#!/usr/bin/python

import logging
import optparse
import os
import sys

from htsworkflow.pipelines import runfolder
from htsworkflow.pipelines.srf import make_srf_commands, make_qseq_commands, \
                                      run_commands, pathname_to_run_name
from htsworkflow.pipelines.srf import ILLUMINA2SRF10, ILLUMINA2SRF11, SOLEXA2SRF

def make_parser():
  usage = '%prog: [options] runfolder -l 1,2,3 [runfolder -l 5,6 ...]'

  parser = optparse.OptionParser(usage)
  parser.add_option('--dry-run', action='store_true',
                    help='print what would be done',
                    default=False)

  parser.add_option('-d', '--dest-dir', dest='dest_dir',
                    help='location to write srf files to',
                    default='.')
  parser.add_option('-s', '--site',
                    help='site name',
                    default='Individual')
  parser.add_option('-l', '--lanes', dest='lanes', action="append",
         default=[],
         help='comma seperated list of lanes to add to srf'
  )
  parser.add_option('-j', '--jobs', default=1, type='int',
                    help='how many jobs to run simultaneously')
  parser.add_option('-r', '--runfolder-version', default=ILLUMINA2SRF11, type='int',
                    help='Which class of srf file should we attempt to create\n'
                         '0 = Solexa pipeline 0.2.6 - 0.3\n'
                         '1 = illumina pipeline 1.0\n'
                         '2 = illumina pipeline 1.1rc1 and later \n')
                     
  parser.add_option('-v', '--verbose', dest='verbose',
                    default=False, action='store_true',
                    help='report more about internals (INFO)')
  parser.add_option('--debug', dest='debug',
                    default=False, action='store_true',
                    help='report even more about internals (DEBUG)')
 
  return parser

def parse_lane_arg(lane_arg):
    """
    Convert comma sperated list of lane ids to a list of integers
    """
    lanes = []
    for lane in lane_arg.split(','):
        try:
            lane = int(lane)
            if lane < 1 or lane > 8:
                parser.error('Lanes must be in range [1..8]')
            lanes.append(lane)
        except ValueError:
            parser.error('Lane selections must be integers')
    return lanes

def main(cmdline=None):
    parser = make_parser()
    opts, args = parser.parse_args(cmdline)
   
    if opts.debug: 
        logging.basicConfig(level=logging.DEBUG)
    elif opts.verbose:
        logging.basicConfig(level=logging.INFO)
    else:
        logging.basicConfig(level=logging.WARNING)

    if len(args) == 0:
        parser.error('need runfolder arguments')

    # parse lane arguemnts
    lanes_list = []
    if len(opts.lanes) == 0:
        lanes_list = [[1,2,3,4,5,6,7,8]] * len(args)
    elif len(opts.lanes) == len(args):
        for lane_arg in opts.lanes:
            lanes_list.append(parse_lane_arg(lane_arg))
    else:
        parser.error(
          "Number of lane arguments must match number of runfolders"
        )

    make_commands = make_qseq_commands
    # build list of commands
    cmds = {}
    for runfolder_path, lanes in zip(args, lanes_list):
        # normalize paths, either relative to home dirs or current dir
        runfolder_path = os.path.abspath(runfolder_path)
        run_name = pathname_to_run_name(runfolder_path)
        # so any bustard directories?
        runs = runfolder.get_runs(runfolder_path)
        # give up if there are anything other than 1 run
        if len(runs) > 1:
          print 'ERROR: Too many run directories in %s' %(runfolder_path,)
          return 1
        elif len(runs) == 1:
          bustard_dir = runs[0].bustard.pathname
          cmds[bustard_dir] = make_commands(run_name,
                                            bustard_dir,
                                            lanes,
                                            opts.site,
                                            opts.dest_dir,
                                            opts.runfolder_version)
        else:
          print "ERROR: Couldn't find a bustard directory in", runfolder_path
          return 1

    if not opts.dry_run:
      for cwd, cmd_list in cmds.items():
        run_commands(cwd, cmd_list, opts.jobs)
    else:
      for cwd, cmd_list in cmds.items():
        print cwd
        print cmd_list
        print 'jobs: ', opts.jobs

    return 0

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