#!/usr/bin/env python
import os
import sys
import re
from htsworkflow.pipelines.configure_run import *
from htsworkflow.pipelines import retrieve_config as _rc
from htsworkflow.pipelines.run_status import startCmdLineStatusMonitor

s_fc = re.compile('FC[0-9]+')

#Turn on built-in command-line parsing.
_rc.DISABLE_CMDLINE = False

GENOME_DIR = '/data-store01/compbio/genomes/'



def main(args=None):
  ci = ConfigInfo()
  ci.analysis_dir = os.getcwd()
  ci.base_analysis_dir, junk = os.path.split(ci.analysis_dir)

  #FIXME: make a better command line tool
  skip_retrieve_config = False
  if len(args) == 1:
    arg = args[0]

    #If FC##### found
    if s_fc.search(arg):
      cfg_filepath = os.path.abspath('config32auto.txt')
      flowcell = arg
    #else, config file provide
    else:
      cfg_filepath = os.path.abspath(args[0])
      skip_retrieve_config = True
  else:
    print "usage:\n" \
          "       configure_pipeline FC#####\n" \
          " or:\n" \
          "       configure_pipeline <conf_filepath>\n"
    return 3

  genome_dir = GENOME_DIR

  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__":
  logging.basicConfig(level=logging.DEBUG,
                    format='%(asctime)s %(levelname)-8s %(message)s',
                    datefmt='%a, %d %b %Y %H:%M:%S',
                    #filename='pipeline_main.log',
                    filemode='w')

  sys.exit(main(sys.argv[1:]))