bin/config_pipeline.py

   1 #!/usr/bin/python
   2 import subprocess
   3 import re
   4 import os
   5 import logging
   6
   7 logging.basicConfig(level=logging.DEBUG,
   8                     format='%(asctime)s %(levelname)-8s %(message)s',
   9                     datefmt='%a, %d %b %Y %H:%M:%S',
  10                     filename='config_pipeline.log',
  11                     filemode='w')
  12
  13 class ConfigInfo:
  14
  15   def __init__(self):
  16     self.run_path = None
  17     self.bustard_path = None
  18     self.config_filepath = None
  19
  20 #Info
  21 s_start = re.compile('Starting Genome Analyzer Pipeline')
  22 s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")
  23 s_generating = re.compile('Generating journals, Makefiles and parameter files')
  24 s_seq_folder = re.compile('^Sequence folder: ')
  25
  26 #Errors
  27 s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
  28
  29 #Ignore
  30 s_skip = re.compile('s_[0-8]_[0-9]+')
  31
  32 def handler(line, conf_info):
  33   """
  34   Processes each line of output from GOAT
  35   and stores useful information using the logging module
  36
  37   Loads useful information into conf_info as well, for future
  38   use outside the function.
  39
  40   returns True if found condition that signifies success.
  41   """
  42
  43   # Irrelevant line
  44   if s_skip.search(line):
  45     pass
  46   elif s_invalid_cmdline.search(line):
  47     logging.error("Invalid commandline options!")
  48   elif s_start.search(line):
  49     logging.info('START: Configuring pipeline')
  50   elif s_gerald.search(line):
  51     logging.info('Running make now')
  52   elif s_generating.search(line):
  53     logging.info('Make files generted')
  54     return True
  55   elif s_seq_folder.search(line):
  56     mo = s_seq_folder.search(line)
  57     conf_info.bustard_path = line[mo.end():]
  58     conf_info.run_path, temp = os.path.split(conf_info.bustard_path)
  59   else:
  60     logging.warning('How to handle: %s' % (line))
  61
  62   return False
  63
  64
  65 def configure(conf_info):
  66   """
  67   Attempts to configure the GA pipeline using goat.
  68
  69   Uses logging module to store information about status.
  70
  71   returns True if configuration successful, otherwise False.
  72   """
  73   #ERROR Test:
  74   #pipe = subprocess.Popen(['goat_pipeline.py',
  75   #                         '--GERALD=config32bk.txt',
  76   #                         '--make .',],
  77   #                         #'.'],
  78   #                        stdout=subprocess.PIPE,
  79   #                        stderr=subprocess.PIPE)
  80
  81   #Not a test; actual run attempt.
  82   pipe = subprocess.Popen(['goat_pipeline.py',
  83                     '--GERALD=%s' % (conf_info.config_filepath),
  84                            '--make',
  85                            '.'],
  86                           stdout=subprocess.PIPE,
  87                           stderr=subprocess.PIPE)
  88
  89   line = pipe.stdout.readline()
  90
  91   complete = False
  92   while line != '':
  93     if handler(line, conf_info):
  94       complete = True
  95     line = pipe.stdout.readline()
  96
  97   error_code = pipe.wait()
  98   if error_code:
  99     logging.error('Recieved error_code: %s' % (error_code))
 100   else:
 101     logging.info ('We are go for launch!')
 102
 103   #If log says complete and we don't have an
 104   # error code (i.e. error_code == False)
 105   status = complete is True and bool(error_code) is False
 106
 107   # If everything was successful, but for some reason
 108   #  we didn't retrieve the path info, log it.
 109   if status is True:
 110     if conf_info.bustard_path is None or conf_info.run_path is None:
 111       logging.error("Failed to retrieve run_path")
 112       return False
 113
 114   return status
 115
 116
 117 if __name__ == '__main__':
 118   ci = ConfigInfo()
 119   ci.config_filepath = 'config32bk.txt'
 120
 121   status = configure(ci)
 122   if status:
 123     print "Configure success"
 124   else:
 125     print "Configure failed"
 126
 127   print 'Run Dir:', ci.run_path
 128   print 'Bustard Dir:', ci.bustard_path