async_system_polymarker_tool.hpp

Go to the documentation of this file.

/*
** 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 SERVER_SRC_SERVICES_POLYMARKER_INCLUDE_SYSTEM_POLYMARKER_TOOL_HPP_
#define SERVER_SRC_SERVICES_POLYMARKER_INCLUDE_SYSTEM_POLYMARKER_TOOL_HPP_
 
#include "polymarker_tool.hpp"
#include "temp_file.hpp"
 
 
class POLYMARKER_SERVICE_LOCAL AsyncSystemPolymarkerTool : public PolymarkerTool
{
public:
  AsyncSystemPolymarkerTool (PolymarkerServiceJob *job_p, const PolymarkerSequence *seq_p, const PolymarkerServiceData *data_p);
 
  AsyncSystemPolymarkerTool (PolymarkerServiceJob *job_p, const PolymarkerSequence *seq_p,  const PolymarkerServiceData *data_p, const json_t *root_p);
 
  virtual ~AsyncSystemPolymarkerTool ();
 
  virtual bool PreRun ();
 
  virtual bool PostRun ();
 
  virtual char *GetLog ();
 
  virtual char *GetResults (PolymarkerFormatter *formatter_p);
 
 
  virtual OperationStatus Run ();
 
  virtual OperationStatus GetStatus (bool update_flag);
 
  virtual bool ParseParameters (const ParameterSet * const param_set_p);
 
 
  virtual bool AddToJSON (json_t *root_p);
 
  virtual PolymarkerToolType GetToolType () const;
 
 
protected:
  const char *aspt_executable_s;
  char *aspt_command_line_args_s;
 
  bool CreateArgs (const char *input_s, char *output_s, char *contigs_s);
  TempFile *GetInputFile (const char *gene_id_s, const char *target_chromosome_s, const char *sequence_s);
  char *GetOutputFolder ();
  bool GetStringParameter (const ParameterSet * const params_p, const char *param_name_s, char **param_value_ss);
  void FreeCommandLineArgs ();
 
  bool SetExecutable (const PolymarkerServiceData *data_p);
 
 
private:
  static uint32 SPT_NUM_ARGS;
 
  static const char * const ASPT_ASYNC_S;
  static const char * const ASPT_LOGFILE_S;
  static const char * const ASPT_EXECUTABLE_S;
 
  char *aspt_async_logfile_s;
  SystemAsyncTask *aspt_task_p;
};
 
 
 
#endif /* SERVER_SRC_SERVICES_POLYMARKER_INCLUDE_SYSTEM_POLYMARKER_TOOL_HPP_ */