[project @ Better handling of configuring pipeline w/ clear success or failure. Loads...

diff --git a/bin/config_pipeline.py b/bin/config_pipeline.py
index c559ebe3e89e705c86fc2af992f5fb48f98df509..a93ce93dfb48b78e2ae0e6c28a6025de38c43609 100644 (file)
--- a/bin/config_pipeline.py
+++ b/bin/config_pipeline.py
@@ -1,6 +1,7 @@
 #!/usr/bin/python
 import subprocess
 import re
+import os
 import logging
 
 logging.basicConfig(level=logging.DEBUG,
@@ -9,10 +10,18 @@ logging.basicConfig(level=logging.DEBUG,
                     filename='config_pipeline.log',
                     filemode='w')
 
+class ConfigInfo:
+  
+  def __init__(self):
+    self.run_path = None
+    self.bustard_path = None
+    self.config_filepath = None
+
 #Info
 s_start = re.compile('Starting Genome Analyzer Pipeline')
 s_gerald = re.compile("[\S\s]+--GERALD[\S\s]+--make[\S\s]+")
 s_generating = re.compile('Generating journals, Makefiles and parameter files')
+s_seq_folder = re.compile('^Sequence folder: ')
 
 #Errors
 s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
@@ -20,7 +29,16 @@ s_invalid_cmdline = re.compile('Usage:[\S\s]*goat_pipeline.py')
 #Ignore
 s_skip = re.compile('s_[0-8]_[0-9]+')
 
-def handler(line):
+def handler(line, conf_info):
+  """
+  Processes each line of output from GOAT
+  and stores useful information using the logging module
+
+  Loads useful information into conf_info as well, for future
+  use outside the function.
+
+  returns True if found condition that signifies success.
+  """
 
   # Irrelevant line
   if s_skip.search(line):
@@ -33,11 +51,25 @@ def handler(line):
     logging.info('Running make now')
   elif s_generating.search(line):
     logging.info('Make files generted')
+    return True
+  elif s_seq_folder.search(line):
+    mo = s_seq_folder.search(line)
+    conf_info.bustard_path = line[mo.end():]
+    conf_info.run_path, temp = os.path.split(conf_info.bustard_path)
   else:
     logging.warning('How to handle: %s' % (line))
-  
 
-def configure():
+  return False
+
+
+def configure(conf_info):
+  """
+  Attempts to configure the GA pipeline using goat.
+
+  Uses logging module to store information about status.
+
+  returns True if configuration successful, otherwise False.
+  """
   #ERROR Test:
   #pipe = subprocess.Popen(['goat_pipeline.py',
   #                         '--GERALD=config32bk.txt',
@@ -48,7 +80,7 @@ def configure():
 
   #Not a test; actual run attempt.
   pipe = subprocess.Popen(['goat_pipeline.py',
-                           '--GERALD=config32bk.txt',
+                    '--GERALD=%s' % (conf_info.config_filepath),
                            '--make',
                            '.'],
                           stdout=subprocess.PIPE,
@@ -56,12 +88,41 @@ def configure():
   
   line = pipe.stdout.readline()
 
+  complete = False
   while line != '':
-    handler(line)
+    if handler(line, conf_info):
+      complete = True
     line = pipe.stdout.readline()
 
-  #print pipe.poll()
+  error_code = pipe.wait()
+  if error_code:
+    logging.error('Recieved error_code: %s' % (error_code))
+  else:
+    logging.info ('We are go for launch!')
+
+  #If log says complete and we don't have an
+  # error code (i.e. error_code == False)
+  status = complete is True and bool(error_code) is False
+
+  # If everything was successful, but for some reason
+  #  we didn't retrieve the path info, log it.
+  if status is True:
+    if conf_info.bustard_path is None or conf_info.run_path is None:
+      logging.error("Failed to retrieve run_path")
+      return False
+  
+  return status
 
 
 if __name__ == '__main__':
-  configure()
+  ci = ConfigInfo()
+  ci.config_filepath = 'config32bk.txt'
+  
+  status = configure(ci)
+  if status:
+    print "Configure success"
+  else:
+    print "Configure failed"
+
+  print 'Run Dir:', ci.run_path
+  print 'Bustard Dir:', ci.bustard_path