--- a/CMakeLists.txt	Mon May 28 16:39:00 2018 +0200
+++ b/CMakeLists.txt	Mon May 28 16:46:54 2018 +0200
@@ -93,6 +93,7 @@
   OrthancServer/ServerJobs/Operations/SystemCallOperation.cpp
   OrthancServer/ServerJobs/OrthancJobUnserializer.cpp
   OrthancServer/ServerJobs/OrthancPeerStoreJob.cpp
+  OrthancServer/ServerJobs/ResourceModificationJob.cpp
   OrthancServer/ServerToolbox.cpp
   OrthancServer/SliceOrdering.cpp
   )

--- a/OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp	Mon May 28 16:39:00 2018 +0200
+++ b/OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp	Mon May 28 16:46:54 2018 +0200
@@ -34,10 +34,10 @@
 #include "../PrecompiledHeadersServer.h"
 #include "OrthancRestApi.h"
 
+#include "../../Core/DicomParsing/FromDcmtkBridge.h"
 #include "../../Core/Logging.h"
-#include "../../Core/DicomParsing/FromDcmtkBridge.h"
 #include "../ServerContext.h"
-#include "../OrthancInitialization.h"
+#include "../ServerJobs/ResourceModificationJob.h"
 
 #include <boost/lexical_cast.hpp>
 #include <boost/algorithm/string/predicate.hpp>
@@ -139,287 +139,6 @@
 
 
 
-  class ResourceModificationJob : public SetOfInstancesJob
-  {
-  public:
-    class Output : public boost::noncopyable
-    {
-    private:
-      boost::mutex  mutex_;
-      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)
-      {
-        boost::mutex::scoped_lock lock(mutex_);
-        
-        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)
-      {
-        boost::mutex::scoped_lock lock(mutex_);
-        
-        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)
-      {
-        boost::mutex::scoped_lock lock(mutex_);
-        
-        if (isFirst_)
-        {
-          return false;
-        }
-        else
-        {
-          id = id_;
-          return true;
-        }
-      }
-    };
-    
-  private:
-    ServerContext&                    context_;
-    std::auto_ptr<DicomModification>  modification_;
-    boost::shared_ptr<Output>         output_;
-    bool                              isAnonymization_;
-    MetadataType                      metadataType_;
-    std::string                       description_;
-    DicomInstanceOrigin               origin_;
-
-  protected:
-    bool HandleInstance(const std::string& instance)
-    {
-      if (modification_.get() == NULL)
-      {
-        LOG(ERROR) << "No modification was provided for this job";
-        throw OrthancException(ErrorCode_BadSequenceOfCalls);
-      }
-
-      
-      LOG(INFO) << "Modifying instance in a job: " << instance;
-
-      std::auto_ptr<ServerContext::DicomCacheLocker> locker;
-
-      try
-      {
-        locker.reset(new ServerContext::DicomCacheLocker(context_, instance));
-      }
-      catch (OrthancException&)
-      {
-        LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
-        return false;
-      }
-
-
-      ParsedDicomFile& original = locker->GetDicom();
-      DicomInstanceHasher originalHasher = original.GetHasher();
-
-
-      /**
-       * Compute the resulting DICOM instance.
-       **/
-
-      std::auto_ptr<ParsedDicomFile> modified(original.Clone(true));
-      modification_->Apply(*modified);
-
-      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 (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
-      {
-        LOG(ERROR) << "Error while storing a modified instance " << instance;
-        throw OrthancException(ErrorCode_CannotStoreInstance);
-      }
-
-      // Sanity checks in debug mode
-      assert(modifiedInstance == modifiedHasher.HashInstance());
-
-
-      if (output_.get() != NULL)
-      {
-        output_->Update(modifiedHasher);
-      }
-
-      return true;
-    }
-    
-  public:
-    ResourceModificationJob(ServerContext& context) :
-      context_(context),
-      isAnonymization_(false)
-    {
-    }
-
-    void SetModification(DicomModification* modification,   // Takes ownership
-                         bool isAnonymization)
-    {
-      if (modification == NULL)
-      {
-        throw OrthancException(ErrorCode_NullPointer);
-      }
-      else if (IsStarted())
-      {
-        throw OrthancException(ErrorCode_BadSequenceOfCalls);
-      }
-      else
-      {
-        modification_.reset(modification);
-        isAnonymization_ = isAnonymization;
-      }
-    }
-
-    void SetOutput(boost::shared_ptr<Output>& output)
-    {
-      if (IsStarted())
-      {
-        throw OrthancException(ErrorCode_BadSequenceOfCalls);
-      }
-      else
-      {
-        output_ = output;
-      }
-    }
-
-    void SetOrigin(const DicomInstanceOrigin& origin)
-    {
-      if (IsStarted())
-      {
-        throw OrthancException(ErrorCode_BadSequenceOfCalls);
-      }
-      else
-      {
-        origin_ = origin;
-      }
-    }
-
-    void SetOrigin(const RestApiCall& call)
-    {
-      DicomInstanceOrigin tmp;
-      tmp.SetRestOrigin(call);      
-      SetOrigin(tmp);
-    }
-
-    virtual void ReleaseResources()
-    {
-    }
-
-    virtual void GetJobType(std::string& target)
-    {
-      target = "ResourceModification";
-    }
-
-    virtual void GetPublicContent(Json::Value& value)
-    {
-      SetOfInstancesJob::GetPublicContent(value);
-
-      value["IsAnonymization"] = isAnonymization_;
-    }
-    
-    virtual void GetInternalContent(Json::Value& value)
-    {
-      SetOfInstancesJob::GetInternalContent(value);
-
-      Json::Value tmp;
-      modification_->Serialize(tmp);
-      value["Modification"] = tmp;
-    }
-  };
-  
-
-
   static void SubmitJob(std::auto_ptr<DicomModification>& modification,
                         bool isAnonymization,
                         ResourceType level,

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancServer/ServerJobs/ResourceModificationJob.cpp	Mon May 28 16:46:54 2018 +0200
@@ -0,0 +1,284 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2018 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"
+
+namespace Orthanc
+{
+  ResourceModificationJob::Output::Output(ResourceType  level) :
+    level_(level),
+    isFirst_(true)
+  {
+    if (level_ != ResourceType_Patient &&
+        level_ != ResourceType_Study &&
+        level_ != ResourceType_Series)
+    {
+      throw OrthancException(ErrorCode_ParameterOutOfRange);
+    }            
+  }
+
+
+  void ResourceModificationJob::Output::Update(DicomInstanceHasher& hasher)
+  {
+    boost::mutex::scoped_lock lock(mutex_);
+        
+    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 ResourceModificationJob::Output::Format(Json::Value& target)
+  {
+    boost::mutex::scoped_lock lock(mutex_);
+        
+    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 ResourceModificationJob::Output::GetIdentifier(std::string& id)
+  {
+    boost::mutex::scoped_lock lock(mutex_);
+        
+    if (isFirst_)
+    {
+      return false;
+    }
+    else
+    {
+      id = id_;
+      return true;
+    }
+  }
+
+
+  bool ResourceModificationJob::HandleInstance(const std::string& instance)
+  {
+    if (modification_.get() == NULL)
+    {
+      LOG(ERROR) << "No modification was provided for this job";
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+
+      
+    LOG(INFO) << "Modifying instance in a job: " << instance;
+
+    std::auto_ptr<ServerContext::DicomCacheLocker> locker;
+
+    try
+    {
+      locker.reset(new ServerContext::DicomCacheLocker(context_, instance));
+    }
+    catch (OrthancException&)
+    {
+      LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
+      return false;
+    }
+
+
+    ParsedDicomFile& original = locker->GetDicom();
+    DicomInstanceHasher originalHasher = original.GetHasher();
+
+
+    /**
+     * Compute the resulting DICOM instance.
+     **/
+
+    std::auto_ptr<ParsedDicomFile> modified(original.Clone(true));
+    modification_->Apply(*modified);
+
+    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 (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
+    {
+      LOG(ERROR) << "Error while storing a modified instance " << instance;
+      throw OrthancException(ErrorCode_CannotStoreInstance);
+    }
+
+    // Sanity checks in debug mode
+    assert(modifiedInstance == modifiedHasher.HashInstance());
+
+
+    if (output_.get() != NULL)
+    {
+      output_->Update(modifiedHasher);
+    }
+
+    return true;
+  }
+    
+
+  
+  void ResourceModificationJob::SetModification(DicomModification* modification,
+                                                bool isAnonymization)
+  {
+    if (modification == NULL)
+    {
+      throw OrthancException(ErrorCode_NullPointer);
+    }
+    else if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      modification_.reset(modification);
+      isAnonymization_ = isAnonymization;
+    }
+  }
+
+
+  void ResourceModificationJob::SetOutput(boost::shared_ptr<Output>& output)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      output_ = output;
+    }
+  }
+
+  
+  void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      origin_ = origin;
+    }
+  }
+
+  
+  void ResourceModificationJob::SetOrigin(const RestApiCall& call)
+  {
+    DicomInstanceOrigin tmp;
+    tmp.SetRestOrigin(call);      
+    SetOrigin(tmp);
+  }
+
+
+  void ResourceModificationJob::GetPublicContent(Json::Value& value)
+  {
+    SetOfInstancesJob::GetPublicContent(value);
+
+    value["IsAnonymization"] = isAnonymization_;
+  }
+
+  
+  void ResourceModificationJob::GetInternalContent(Json::Value& value)
+  {
+    SetOfInstancesJob::GetInternalContent(value);
+
+    Json::Value tmp;
+    modification_->Serialize(tmp);
+    value["Modification"] = tmp;
+  }
+}

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancServer/ServerJobs/ResourceModificationJob.h	Mon May 28 16:46:54 2018 +0200
@@ -0,0 +1,109 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2018 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/>.
+ **/
+
+
+#pragma once
+
+#include "../../Core/JobsEngine/SetOfInstancesJob.h"
+#include "../ServerContext.h"
+
+namespace Orthanc
+{
+  class ResourceModificationJob : public SetOfInstancesJob
+  {
+  public:
+    class Output : public boost::noncopyable
+    {
+    private:
+      boost::mutex  mutex_;
+      ResourceType  level_;
+      bool          isFirst_;
+      std::string   id_;
+      std::string   patientId_;
+
+    public:
+      Output(ResourceType  level);
+
+      ResourceType GetLevel() const
+      {
+        return level_;
+      }
+
+      void Update(DicomInstanceHasher& hasher);
+
+      bool Format(Json::Value& target);
+
+      bool GetIdentifier(std::string& id);
+    };
+    
+  private:
+    ServerContext&                    context_;
+    std::auto_ptr<DicomModification>  modification_;
+    boost::shared_ptr<Output>         output_;
+    bool                              isAnonymization_;
+    MetadataType                      metadataType_;
+    std::string                       description_;
+    DicomInstanceOrigin               origin_;
+
+  protected:
+    virtual bool HandleInstance(const std::string& instance);
+    
+  public:
+    ResourceModificationJob(ServerContext& context) :
+      context_(context),
+      isAnonymization_(false)
+    {
+    }
+
+    void SetModification(DicomModification* modification,   // Takes ownership
+                         bool isAnonymization);
+
+    void SetOutput(boost::shared_ptr<Output>& output);
+
+    void SetOrigin(const DicomInstanceOrigin& origin);
+
+    void SetOrigin(const RestApiCall& call);
+
+    virtual void ReleaseResources()
+    {
+    }
+
+    virtual void GetJobType(std::string& target)
+    {
+      target = "ResourceModification";
+    }
+
+    virtual void GetPublicContent(Json::Value& value);
+    
+    virtual void GetInternalContent(Json::Value& value);
+  };
+}