#!/usr/bin/python
+__docformat__ = "restructuredtext en"
+
import subprocess
import logging
import time
import re
import os
-from htsworkflow.pipelines.retrieve_config import getCombinedOptions, saveConfigFile
-from htsworkflow.pipelines.retrieve_config import FlowCellNotFound, WebError404
+from htsworkflow.pipelines.retrieve_config import \
+ CONFIG_SYSTEM, CONFIG_USER, \
+ FlowCellNotFound, getCombinedOptions, saveConfigFile, WebError404
from htsworkflow.pipelines.genome_mapper import DuplicateGenome, getAvailableGenomes, constructMapperDict
from htsworkflow.pipelines.run_status import GARunStatus
from pyinotify import WatchManager, ThreadedNotifier
from pyinotify import EventsCodes, ProcessEvent
+LOGGER = logging.getLogger(__name__)
+
class ConfigInfo:
-
+
def __init__(self):
#run_path = firecrest analysis directory to run analysis from
self.run_path = None
self._ci = conf_info
ProcessEvent.__init__(self)
-
+
def process_IN_CREATE(self, event):
fullpath = os.path.join(event.path, event.name)
if s_finished.search(fullpath):
- logging.info("File Found: %s" % (fullpath))
+ LOGGER.info("File Found: %s" % (fullpath))
if s_firecrest_finished.search(fullpath):
self.run_status_dict['firecrest'] = True
self._ci.status.updateBustard(event.name)
elif s_firecrest_all.search(fullpath):
self._ci.status.updateFirecrest(event.name)
-
+
#print "Create: %s" % (os.path.join(event.path, event.name))
def process_IN_DELETE(self, event):
# Detect invalid command-line arguments
elif s_invalid_cmdline.search(line):
- logging.error("Invalid commandline options!")
+ LOGGER.error("Invalid commandline options!")
# Detect starting of configuration
elif s_start.search(line):
- logging.info('START: Configuring pipeline')
+ LOGGER.info('START: Configuring pipeline')
# Detect it made it past invalid arguments
elif s_gerald.search(line):
- logging.info('Running make now')
+ LOGGER.info('Running make now')
# Detect that make files have been generated (based on output)
elif s_generating.search(line):
- logging.info('Make files generted')
+ LOGGER.info('Make files generted')
return True
# Capture run directory
conf_info.bustard_path = firecrest_bustard
conf_info.run_path = firecrest
-
+
#Standard output handling
else:
- print 'Sequence line:', line
+ 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('CONF:?: %s' % (line))
+ LOGGER.warning('CONF:?: %s' % (line))
return False
# Detect invalid species directory error
if s_species_dir_err.search(line):
- logging.error(line)
+ LOGGER.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")
+ LOGGER.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)')
+ LOGGER.info('Configure step successful (from: stderr)')
return True
# Detect missing cycles
elif s_missing_cycles.search(line):
# Only display error once
if not SUPPRESS_MISSING_CYCLES:
- logging.error("Missing cycles detected; Not all cycles copied?")
- logging.debug("CONF:STDERR:MISSING_CYCLES: %s" % (line))
+ LOGGER.error("Missing cycles detected; Not all cycles copied?")
+ LOGGER.debug("CONF:STDERR:MISSING_CYCLES: %s" % (line))
SUPPRESS_MISSING_CYCLES = True
return RUN_ABORT
-
+
# Log all other output as debug output
else:
- logging.debug('CONF:STDERR:?: %s' % (line))
+ LOGGER.debug('CONF:STDERR:?: %s' % (line))
# Neutral (not failure; nor success)
return False
if pl_stderr_ignore(line):
pass
elif s_make_error.search(line):
- logging.error("make error detected; run failed")
+ LOGGER.error("make error detected; run failed")
return RUN_FAILED
elif s_no_gnuplot.search(line):
- logging.error("gnuplot not found")
+ LOGGER.error("gnuplot not found")
return RUN_FAILED
elif s_no_convert.search(line):
- logging.error("imagemagick's convert command not found")
+ LOGGER.error("imagemagick's convert command not found")
return RUN_FAILED
elif s_no_ghostscript.search(line):
- logging.error("ghostscript not found")
+ LOGGER.error("ghostscript not found")
return RUN_FAILED
else:
- logging.debug('PIPE:STDERR:?: %s' % (line))
+ LOGGER.debug('PIPE:STDERR:?: %s' % (line))
return False
options = getCombinedOptions()
if options.url is None:
- logging.error("~/.ga_frontend.conf or /etc/ga_frontend/ga_frontend.conf" \
- " missing base_host_url option")
+ LOGGER.error("%s or %s missing base_host_url option" % \
+ (CONFIG_USER, CONFIG_SYSTEM))
return False
try:
saveConfigFile(flowcell, options.url, cfg_filepath)
conf_info.config_filepath = cfg_filepath
- except FlowCellNotFound, e:
- logging.error(e)
+ except FlowCellNotFound as e:
+ LOGGER.error(e)
return False
- except WebError404, e:
- logging.error(e)
+ except WebError404 as e:
+ LOGGER.error(e)
return False
- except IOError, e:
- logging.error(e)
+ except IOError as e:
+ LOGGER.error(e)
return False
- except Exception, e:
- logging.error(e)
+ except Exception as e:
+ LOGGER.error(e)
return False
f = open(cfg_filepath, 'r')
genome_dict = getAvailableGenomes(genome_dir)
mapper_dict = constructMapperDict(genome_dict)
- logging.debug(data)
+ LOGGER.debug(data)
f = open(cfg_filepath, 'w')
f.write(data % (mapper_dict))
f.close()
-
+
return True
-
+
def configure(conf_info):
fout = open(stdout_filepath, 'w')
ferr = open(stderr_filepath, 'w')
-
+
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',
+ '--GERALD=%s' % (conf_info.config_filepath),
'--make',
conf_info.analysis_dir],
- stdout=fout,
- stderr=ferr)
+ stdout=fout,
+ stderr=ferr)
- print "Configuring pipeline: %s" % (time.ctime())
+ print("Configuring pipeline: %s" % (time.ctime()))
error_code = pipe.wait()
# Clean up
fout.close()
ferr.close()
-
-
+
+
##################
# Process stdout
fout = open(stdout_filepath, 'r')
-
+
stdout_line = fout.readline()
complete = False
#error_code = pipe.wait()
if error_code:
- logging.error('Recieved error_code: %s' % (error_code))
+ LOGGER.error('Recieved error_code: %s' % (error_code))
else:
- logging.info('We are go for launch!')
+ LOGGER.info('We are go for launch!')
#Process stderr
ferr = open(stderr_filepath, 'r')
# 1) The stdout completed without error
# 2) The program exited with status 0
# 3) No errors found in stdout
- print '#Expect: True, False, True, True'
- print complete, bool(error_code), abort != RUN_ABORT, stderr_success is True
+ print('#Expect: True, False, True, True')
+ print(complete, bool(error_code), abort != RUN_ABORT, stderr_success is True)
status = complete is True and \
bool(error_code) is False and \
abort != RUN_ABORT and \
# 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")
+ LOGGER.error("Failed to retrieve run_path")
return False
-
+
return 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' \
+ LOGGER.error('Run path does not exist: %s' \
% (conf_info.run_path))
return False
wdd = wm.add_watch(conf_info.run_path, mask, rec=True)
# Log pipeline starting
- logging.info('STARTING PIPELINE @ %s' % (time.ctime()))
-
+ LOGGER.info('STARTING PIPELINE @ %s' % (time.ctime()))
+
# Start the pipeline (and hide!)
#pipe = subprocess.Popen(['make',
# '-j8',
ferr.close()
# Finished file check!
- print 'RUN SUCCESS CHECK:'
- for key, value in event.run_status_dict.items():
- print ' %s: %s' % (key, value)
+ print('RUN SUCCESS CHECK:')
+ for key, value in list(event.run_status_dict.items()):
+ print(' %s: %s' % (key, value))
dstatus = event.run_status_dict
projects / htsworkflow.git / blobdiff