#!/usr/bin/env python
import sys
from htsworkflow.pipelines.retrieve_config import *
from htsworkflow.pipelines import retrieve_config
from htsworkflow.pipelines.genome_mapper import getAvailableGenomes
from htsworkflow.pipelines.genome_mapper import constructMapperDict

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

def main(args=None):
  #Display help if no args are presented
  if len(sys.argv) == 1:
    sys.argv.append('-h')
    
  options = getCombinedOptions()
  msg_list = ['ERROR MESSAGES:']
  if options.output_filepath is None:
    msg_list.append("  Output filepath argument required. -o <filepath> or --output=<filepath>")
    
  if options.flowcell is None:
    msg_list.append("  Flow cell argument required. -f <flowcell> or --flowcell=<flowcell>")
    
  if options.url is None:
    msg_list.append("  URL argument required (-u <url> or --url=<url>), or entry\n" \
                    "    in /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
  if options.genome_dir is None:
    msg_list.append("  genome_dir argument required (-g <genome_dir> or \n" \
                    "    --genome_dir=<genome_dir>, or entry in \n" \
                    "    /etc/ga_frontend/ga_frontend.conf or ~/.ga_frontend.conf")
    
  if len(msg_list) > 1:
    print '\n'.join(msg_list)
    return 1
  
  saveConfigFile(options.flowcell, options.url, options.output_filepath)

  f = open(options.output_filepath, 'r')
  data = f.read()
  f.close()

  genome_dict = getAvailableGenomes(options.genome_dir)
  mapper_dict = constructMapperDict(genome_dict)

  f = open(options.output_filepath, 'w')
  f.write(data % (mapper_dict))
  f.close()
  
  return 0
  
if __name__ == "__main__":
  sys.exit(main(sys.argv[1:]))