#!/usr/bin/env python
import os
import sys
from gaworkflow.pipeline.configure_run import *
from gaworkflow.pipeline.monitors import startCmdLineStatusMonitor


def main(args=None):
  ci = ConfigInfo()

  #FIXME: make a better command line tool
  skip_retrieve_config = False
  if len(args) == 1:
    cfg_filepath = os.path.abspath(args[0])
    skip_retrieve_config = True
  else:
    cfg_filepath = os.path.abspath('config32auto.txt')

  flowcell = 'FC12150'
  genome_dir = '/home/king/trog_drive/'

  if not skip_retrieve_config:
    status_retrieve_cfg = retrieve_config(ci, flowcell, cfg_filepath, genome_dir)
    if status_retrieve_cfg:
      print "Retrieve config file successful"
    else:
      print "Failed to retrieve config file"
  else:
    print "Config file %s provided from command-line" % (cfg_filepath)
    ci.config_filepath = cfg_filepath
    status_retrieve_cfg = True
  
  if status_retrieve_cfg:
    status = configure(ci)
    if status:
      print "Configure success"
    else:
      print "Configure failed"
    
    print 'Run Dir:', ci.run_path
    print 'Bustard Dir:', ci.bustard_path
    
    if status:
      # Setup status cmdline status monitor
      startCmdLineStatusMonitor(ci)
      
      print 'Running pipeline now!'
      run_status = run_pipeline(ci)
      if run_status is True:
        print 'Pipeline ran successfully.'
        return 0
      else:
        print 'Pipeline run failed.'
        return 1

    return 2

if __name__ == "__main__":
  sys.exit(main(sys.argv[1:]))