blast_tool.hpp

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/*
** Copyright 2014-2016 The Earlham Institute
** 
** Licensed under the Apache License, Version 2.0 (the "License");
** you may not use this file except in compliance with the License.
** You may obtain a copy of the License at
** 
**     http://www.apache.org/licenses/LICENSE-2.0
** 
** Unless required by applicable law or agreed to in writing, software
** distributed under the License is distributed on an "AS IS" BASIS,
** WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
** See the License for the specific language governing permissions and
** limitations under the License.
*/
 
#ifndef BLAST_TOOL_HPP
#define BLAST_TOOL_HPP
 
#include <vector>
 
#include "blast_app_parameters.h"
#include "blast_formatter.h"
#include "blast_service_api.h"
#include "byte_buffer.h"
 
#include "service_job.h"
 
 
/* forward declaration */
struct BlastServiceData;
struct BlastServiceJob;
 
class BLAST_SERVICE_LOCAL BlastTool
{
public:
 
  BlastTool (BlastServiceJob *job_p, const char *name_s, const char *factory_s, const BlastServiceData *data_p, const uint32 output_format, const char *custom_output_s);
 
 
  BlastTool (BlastServiceJob *job_p, const BlastServiceData *data_p, const json_t *json_p);
 
 
  virtual ~BlastTool ();
 
 
  uint32 GetOutputFormat () const;
 
 
  virtual OperationStatus Run () = 0;
 
 
  virtual bool ParseParameters (ParameterSet *param_set_p, BlastAppParameters *app_params_p) = 0;
 
  virtual bool SetInputFilename (const char * const filename_s) = 0;
 
 
  virtual bool SetUpOutputFile () = 0;
 
 
  virtual bool PreRun ();
  
 
  virtual void PostRun ();
 
  virtual OperationStatus GetStatus (bool update_flag = true);
 
 
  virtual char *GetResults (BlastFormatter *formatter_p) = 0;
 
  virtual char *GetLog () = 0;
 
 
  virtual bool AddErrorDetails ();
 
 
  const uuid_t &GetUUID () const;
 
  const char *GetName () const;
 
 
  json_t *GetAsJSON ();
 
 
  const char *GetFactoryName () const;
 
 
  bool SetCustomOutputColumns (const char *custom_columns_s);
 
 
 
protected:
 
 
  char *bt_name_s;
 
  char *bt_factory_name_s;
 
 
  uint32 bt_output_format;
 
 
  char *bt_custom_output_columns_s;
 
 
  BlastServiceJob *bt_job_p;
 
  const BlastServiceData *bt_service_data_p;
 
 
  virtual bool AddToJSON (json_t *root_p);
 
private:
  static const char * const BT_NAME_S;
  static const char * const BT_FACTORY_NAME_S;
  static const char * const BT_OUTPUT_FORMAT_S;
  static const char * const BT_CUSTOM_OUTPUT_COLUMNS_S;
 
};
 
 
/*
* I can see that potentially we could use a variety of methods:
* 
* 1. Fork a new process.
* 2. Create a DBApplication and run it inline.
* 3. Create a DBApplication and run it in a separate thread using pthreads or similar.
* 4. Create a job submission script and call it, this would be on HPC or similar.
* 
* So we need a way to call any of these and check on their status, the obvious answer
* is subclassing with virtual calls.
*/
 
 
#ifdef __cplusplus
extern "C" 
{
#endif
 
 
BLAST_SERVICE_LOCAL void FreeBlastTool (BlastTool *tool_p);
 
 
 
BLAST_SERVICE_LOCAL OperationStatus RunBlast (BlastTool *tool_p);
 
BLAST_SERVICE_LOCAL OperationStatus GetBlastStatus (BlastTool *tool_p);
 
 
BLAST_SERVICE_LOCAL bool IsBlastToolSynchronous (BlastTool *tool_p);
 
 
#ifdef __cplusplus
}
#endif
 
 
#endif    /* #ifndef BLAST_TOOL_HPP */