Skip to content

Commit

Permalink
removed code smells
Browse files Browse the repository at this point in the history
  • Loading branch information
Felix Simkovic committed Apr 15, 2017
1 parent 87e0781 commit ae497a4
Showing 1 changed file with 33 additions and 27 deletions.
60 changes: 33 additions & 27 deletions simbad/util/mtz_util.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@

from simbad.util import simbad_util # Avoid circular dependencies

_logger = logging.getLogger()
_logger.setLevel(logging.DEBUG)
logger = logging.getLogger()
logger.setLevel(logging.DEBUG)



Expand Down Expand Up @@ -81,8 +81,8 @@ def del_column(file_name, column, overwrite=True):
retcode = simbad_util.run_command(cmd, stdin=stdin, logfile=logfile)
if retcode != 0:
msg = "Error running mtzutils. Check the logfile: {0}".format(logfile)
_logger.critical(msg)
raise RuntimeError, msg
logger.critical(msg)
raise RuntimeError(msg)

if overwrite:
shutil.move(mtzDel,file_name)
Expand All @@ -99,8 +99,8 @@ def add_rfree(file_name,directory=None,overwrite=True):
retcode = simbad_util.run_command(cmd, logfile=logfile)
if retcode != 0:
msg = "Error running command: {0}. Check the logfile: {1}".format(" ".join(cmd),logfile)
_logger.critical(msg)
raise RuntimeError, msg
logger.critical(msg)
raise RuntimeError(msg)

if overwrite:
shutil.move(mtzUnique,file_name)
Expand All @@ -115,7 +115,7 @@ def get_labels(file_name):
if not reflection_file.file_type()=="ccp4_mtz":
msg="File is not of type ccp4_mtz: {0}".format(file_name)
logging.critical(msg)
raise RuntimeError,msg
raise RuntimeError(msg)

content=reflection_file.file_content()
ctypes=content.column_types()
Expand All @@ -124,23 +124,28 @@ def get_labels(file_name):
dtype='D'

if not ftype in ctypes:
raise RuntimeError,"Cannot find any structure amplitudes in: {0}".format(file_name)
msg = "Cannot find any structure amplitudes in: {0}".format(file_name)
raise RuntimeError(msg)
F=clabels[ctypes.index(ftype)]

# FP derived from F
FP='SIG'+F
if not FP in clabels:
raise RuntimeError,"Cannot find label {0} in file: {1}".format(FP,file_name)
msg = "Cannot find label {0} in file: {1}".format(FP,file_name)
raise RuntimeError(msg)

try:
if not dtype in ctypes:
raise RuntimeError, "Cannot find any structure amplitudes in: {0}".format(file_name)
msg = "Cannot find any structure amplitudes in: {0}".format(file_name)
raise RuntimeError(msg)

DANO = clabels[ctypes.index(dtype)]

# SIGDANO derived from DANO
SIGDANO = 'SIG' + DANO
if not SIGDANO in clabels:
raise RuntimeError, "Cannot find label {0} in file: {1}".format(SIGDANO, file_name)
msg = "Cannot find label {0} in file: {1}".format(SIGDANO, file_name)
raise RuntimeError(msg)
except RuntimeError:
DANO, SIGDANO = None, None

Expand All @@ -154,9 +159,9 @@ def get_rfree(file_name):

reflection_file = reflection_file_reader.any_reflection_file(file_name=file_name)
if not reflection_file.file_type()=="ccp4_mtz":
msg="File is not of type ccp4_mtz: {0}".format(file_name)
msg = "File is not of type ccp4_mtz: {0}".format(file_name)
logging.critical(msg)
raise RuntimeError,msg
raise RuntimeError(msg)

# Read the file
content=reflection_file.file_content()
Expand All @@ -179,7 +184,7 @@ def _get_rfree(content):
#print float(n0)/float(n1)*100
if n0>0 and n1>0:
if rfree_label:
_logger.warning("FOUND >1 RFREE label in file!")
logger.warning("FOUND >1 RFREE label in file!")
rfree_label=label
return rfree_label

Expand All @@ -203,10 +208,11 @@ def to_hkl(mtz_file,hkl_file=None,directory=None,F=None,SIGF=None,FREE=None):
END""".format(F,SIGF,FREE)

ret = simbad_util.run_command(cmd=cmd, logfile=logfile, directory=None, dolog=False, stdin=stdin)
if not ret==0:
raise RuntimeError,"Error converting {0} to HKL format - see log: {1}".format(mtz_file,logfile)
else:
if ret == 0:
os.unlink(logfile)
else:
msg = "Error converting {0} to HKL format - see log: {1}".format(mtz_file,logfile)
raise RuntimeError(msg)

return hkl_file

Expand All @@ -218,14 +224,14 @@ def processReflectionFile(amoptd):

# Now have an mtz so check it's valid
if not amoptd['mtz'] or not os.path.isfile( amoptd['mtz'] ):
_logger.critical("Cannot find MTZ file: {0}".format( amoptd['mtz'] ) )
logger.critical("Cannot find MTZ file: %s", amoptd['mtz'])
sys.exit(1)


# Get column label info
reflection_file = reflection_file_reader.any_reflection_file(file_name=amoptd['mtz'])
if not reflection_file.file_type()=="ccp4_mtz":
_logger.critical("File is not of type ccp4_mtz: {0}".format( amoptd['mtz'] ) )
logger.critical("File is not of type ccp4_mtz: %s", amoptd['mtz'])
sys.exit(1)

# Read the file
Expand All @@ -235,54 +241,54 @@ def processReflectionFile(amoptd):

for flag in ['F','SIGF','FREE']:
if amoptd[flag] and amoptd[flag] not in content.column_labels():
_logger.critical("Cannot find flag {0} label {1} in mtz file {2}".format( flag, amoptd[flag], amoptd['mtz'] ) )
logger.critical("Cannot find flag %s label %s in mtz file %s", flag, amoptd[flag], amoptd['mtz'])
sys.exit(1)

# If any of the flags aren't given we set defaults based on what's in the file
if not amoptd['F']:
if 'F' not in content.column_types():
_logger.critical("Cannot find column type F for flag F in mtz file: {0}".format( amoptd['mtz'] ) )
logger.critical("Cannot find column type F for flag F in mtz file: %s", amoptd['mtz'])
sys.exit(1)
amoptd['F'] = content.column_labels()[content.column_types().index('F')]
if not amoptd['SIGF']:
l='SIG'+amoptd['F']
if not l in content.column_labels():
_logger.critical("Cannot find column type {0} for flag SIGF in mtz file: {0}".format( l, amoptd['mtz'] ) )
logger.critical("Cannot find column type %s for flag SIGF in mtz file: %s", l, amoptd['mtz'])
sys.exit(1)
amoptd['SIGF'] = l

if amoptd['FREE']:
# Check is valid
rfree=_get_rfree(content)
if not rfree or not rfree==amoptd['FREE']:
_logger.critical("Given RFREE label {0} is not valid for mtz file: {0}".format( amoptd['FREE'], amoptd['mtz'] ) )
logger.critical("Given RFREE label %s is not valid for mtz file: %s", amoptd['FREE'], amoptd['mtz'])
sys.exit(1)
else:
# See if we can find a valid label in the file
rfree=_get_rfree(content)
if not rfree:
# Need to generate RFREE
_logger.warning("Cannot find a valid FREE flag - running uniquefy to generate column with RFREE data." )
logger.warning("Cannot find a valid FREE flag - running uniquefy to generate column with RFREE data.")
amoptd['mtz'] = add_rfree( amoptd['mtz'], directory=amoptd['work_dir'],overwrite=False)

# Check file and get new FREE flag
rfree=get_rfree(amoptd['mtz'])
if not rfree:
_logger.critical("Cannot find valid rfree flag in mtz file {0} after running uniquiefy".format(amoptd['mtz']))
logger.critical("Cannot find valid rfree flag in mtz file %s after running uniquiefy", amoptd['mtz'])
sys.exit(1)
amoptd['FREE'] = rfree

# Return anomalous data labels if the columns exist in the file
if not amoptd['DANO']:
if 'D' not in content.column_types():
_logger.critical("Cannot find column type D for flag DANO in mtz file: {0}".format(amoptd['mtz']))
logger.critical("Cannot find column type D for flag DANO in mtz file: %s", amoptd['mtz'])
else:
amoptd['DANO'] = content.column_labels()[content.column_types().index('D')]

if not amoptd['SIGDANO'] and amoptd['DANO']:
l = 'SIG' + amoptd['DANO']
if not l in content.column_labels():
_logger.critical("Cannot find column type {0} for flag SIGDANO in mtz file: {0}".format( l, amoptd['mtz'] ) )
logger.critical("Cannot find column type %s for flag SIGDANO in mtz file: %s", l, amoptd['mtz'])
else:
amoptd['SIGDANO'] = l

Expand Down

0 comments on commit ae497a4

Please sign in to comment.