#!/usr/bin/python

from glob import glob
import logging
import optparse
import os
import subprocess
import sys

from htsworkflow.util import queuecommands
from htsworkflow.pipelines import runfolder

def make_commands(run_name, lanes, site_name, destdir):
  """
  make a subprocess-friendly list of command line arguments to run solexa2srf
  generates files like: 
  woldlab:080514_HWI-EAS229_0029_20768AAXX:8.srf
   site        run name                    lane
             
  run_name - most of the file name (run folder name is a good choice)
  lanes - list of integers corresponding to which lanes to process
  site_name - name of your "sequencing site" or "Individual"
  destdir - where to write all the srf files
  """
  cmd_list = []
  for lane in lanes:
    name_prefix = '%s_%%l_%%t_' % (run_name,)
    destname = '%s_%s_%d.srf' % (site_name, run_name, lane)
    destdir = os.path.normpath(destdir)
    dest_path = os.path.join(destdir, destname)
    seq_pattern = 's_%d_*_seq.txt' % (lane,)

    cmd = ['solexa2srf', 
           '-N', name_prefix,
           '-n', '%3x:%3y', 
           '-o', dest_path, 
	   seq_pattern]

    cmd_list.append(" ".join(cmd))
  return cmd_list

def pathname_to_run_name(base):
  """
  Convert a pathname to a base runfolder name
  handle the case with a trailing /
  """
  name = ""
  while len(name) == 0:
    base, name = os.path.split(base)
    if len(base) == 0:
      return None
  return name

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')
                     

  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 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"
        )
    
    # 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)
        # the last part of the path should be a runfolder name
        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(name, lanes, opts.site, opts.dest_dir)
        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():
        curdir = os.getcwd()
        os.chdir(cwd)
        q = queuecommands.QueueCommands(cmd_list, opts.jobs)
        q.run()
        os.chdir(curdir)
    else:
      for cwd, cmd_list in cmds.items():
        print cwd
        print cmd_list
        print 'jobs: ', opts.jobs

    return 0

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