def main():
"""Validates config file"""
config = ConfigParser()
config.read(CONFIG_PATH)
# Type validate each entry not in the keymap
for section in filter(
lambda s: s != 'BIT2KEY_MAP',
config.sections()
):
for option in filter(
lambda o: not o.startswith('type_'),
config.options(section)
):
if "GPIO_attr" in config.get(section, 'type_' + option):
assert hasattr(GPIO, config.get(section, option)), (
"Config validation failed. GPIO does not have "
"attr {}.".format(GPIO, config.get(section, option))
)
assert str(type(safe_eval(config.get(section, option)))) == \
"<type '{}'>".format(config.get(section, 'type_' + option)),\
("Config validation failed. {} expected type was <type '{}'>"
", got {} instead.".format(
option,
config.get(section, 'type_' + option),
str(type(safe_eval(
config.get(section, option))))))
# Validate keymap length
actual = sorted([int(option) for option in config.options('BIT2KEY_MAP')])
expected = range(int(config.get(
'RASPBERRY_CEREAL', 'bus_width')) * int(config.get(
'RASPBERRY_CEREAL', 'shift_registers')))
assert actual == expected, \
("KEY2BIT_MAP does not have items matching specification from"
" bus_width and shift_registers.\nactual: {}\nexpected: {}".format(
actual,
expected))
# Ensure keys in keymap actually exist
for key in [
config.get('BIT2KEY_MAP', key) for key in
config.options('BIT2KEY_MAP')]:
assert hasattr(uinput, key), ("The key, {}, is not valid."
.format(key))
def _parse_args(func, args, usage=None):
"""Parse the arguments given to a magic function"""
if isinstance(args, list):
args = ' '.join(args)
args = _split_args(args)
kwargs = dict()
if getattr(func, 'has_options', False):
parser = MagicOptionParser(usage=usage, conflict_handler="resolve")
parser.add_options(func.options)
left = []
value = None
if '--' in args:
left = args[:args.index('--')]
value, args = parser.parse_args(args[args.index('--') + 1:])
else:
while args:
try:
value, args = parser.parse_args(args)
except Exception:
left.append(args.pop(0))
else:
break
args = left + args
if value:
kwargs = value.__dict__
new_args = []
for arg in args:
try:
new_args.append(safe_eval(arg))
except:
new_args.append(arg)
for (key, value) in kwargs.items():
try:
kwargs[key] = safe_eval(value)
except:
pass
return new_args, kwargs
def _parse_args(func, args, usage=None):
"""Parse the arguments given to a magic function"""
if isinstance(args, list):
args = ' '.join(args)
args = _split_args(args)
kwargs = dict()
if getattr(func, 'has_options', False):
parser = MagicOptionParser(usage=usage, conflict_handler="resolve")
parser.add_options(func.options)
left = []
value = None
if '--' in args:
left = args[:args.index('--')]
value, args = parser.parse_args(args[args.index('--') + 1:])
else:
while args:
try:
value, args = parser.parse_args(args)
except Exception:
left.append(args.pop(0))
else:
break
args = left + args
if value:
kwargs = value.__dict__
new_args = []
for arg in args:
try:
new_args.append(safe_eval(arg))
except:
new_args.append(arg)
for (key, value) in kwargs.items():
try:
kwargs[key] = safe_eval(value)
except:
pass
return new_args, kwargs
def _split_args(args):
try:
# do not use posix mode, to avoid eating quote characters
args = shlex.split(args, posix=False)
except:
# parse error; let's pass args along rather than crashing
args = args.split()
new_args = []
temp = ''
for arg in args:
if arg.startswith('-'):
new_args.append(arg)
elif temp:
arg = temp + ' ' + arg
try:
safe_eval(arg)
except:
temp = arg
else:
new_args.append(arg)
temp = ''
elif arg.startswith(('(', '[', '{')) or '(' in arg:
try:
safe_eval(arg)
except:
temp = arg
else:
new_args.append(arg)
else:
new_args.append(arg)
if temp:
new_args.append(temp)
return new_args
def _split_args(args):
try:
# do not use posix mode, to avoid eating quote characters
args = shlex.split(args, posix=False)
except:
# parse error; let's pass args along rather than crashing
args = args.split()
new_args = []
temp = ''
for arg in args:
if arg.startswith('-'):
new_args.append(arg)
elif temp:
arg = temp + ' ' + arg
try:
safe_eval(arg)
except:
temp = arg
else:
new_args.append(arg)
temp = ''
elif arg.startswith(('(', '[', '{')) or '(' in arg:
try:
safe_eval(arg)
except:
temp = arg
else:
new_args.append(arg)
else:
new_args.append(arg)
if temp:
new_args.append(temp)
return new_args
def main():
"""Polls shift register for serial data and emit_clicks HIGHs"""
if os.geteuid() != 0:
exit("Must be run as root!")
print "[WAIT] Setting up..."
# argparse
parser = argparse.ArgumentParser()
for arg in ARGS.keys():
parser.add_argument(*ARGS[arg][0], dest=arg, action='store_true',
help=ARGS[arg][1])
args = parser.parse_args()
# Validate config
validate_config()
# Read config file
config = ConfigParser()
config.read(CONFIG_PATH)
#
active_low = int(safe_eval(config.get('RASPBERRY_CEREAL', 'active_low')))
# Create device
events = []
for key in [config.get('BIT2KEY_MAP', num)
for num in config.options('BIT2KEY_MAP')
if config.get('BIT2KEY_MAP', num) != "NONE"]:
events.append(getattr(uinput, key.upper()))
device = uinput.Device(events)
print "[OK] Configuration options type-validated."
# Setup GPIO
sr_config = gpio_setup()
# Set poll time
poll_time = float(config.get('RASPBERRY_CEREAL', 'poll_time'))
print ("[OK] If you opened {0} with {1}, you may safely hit Ctrl-C and"
" {0} will continue to run in the background. Remember to kill"
" the job when you are done. Polling every {2} ms.".format(
"raspberry-cereal",
"'sudo raspberry-cereal &'",
int(poll_time * 1000)))
# PERFORMANCE: Moved main_loop so that there are no longer
# two loops.
try:
main_loop(sr_config, active_low, poll_time, device, config, args)
except KeyboardInterrupt:
exit("[OK] raspberry-cereal bids you adieu.")
def _get_search_engines(self):
try:
lang = MyConfig.get("document_retrieval", "lang")
engines = safe_eval(MyConfig.get("document_retrieval", "engines"))
throttle = MyConfig.get("document_retrieval", "throttle")
l = []
for (engine, license) in engines:
# Eval to something like this:
# Google(google_license, throttle, lang)
l.append(eval(engine + "(\"" + license + "\", " + throttle + ", " + lang + ")"))
return l
except MyConfigException:
sys.exit("_get_search_engines: config error")
except:
logger = logging.getLogger("qa_logger")
logger.exception("_get_search_engines: fatal error")
sys.exit(2)
def _get_search_engines(self):
try:
lang = MyConfig.get("document_retrieval", "lang")
engines = safe_eval(MyConfig.get("document_retrieval", "engines"))
throttle = MyConfig.get("document_retrieval", "throttle")
l = []
for (engine, license) in engines:
# Eval to something like this:
# Google(google_license, throttle, lang)
l.append(
eval(engine + "(\"" + license + "\", " + throttle + ", " +
lang + ")"))
return l
except MyConfigException:
sys.exit("_get_search_engines: config error")
except:
logger = logging.getLogger("qa_logger")
logger.exception("_get_search_engines: fatal error")
sys.exit(2)
def fix_code_style_list(key, data, errors, context):
"""Grant's code style fix converter"""
from ast import literal_eval as safe_eval
# As per method signature this is for editing data, not returning a value
raw = data.get(key)
try:
py_list = safe_eval(raw)
except ValueError as e:
# only warnings seem to make it through the CKAN logging (and appear
# in /var/log/apache2/ckan_default.error.log)
log.info(
"Unable to clean value {} - already a clean string? {}".format(
raw, e))
return None
except Exception as e:
log.info(u"Unable to clean value {} - {}".format(raw, e))
return None
else:
if isinstance(py_list, list):
log.info(
u"Converted code-style list '{}' into text format".format(raw))
data[key] = u' & '.join(py_list)
def gpio_setup():
"""Performs GPIO setup
returns:
Shift register config
"""
sr_config = {}
config = ConfigParser()
config.read(CONFIG_PATH)
sr_config['ploadpin'] = int(config.get('74HC165N', 'ploadpin'))
sr_config['datapin'] = int(config.get('74HC165N', 'datapin'))
sr_config['clockpin'] = int(config.get('74HC165N', 'clockpin'))
sr_config['triggerpulsewidth'] = float(
config.get('74HC165N',
'triggerpulsewidth')
)
sr_config['bus_width'] = int(config.get('RASPBERRY_CEREAL', 'bus_width'))
sr_config['shift_registers'] = int(config.get(
'RASPBERRY_CEREAL',
'shift_registers'
)
)
# PERFORMANCE: Perform this operation here so it only needs to be
# performed once
sr_config['full_width'] = sr_config[
'bus_width'] * sr_config['shift_registers']
GPIO.setmode(getattr(GPIO, config.get('GPIO', 'setmode')))
GPIO.setwarnings(safe_eval(config.get('GPIO', 'setwarnings')))
GPIO.setup(sr_config['ploadpin'], GPIO.OUT)
GPIO.setup(sr_config['datapin'], GPIO.IN)
GPIO.setup(sr_config['clockpin'], GPIO.OUT)
GPIO.output(sr_config['clockpin'], 0)
GPIO.output(sr_config['ploadpin'], 1)
return sr_config
def server_version(self):
detected = tuple(
int(x) for x in self._server_version.relVersion.replace(
'rods', '').split('.'))
return (safe_eval(os.environ.get('IRODS_SERVER_VERSION', '()'))
or detected)
def parse_strelka(self, fname):
'''
extracts all the information about each mutations from line
'''
mode = self.__parse_header_strelka(fname)
if self.is_gzip(fname):
freader = gzip.open(fname, 'rb')
else:
freader = open(fname)
for line in freader:
if line[0] == '#':
continue
line = line.strip().split('\t')
line[7] = line[7].split(';')
line[8] = Utils.build_indices(line[8].split(':'))
#normal
line[9] = [safe_eval(val) for val in line[9].split(':')]
#tumour
line[10] = [safe_eval(val) for val in line[10].split(':')]
if mode == 'strelka_indel':
#TR = (DP+DP2)-sum(TIR)
tum_alt = line[10][line[8]['TIR']][0]
tum_ref = line[10][line[8]['DP']] - tum_alt
norm_alt = line[9][line[8]['TIR']][0]
norm_ref = line[9][line[8]['DP']] - norm_alt
else:
tum_ref = line[10][line[8][line[3] + 'U']][0]
norm_ref = line[9][line[8][line[3] + 'U']][0]
if line[4] == '.':
tum_alt = 'N/A'
norm_alt = 'N/A'
else:
tum_alt = max([
line[10][line[8][val + 'U']][0]
for val in line[4].split(',')
])
norm_alt = max([
line[9][line[8][val + 'U']][0]
for val in line[4].split(',')
])
subpat, _ = Utils.get_sub_pattern(line[3], line[4])
#get snpeff annotations
snpeff = self.parse_snpeff(line[7])
snpeff = self.sort_snpeff(snpeff)
#only keep the highest ranked annotation when removing duplicates
if self.rmdups:
snpeff = [snpeff[0]]
anns = self.get_annotations(line[7])
for snpval in snpeff:
outval = [
self.case_id, self.normal_id, self.tumour_id, line[0],
line[1], line[1], snpval[1], snpval[2], snpval[0], line[3],
line[4], tum_ref, tum_alt, norm_ref, norm_alt, anns[0],
anns[1], anns[2], mode, snpval[4], snpval[5], snpval[6],
self.project, snpval[7], snpval[8], line[6], snpval[3],
subpat
] + [None] * 5 + self.lab_vals
outval = [val if val else 'N/A' for val in outval]
yield outval
freader.close()
