#!/usr/bin/python
import subprocess
+import logging
+import time
import re
import os
-import logging
+
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(levelname)-8s %(message)s',
#FLAGS
RUN_ABORT = 'abort'
+RUN_FAILED = 'failed'
+
+#####################################
+# Configure Step (goat_pipeline.py)
#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: ')
+s_seq_folder_sub = re.compile('want to make ')
s_stderr_taskcomplete = re.compile('^Task complete, exiting')
#Errors
#Ignore
s_skip = re.compile('s_[0-8]_[0-9]+')
+##########################################
+# Pipeline Run Step (make -j8 recursive)
+
+##Info
+
+
+##Errors
+s_make_error = re.compile('^make[\S\s]+Error')
+s_no_gnuplot = re.compile('gnuplot: command not found')
+s_no_convert = re.compile('^Can\'t exec "convert"')
+
+##Ignore
+PL_STDERR_IGNORE_LIST = []
+# Info: PF 11802
+PL_STDERR_IGNORE_LIST.append( re.compile('^Info: PF') )
+# About to analyse intensity file s_4_0101_sig2.txt
+PL_STDERR_IGNORE_LIST.append( re.compile('^About to analyse intensity file') )
+# Will send output to standard output
+PL_STDERR_IGNORE_LIST.append( re.compile('^Will send output to standard output') )
+# Found 31877 clusters
+PL_STDERR_IGNORE_LIST.append( re.compile('^Found [0-9]+ clusters') )
+# Will use quality criterion ((CHASTITY>=0.6)
+PL_STDERR_IGNORE_LIST.append( re.compile('^Will use quality criterion') )
+# Quality criterion translated to (($F[5]>=0.6))
+PL_STDERR_IGNORE_LIST.append( re.compile('^Quality criterion translated to') )
+# opened /woldlab/trog/data1/king/070924_USI-EAS44_0022_FC12150/Data/C1-36_Firecrest1.9.1_14-11-2007_king.4/Bustard1.9.1_14-11-2007_king/s_4_0101_qhg.txt
+# AND
+# opened s_4_0103_qhg.txt
+PL_STDERR_IGNORE_LIST.append( re.compile('^opened[\S\s]+qhg.txt') )
+
+
+def pl_stderr_ignore(line):
+ """
+ Searches lines for lines to ignore (i.e. not to log)
+
+ returns True if line should be ignored
+ returns False if line should NOT be ignored
+ """
+ for s in PL_STDERR_IGNORE_LIST:
+ if s.search(line):
+ return True
+ return False
+
+
def config_stdout_handler(line, conf_info):
"""
Processes each line of output from GOAT
returns True if found condition that signifies success.
"""
- # Irrelevant line
+ # Skip irrelevant line (without logging)
if s_skip.search(line):
pass
+
+ # Detect invalid command-line arguments
elif s_invalid_cmdline.search(line):
logging.error("Invalid commandline options!")
+
+ # Detect starting of configuration
elif s_start.search(line):
logging.info('START: Configuring pipeline')
+
+ # Detect it made it past invalid arguments
elif s_gerald.search(line):
logging.info('Running make now')
+
+ # Detect that make files have been generated (based on output)
elif s_generating.search(line):
logging.info('Make files generted')
return True
+
+ # Capture run directory
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)
+ mo = s_seq_folder_sub.search(line)
+ #Output changed when using --tiles=<tiles>
+ # at least in pipeline v0.3.0b2
+ if mo:
+ firecrest_bustard_gerald_makefile = line[mo.end():]
+ firecrest_bustard_gerald, junk = \
+ os.path.split(firecrest_bustard_gerald_makefile)
+ firecrest_bustard, junk = os.path.split(firecrest_bustard_gerald)
+ firecrest, junk = os.path.split(firecrest_bustard)
+
+ conf_info.bustard_path = firecrest_bustard
+ conf_info.run_path = firecrest
+
+ #Standard output handling
+ else:
+ print 'Sequence line:', 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)
+
+ # Log all other output for debugging purposes
else:
- logging.warning('How to handle: %s' % (line))
+ logging.warning('CONF:?: %s' % (line))
return False
Loads useful information into conf_info as well, for future
use outside the function.
- returns RUN_ABORT upon detecting failure; True on success message
+ returns RUN_ABORT upon detecting failure;
+ True on success message;
+ False if neutral message
+ (i.e. doesn't signify failure or success)
"""
+ # Detect invalid species directory error
if s_species_dir_err.search(line):
logging.error(line)
return RUN_ABORT
+ # Detect goat_pipeline.py traceback
elif s_goat_traceb.search(line):
logging.error("Goat config script died, traceback in debug output")
return RUN_ABORT
+ # Detect indication of successful configuration (from stderr; odd, but ok)
elif s_stderr_taskcomplete.search(line):
logging.info('Configure step successful (from: stderr)')
return True
+ # Log all other output as debug output
else:
- logging.debug('STDERR: How to handle: %s' % (line))
+ logging.debug('CONF:STDERR:?: %s' % (line))
+ # Neutral (not failure; nor success)
return False
+
#FIXME: Temperary hack
-f = open('pipeline_run.log', 'w')
-ferr = open('pipeline_err.log', 'w')
+f = open('pipeline_run.log.1', 'w')
+#ferr = open('pipeline_err.log.1', 'w')
+
-def pipeline_handler(line, conf_info):
+
+def pipeline_stdout_handler(line, conf_info):
"""
Processes each line of output from running the pipeline
and stores useful information using the logging module
return True
+
+def pipeline_stderr_handler(line, conf_info):
+ """
+ """
+
+ if pl_stderr_ignore(line):
+ pass
+ elif s_make_error.search(line):
+ logging.error("make error detected; run failed")
+ return RUN_FAILED
+ elif s_no_gnuplot.search(line):
+ logging.error("gnuplot not found")
+ return RUN_FAILED
+ elif s_no_convert.search(line):
+ logging.error("imagemagick's convert command not found")
+ return RUN_FAILED
+ else:
+ logging.debug('PIPE:STDERR:?: %s' % (line))
+
+ return False
+
+
def configure(conf_info):
"""
Attempts to configure the GA pipeline using goat.
# stdout=subprocess.PIPE,
# stderr=subprocess.PIPE)
- #Not a test; actual run attempt.
- pipe = subprocess.Popen(['goat_pipeline.py',
- '--GERALD=%s' % (conf_info.config_filepath),
- '--make',
- '.'],
- stdout=subprocess.PIPE,
- stderr=subprocess.PIPE)
-
- # CONTINUE HERE
- #FIXME: this only does a run on 5 tiles on lane 4
+ ##########################
+ # Run configuration step
+ # Not a test; actual configure attempt.
#pipe = subprocess.Popen(['goat_pipeline.py',
# '--GERALD=%s' % (conf_info.config_filepath),
- # '--tiles=s_4_0100,s_4_0101,s_4_0102,s_4_103,s_4_104',
# '--make',
# '.'],
# stdout=subprocess.PIPE,
# stderr=subprocess.PIPE)
- #Process stdout
+ # CONTINUE HERE
+ #FIXME: this only does a run on 5 tiles on lane 4
+ pipe = subprocess.Popen(['goat_pipeline.py',
+ '--GERALD=%s' % (conf_info.config_filepath),
+ '--tiles=s_4_0100,s_4_0101,s_4_0102,s_4_0103,s_4_0104',
+ '--make',
+ '.'],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+ ##################
+ # Process stdout
stdout_line = pipe.stdout.readline()
complete = False
if error_code:
logging.error('Recieved error_code: %s' % (error_code))
else:
- logging.info ('We are go for launch!')
+ logging.info('We are go for launch!')
#Process stderr
stderr_line = pipe.stderr.readline()
def run_pipeline(conf_info):
-
+ """
+ Run the pipeline and monitor status.
+ """
# Fail if the run_path doesn't actually exist
if not os.path.exists(conf_info.run_path):
logging.error('Run path does not exist: %s' \
# Change cwd to run_path
os.chdir(conf_info.run_path)
+ # Log pipeline starting
+ logging.info('STARTING PIPELINE @ %s' % (time.ctime()))
+
# Start the pipeline (and hide!)
pipe = subprocess.Popen(['make',
'-j8',
complete = False
while line != '':
- if pipeline_handler(line, conf_info):
+ if pipeline_stdout_handler(line, conf_info):
complete = True
line = pipe.stdout.readline()
error_code = pipe.wait()
- ferr.write(pipe.stderr.read())
- ferr.close()
+ #ferr.write(pipe.stderr.read())
+ #ferr.close()
+
+ stderr_line = pipe.stderr.readline()
+
+ run_succeded = False
+ run_failed = False
+ while stderr_line != '':
+ stderr_status = pipeline_stderr_handler(stderr_line, conf_info)
+ if stderr_status is True:
+ run_succeded = True
+ if stderr_status == RUN_FAILED:
+ run_failed = True
+ stderr_line = pipe.stderr.readline()
+
+ ###DEBUG###
+ print 'RUN STATUS: expect: True, True, True, True'
+ print ' Status:',
+ print complete is True, error_code == 0,
+ print run_succeded is True, run_failed is False
+ ###END_DEBUG###
+
+ status = complete is True and \
+ error_code == 0 and \
+ run_succeded is True and \
+ run_failed is False
+
+ return status
+
if __name__ == '__main__':
projects / htsworkflow.git / commitdiff