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code smells removed
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Felix Simkovic committed Apr 15, 2017
1 parent ae497a4 commit cafc7c0
Showing 1 changed file with 24 additions and 31 deletions.
55 changes: 24 additions & 31 deletions simbad/main.py
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@
__email__ = "hlasimpk@liv.ac.uk"
__version__ = version.__version__

LOGGER = logging_util.setup_console_logging()
logger = logging_util.setup_console_logging()
monitor = None


Expand All @@ -54,17 +54,15 @@ def __init__(self):
def setup(self, optd):

if optd['work_dir']:
LOGGER.info('Making a named work directory: {0}'.format(optd['work_dir']))
try:
os.mkdir(optd['work_dir'])
except:
logger.info('Making a named work directory: {0}'.format(optd['work_dir']))
if os.path.isdir(optd['work_dir']):
msg = "Cannot create work_dir {0}".format(optd['work_dir'])
exit_util.exit_error(msg, sys.exc_info()[2])
else:
if not os.path.exists(optd['run_dir']):
msg = "Cannot find run directory: {0}".format(optd['run_dir'])
exit_util.exit_error(msg, sys.exc_info()[2])
LOGGER.info('Making a run_directory: checking for previous runs...')
logger.info('Making a run_directory: checking for previous runs...')
optd['work_dir'] = simbad_util.make_workdir(optd['run_dir'],
ccp4_jobid=optd['ccp4_jobid'])

Expand All @@ -88,22 +86,22 @@ def setup(self, optd):
ccp4_version = ".".join([str(x) for x in optd['ccp4_version']])

# Print out Version and invocation
LOGGER.info(simbad_util.header)
LOGGER.info("SIMBAD version: {0}".format(version.__version__))
LOGGER.info("Running with CCP4 version: {0} from directory: {1}".format(ccp4_version, ccp4_home))
LOGGER.info("Running on host: {0}".format(platform.node()))
LOGGER.info("Running on platform: {0}".format(platform.platform()))
LOGGER.info("Job started at: {0}".format(time.strftime("%a, %d %b %Y %H:%M:%S", time.gmtime())))
LOGGER.info("Invoked with command-line:\n{0}\n".format(" ".join(sys.argv)))
LOGGER.info("Running in directory: {0}\n".format(optd['work_dir']))
logger.info(simbad_util.header)
logger.info("SIMBAD version: %s", version.__version__)
logger.info("Running with CCP4 version: %s from directory: %s", ccp4_version, ccp4_home))
logger.info("Running on host: %s", platform.node())
logger.info("Running on platform: %s", platform.platform())
logger.info("Job started at: %s", time.strftime("%a, %d %b %Y %H:%M:%S", time.gmtime()))
logger.info("Invoked with command-line:\n%s\n", " ".join(sys.argv))
logger.info("Running in directory: %s\n", optd['work_dir'])

################################################################################################################
# SHOULD ADD IN CODE HERE TO REPORT THE OUTPUT OF SIMBAD ON THE FLY
################################################################################################################

optd = options_processor.process_options(optd)

LOGGER.info('All needed programs are found, continuing...')
logger.info('All needed programs are found, continuing...')

return optd

Expand All @@ -129,7 +127,7 @@ def main(self, args=None):
self.setup(sopt.d)

# Display the parameters used
LOGGER.debug(sopt.prettify_parameters())
logger.debug(sopt.prettify_parameters())

sopt.write_config_file()

Expand Down Expand Up @@ -175,10 +173,10 @@ def main(self, args=None):
pass

else:
LOGGER.info("No results found - lattice search was unsuccessful")
logger.info("No results found - lattice search was unsuccessful")

elif sopt.d["lattice"] != "True":
LOGGER.info("Lattice run set to {0}: Skipping...".format(sopt.d["lattice"]))
logger.info("Lattice run set to %s: Skipping...", sopt.d["lattice"])

if sopt.d['solution'] and sopt.d['early_term'] or sopt.d['contaminant'] == 'False' and sopt.d['full'] == 'False':
self.finished = True
Expand Down Expand Up @@ -220,10 +218,10 @@ def main(self, args=None):
except:
pass
else:
LOGGER.info("No results found - Contaminant search was unsuccessful")
logger.info("No results found - Contaminant search was unsuccessful")

elif sopt.d["contaminant"] != "True":
LOGGER.info("Contaminant run set to {0}: Skipping...".format(sopt.d["contaminant"]))
logger.info("Contaminant run set to %s: Skipping...", sopt.d["contaminant"])

if sopt.d['solution'] and sopt.d['early_term'] or sopt.d['full'] == 'False':
self.finished = True
Expand All @@ -232,7 +230,7 @@ def main(self, args=None):
# Full search
########################################################################

if sopt.d['full'] == True and not (sopt.d['early_term'] and sopt.d['solution']):
if sopt.d['full'] and not (sopt.d['early_term'] and sopt.d['solution']):
# Create work directories
os.mkdir(os.path.join(sopt.d['work_dir'], 'output'))
os.mkdir(os.path.join(sopt.d['work_dir'], 'logs'))
Expand All @@ -245,23 +243,18 @@ def main(self, args=None):
for e in os.walk(sopt.d['morda_db']):
if first:
first = False
pass
else:
if count < 1:
pdb_dir = e[0]
count += 1


elif sopt.d['sphere_database']:
pass



self.finished = True

elif sopt.d["full"] != "True" and not self.finished:
LOGGER.info("Full run set to {0}: Skipping...".format(sopt.d["full"]))

logger.info("Full run set to %s: Skipping...", sopt.d["full"])

########################################################################
# Finish up
Expand All @@ -279,7 +272,7 @@ def main(self, args=None):
msg = os.linesep + 'All processing completed (in {0:6.2F} hours)'.format(run_in_hours) + os.linesep
msg += '----------------------------------------' + os.linesep
msg += 'Results can be viewed in {0}'.format(os.path.join(sopt.d['work_dir'], 'SIMBAD.log')) + os.linesep
LOGGER.info(msg)
logger.info(msg)


exit()
Expand All @@ -306,11 +299,11 @@ def setup_ccp4(self, amoptd):
# type: (object) -> object
"""Check CCP4 is available and return the top CCP4 directory"""
# Make sure CCP4 is around
if not "CCP4" in os.environ:
if "CCP4" not in os.environ:
msg = "Cannot find CCP4 installation - please make sure CCP4 is installed and the setup scripts have been run!"
exit_util.exit_error(msg)

if not "CCP4_SCR" in os.environ:
if "CCP4_SCR" not in os.environ:
msg = "$CCP4_SCR environement variable not set - please make sure CCP4 is installed and the setup scripts have been run!"
exit_util.exit_error(msg)

Expand All @@ -319,7 +312,7 @@ def setup_ccp4(self, amoptd):
msg += "Cannot find the $CCP4_SCR directory: {0}\n".format(os.environ['CCP4_SCR'])
msg += "The directory will be created, but it should have already been created by the CCP4 startup scripts\n"
msg += "Please make sure CCP4 is installed and the setup scripts have been run."
LOGGER.critical(msg)
logger.critical(msg)
os.mkdir(os.environ['CCP4_SCR'])
# exit_util.exit_error(msg)

Expand Down

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