def clean(self):
try:
cmd_check('rm -rf {}', self.ds_path)
# cmd_check("find {} -type f ! -name '*.json' -delete", self.ds_path)
except CalledProcessError as e:
logger.warning('Deleting interim local data files error: %s',
e.message)
def isotope_peaks(self, sf, adduct):
"""
Args
----
sf : str
Sum formula
adduct : str
Molecule adduct. One of isotope_generation.adducts from a dataset config file
Returns
-------
: dict
A dict with keys:
- centroid mzs
- centroid intensities
In case of any errors returns a dict of empty lists.
"""
centroids = Centroids([], [])
try:
isotope_ms = self._isodist(sf + adduct)
centroids = Centroids(*map(lambda l: l[:6],
isotope_ms.get_spectrum(source='centroids')))
except InvalidFormulaError as e:
logger.warning('(%s, %s) - %s', sf, adduct, e)
except Exception as e:
logger.error('(%s, %s) - %s', sf, adduct, e)
logger.error(format_exc())
finally:
return centroids
def parsable(sf):
try:
parseSumFormula(sf)
return True
except Exception as e:
logger.warning(e)
return False
def clean(self):
try:
bucket_obj = self.s3.Bucket(self.bucket)
for obj in bucket_obj.objects.filter(Prefix=self.ds_path):
self.s3.Object(self.bucket, obj.key).delete()
logger.info('Successfully deleted interim data')
except CalledProcessError as e:
logger.warning('Deleting interim data files error: %s', e.message)
def clean(self):
try:
bucket_obj = self.s3.Bucket(self.bucket)
for obj in bucket_obj.objects.filter(Prefix=self.ds_path):
self.s3.Object(self.bucket, obj.key).delete()
logger.info('Successfully deleted interim data')
except CalledProcessError as e:
logger.warning('Deleting interim data files error: %s', e.message)
def _valid_sf_adduct(cls, sf, adduct):
if sf is None or adduct is None or sf == 'None' or adduct == 'None':
logger.warning('Invalid sum formula or adduct: sf=%s, adduct=%s', sf, adduct)
return False
if '-' in adduct and adduct.strip('-') not in cls._sf_elements(sf):
logger.info('No negative adduct element in the sum formula: sf=%s, adduct=%s', sf, adduct)
return False
return True
def _valid_sf_adduct(cls, sf, adduct):
if sf is None or adduct is None or sf == 'None' or adduct == 'None':
logger.warning('Invalid sum formula or adduct: sf=%s, adduct=%s',
sf, adduct)
return False
if '-' in adduct and adduct.strip('-') not in cls._sf_elements(sf):
logger.info(
'No negative adduct element in the sum formula: sf=%s, adduct=%s',
sf, adduct)
return False
return True
def wrapper(*args, **kwargs):
for i in range(num_retries):
try:
return func(*args, **kwargs)
except exception_type as e:
wait_initial, wait_increase, jitter = retry_wait_params
min_wait = wait_initial + i * wait_increase
delay = random.uniform(min_wait, min_wait + jitter)
logger.warning(
f'{func_name} raised {type(e)} on attempt {i+1}. '
f'Retrying after {delay:.1f} seconds...'
)
sleep(delay)
# Last attempt, don't catch the exception
return func(*args, **kwargs)
def clean(self):
try:
cmd_check('rm -rf {}', self.ds_path)
# cmd_check("find {} -type f ! -name '*.json' -delete", self.ds_path)
except CalledProcessError as e:
logger.warning('Deleting interim local data files error: %s', e.message)
def _uniq_coord(self, x, y):
if (x, y) in self.coord_set:
logger.warning('Duplicated x,y = ({},{}) pair'.format(x, y))
return False
self.coord_set.add((x, y))
return True
def _uniq_coord(self, x, y):
if (x, y) in self.coord_set:
logger.warning('Duplicated x,y = ({},{}) pair'.format(x, y))
return False
self.coord_set.add((x, y))
return True