text_prompt stringlengths 157 13.1k | code_prompt stringlengths 7 19.8k ⌀ |
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def clear_layout(layout: QLayout) -> None: """Clear the layout off all its components""" |
if layout is not None:
while layout.count():
item = layout.takeAt(0)
widget = item.widget()
if widget is not None:
widget.deleteLater()
else:
clear_layout(item.layout()) |
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def _get_hangul_syllable_type(hangul_syllable):
""" Function for taking a Unicode scalar value representing a Hangul syllable and determining the correct value f... |
if not _is_hangul_syllable(hangul_syllable):
raise ValueError("Value 0x%0.4x does not represent a Hangul syllable!" % hangul_syllable)
if not _hangul_syllable_types:
_load_hangul_syllable_types()
return _hangul_syllable_types[hangul_syllable] |
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def _get_jamo_short_name(jamo):
""" Function for taking a Unicode scalar value representing a Jamo and determining the correct value for its Jamo_Short_Name prop... |
if not _is_jamo(jamo):
raise ValueError("Value 0x%0.4x passed in does not represent a Jamo!" % jamo)
if not _jamo_short_names:
_load_jamo_short_names()
return _jamo_short_names[jamo] |
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def compose_hangul_syllable(jamo):
""" Function for taking a tuple or list of Unicode scalar values representing Jamo and composing it into a Hangul syllable. If... |
fmt_str_invalid_sequence = "{0} does not represent a valid sequence of Jamo!"
if len(jamo) == 3:
l_part, v_part, t_part = jamo
if not (l_part in range(0x1100, 0x1112 + 1) and
v_part in range(0x1161, 0x1175 + 1) and
t_part in range(0x11a8, 0x11c2 + 1)):
... |
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def _get_hangul_syllable_name(hangul_syllable):
""" Function for taking a Unicode scalar value representing a Hangul syllable and converting it to its syllable n... |
if not _is_hangul_syllable(hangul_syllable):
raise ValueError("Value passed in does not represent a Hangul syllable!")
jamo = decompose_hangul_syllable(hangul_syllable, fully_decompose=True)
result = ''
for j in jamo:
if j is not None:
result += _get_jamo_short_name(j)
r... |
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def generate_client_callers(spec, timeout, error_callback, local, app):
"""Return a dict mapping method names to anonymous functions that will call the server's ... |
callers_dict = {}
def mycallback(endpoint):
if not endpoint.handler_client:
return
callers_dict[endpoint.handler_client] = _generate_client_caller(spec, endpoint, timeout, error_callback, local, app)
spec.call_on_each_endpoint(mycallback)
return callers_dict |
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| def calculate_new_length(gene_split, gene_results, hit):
''' Function for calcualting new length if the gene is split on several
contigs
'''
# Looping over splitted hits and calculate new length
first = 1
for split in gene_split[hit['sbjct_header']]:
new_start = int(gene_results[split]['sbjct_st... |
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def stream_to_packet(data):
""" Chop a stream of data into MODBUS packets. :param data: stream of data :returns: a tuple of the data that is a packet with the re... |
if len(data) < 6:
return None
# unpack the length
pktlen = struct.unpack(">H", data[4:6])[0] + 6
if (len(data) < pktlen):
return None
return (data[:pktlen], data[pktlen:]) |
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def to_primitive(value, convert_instances=False, convert_datetime=True, level=0, max_depth=3):
"""Convert a complex object into primitives. Handy for JSON serial... |
# handle obvious types first - order of basic types determined by running
# full tests on nova project, resulting in the following counts:
# 572754 <type 'NoneType'>
# 460353 <type 'int'>
# 379632 <type 'unicode'>
# 274610 <type 'str'>
# 199918 <type 'dict'>
# 114200 <type 'datetime.dat... |
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| def stress(syllabified_simplex_word):
'''Assign primary and secondary stress to 'syllabified_simplex_word'.'''
syllables = syllabified_simplex_word.split('.')
stressed = '\'' + syllables[0] # primary stress
try:
n = 0
medial = syllables[1:-1]
for i, syll in enumerate(medial):
... |
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def confindr_reporter(self, analysistype='confindr'):
""" Creates a final report of all the ConFindr results """ |
# Initialise the data strings
data = 'Strain,Genus,NumContamSNVs,ContamStatus,PercentContam,PercentContamSTD\n'
with open(os.path.join(self.reportpath, analysistype + '.csv'), 'w') as report:
# Iterate through all the results
for sample in self.runmetadata.samples:
... |
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def methodreporter(self):
""" Create final reports collating results from all the individual iterations through the method pipeline """ |
# Ensure that the analyses are set to complete
self.analysescomplete = True
# Reset the report path to original value
self.reportpath = os.path.join(self.path, 'reports')
# Clear the runmetadata - it will be populated with all the metadata from completemetadata
self.runm... |
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def main(self):
""" Run the methods required to create the genesippr report summary image """ |
self.dataframe_setup()
self.figure_populate(self.outputfolder,
self.image_report,
self.header_list,
self.samples,
'genesippr',
'report',
... |
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def dir_exists(location, use_sudo=False):
"""Tells if there is a remote directory at the given location.""" |
with settings(hide('running', 'stdout', 'stderr'), warn_only=True):
if use_sudo:
# convert return code 0 to True
return not bool(sudo('test -d %s' % (location)).return_code)
else:
return not bool(run('test -d %s' % (location)).return_code) |
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def disable_requiretty_on_sudoers(log=False):
""" allow sudo calls through ssh without a tty """ |
if log:
bookshelf2.logging_helpers.log_green(
'disabling requiretty on sudo calls')
comment_line('/etc/sudoers',
'^Defaults.*requiretty', use_sudo=True)
return True |
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def linux_distribution():
""" returns the linux distribution in lower case """ |
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
warn_only=True, capture=True):
data = os_release()
return(data['ID']) |
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def systemd(service, start=True, enabled=True, unmask=False, restart=False):
""" manipulates systemd services """ |
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
warn_only=True, capture=True):
if restart:
sudo('systemctl restart %s' % service)
else:
if start:
sudo('systemctl start %s' % service)
else:
sudo('s... |
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def install_os_updates(distribution, force=False):
""" installs OS updates """ |
if ('centos' in distribution or
'rhel' in distribution or
'redhat' in distribution):
bookshelf2.logging_helpers.log_green('installing OS updates')
sudo("yum -y --quiet clean all")
sudo("yum group mark convert")
sudo("yum -y --quiet update")
if ('ubuntu' ... |
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def put(self):
"""Updates this task whitelist on the saltant server. Returns: :class:`saltant.models.task_whitelist.TaskWhitelist`: A task whitelist model instan... |
return self.manager.put(
id=self.id,
name=self.name,
description=self.description,
whitelisted_container_task_types=(
self.whitelisted_container_task_types
),
whitelisted_executable_task_types=(
self.whiteli... |
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def create( self, name, description="", whitelisted_container_task_types=None, whitelisted_executable_task_types=None, ):
"""Create a task whitelist. Args: name ... |
# Translate whitelists None to [] if necessary
if whitelisted_container_task_types is None:
whitelisted_container_task_types = []
if whitelisted_executable_task_types is None:
whitelisted_executable_task_types = []
# Create the object
request_url = self... |
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def patch( self, id, name=None, description=None, whitelisted_container_task_types=None, whitelisted_executable_task_types=None, ):
"""Partially updates a task w... |
# Update the object
request_url = self._client.base_api_url + self.detail_url.format(id=id)
data_to_patch = {}
if name is not None:
data_to_patch["name"] = name
if description is not None:
data_to_patch["description"] = description
if whitelis... |
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def enable_logging( level='WARNING' ):
"""Enable sending logs to stderr. Useful for shell sessions. level Logging threshold, as defined in the logging module of ... |
log = logging.getLogger( 'mrcrowbar' )
log.setLevel( level )
out = logging.StreamHandler()
out.setLevel( level )
form = logging.Formatter( '[%(levelname)s] %(name)s - %(message)s' )
out.setFormatter( form )
log.addHandler( out ) |
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def find_all_iter( source, substring, start=None, end=None, overlap=False ):
"""Iterate through every location a substring can be found in a source string. sourc... |
data = source
base = 0
if end is not None:
data = data[:end]
if start is not None:
data = data[start:]
base = start
pointer = 0
increment = 1 if overlap else (len( substring ) or 1)
while True:
pointer = data.find( substring, pointer )
if pointer == -... |
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def find_all( source, substring, start=None, end=None, overlap=False ):
"""Return every location a substring can be found in a source string. source The source s... |
return [x for x in find_all_iter( source, substring, start, end, overlap )] |
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def pixdump_iter( source, start=None, end=None, length=None, width=64, height=None, palette=None ):
"""Return the contents of a byte string as a 256 colour image... |
assert is_bytes( source )
if not palette:
palette = colour.TEST_PALETTE
start = 0 if (start is None) else start
if (end is not None) and (length is not None):
raise ValueError( 'Can\'t define both an end and a length!' )
elif (length is not None):
end = start+length
el... |
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def pixdump( source, start=None, end=None, length=None, width=64, height=None, palette=None ):
"""Print the contents of a byte string as a 256 colour image. sour... |
for line in pixdump_iter( source, start, end, length, width, height, palette ):
print( line ) |
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def put_bits( self, value, count ):
"""Push bits into the target. value Integer containing bits to push, ordered from least-significant bit to most-significant b... |
for _ in range( count ):
# bits are retrieved from the source LSB first
bit = (value & 1)
value >>= 1
# however, bits are put into the result based on the rule
if self.bits_reverse:
if self.insert_at_msb:
self.cur... |
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def get_buffer( self ):
"""Return a byte string containing the target as currently written.""" |
last_byte = self.current_bits if (self.bits_remaining < 8) else None
result = self.output
if last_byte is not None:
result = bytearray( result )
result.append( last_byte )
if self.bytes_reverse:
return bytes( reversed( result ) )
else:
... |
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def convert_case(name):
"""Converts name from CamelCase to snake_case""" |
s1 = re.sub('(.)([A-Z][a-z]+)', r'\1_\2', name)
return re.sub('([a-z0-9])([A-Z])', r'\1_\2', s1).lower() |
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def table_name(self):
"""Pluralises the class_name using utterly simple algo and returns as table_name""" |
if not self.class_name:
raise ValueError
else:
tbl_name = ModelCompiler.convert_case(self.class_name)
last_letter = tbl_name[-1]
if last_letter in ("y",):
return "{}ies".format(tbl_name[:-1])
elif last_letter in ("s",):
return "{}e... |
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def types(self):
"""All the unique types found in user supplied model""" |
res = []
for column in self.column_definitions:
tmp = column.get('type', None)
res.append(ModelCompiler.get_column_type(tmp)) if tmp else False
res = list(set(res))
return res |
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def basic_types(self):
"""Returns non-postgres types referenced in user supplied model """ |
if not self.foreign_key_definitions:
return self.standard_types
else:
tmp = self.standard_types
tmp.append('ForeignKey')
return tmp |
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def primary_keys(self):
"""Returns the primary keys referenced in user supplied model""" |
res = []
for column in self.column_definitions:
if 'primary_key' in column.keys():
tmp = column.get('primary_key', None)
res.append(column['name']) if tmp else False
return res |
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def compiled_columns(self):
"""Returns compiled column definitions""" |
def get_column_args(column):
tmp = []
for arg_name, arg_val in column.items():
if arg_name not in ('name', 'type'):
if arg_name in ('server_default', 'server_onupdate'):
arg_val = '"{}"'.format(arg_val)
tmp... |
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def compiled_foreign_keys(self):
"""Returns compiled foreign key definitions""" |
def get_column_args(column):
tmp = []
for arg_name, arg_val in column.items():
if arg_name not in ('name', 'type', 'reference'):
if arg_name in ('server_default', 'server_onupdate'):
arg_val = '"{}"'.format(arg_val)
... |
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def compiled_relationships(self):
"""Returns compiled relationship definitions""" |
def get_column_args(column):
tmp = []
for arg_name, arg_val in column.items():
if arg_name not in ('name', 'type', 'reference', 'class'):
if arg_name in ('back_populates', ):
arg_val = "'{}'".format(arg_val)
... |
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def compiled_init_func(self):
"""Returns compiled init function""" |
def get_column_assignment(column_name):
return ALCHEMY_TEMPLATES.col_assignment.safe_substitute(col_name=column_name)
def get_compiled_args(arg_name):
return ALCHEMY_TEMPLATES.func_arg.safe_substitute(arg_name=arg_name)
join_string = "\n" + self.tab + self.tab
... |
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def compiled_update_func(self):
"""Returns compiled update function""" |
def get_not_none_col_assignment(column_name):
return ALCHEMY_TEMPLATES.not_none_col_assignment.safe_substitute(col_name=column_name)
def get_compiled_args(arg_name):
return ALCHEMY_TEMPLATES.func_arg.safe_substitute(arg_name=arg_name)
join_string = "\n" + self.tab + s... |
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def compiled_hash_func(self):
"""Returns compiled hash function based on hash of stringified primary_keys. This isn't the most efficient way""" |
def get_primary_key_str(pkey_name):
return "str(self.{})".format(pkey_name)
hash_str = "+ ".join([get_primary_key_str(n) for n in self.primary_keys])
return ALCHEMY_TEMPLATES.hash_function.safe_substitute(concated_primary_key_strs=hash_str) |
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def compiled_model(self):
"""Returns compile ORM class for the user supplied model""" |
return ALCHEMY_TEMPLATES.model.safe_substitute(class_name=self.class_name,
table_name=self.table_name,
column_definitions=self.compiled_columns,
i... |
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def put(self):
"""Updates this task queue on the saltant server. Returns: :class:`saltant.models.task_queue.TaskQueue`: A task queue model instance representing ... |
return self.manager.put(
id=self.id,
name=self.name,
description=self.description,
private=self.private,
runs_executable_tasks=self.runs_executable_tasks,
runs_docker_container_tasks=self.runs_docker_container_tasks,
runs_singu... |
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def get(self, id=None, name=None):
"""Get a task queue. Either the id xor the name of the task type must be specified. Args: id (int, optional):
The id of the t... |
# Validate arguments - use an xor
if not (id is None) ^ (name is None):
raise ValueError("Either id or name must be set (but not both!)")
# If it's just ID provided, call the parent function
if id is not None:
return super(TaskQueueManager, self).get(id=id)
... |
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def create( self, name, description="", private=False, runs_executable_tasks=True, runs_docker_container_tasks=True, runs_singularity_container_tasks=True, active... |
# Translate whitelists None to [] if necessary
if whitelists is None:
whitelists = []
# Create the object
request_url = self._client.base_api_url + self.list_url
data_to_post = {
"name": name,
"description": description,
"private"... |
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def patch( self, id, name=None, description=None, private=None, runs_executable_tasks=None, runs_docker_container_tasks=None, runs_singularity_container_tasks=Non... |
# Update the object
request_url = self._client.base_api_url + self.detail_url.format(id=id)
data_to_patch = {}
if name is not None:
data_to_patch["name"] = name
if description is not None:
data_to_patch["description"] = description
if private ... |
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def put( self, id, name, description, private, runs_executable_tasks, runs_docker_container_tasks, runs_singularity_container_tasks, active, whitelists, ):
"""Up... |
# Update the object
request_url = self._client.base_api_url + self.detail_url.format(id=id)
data_to_put = {
"name": name,
"description": description,
"private": private,
"runs_executable_tasks": runs_executable_tasks,
"runs_docker_cont... |
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def main(self):
""" Run the required methods in the appropriate order """ |
self.targets()
self.bait(k=49)
self.reversebait(maskmiddle='t', k=19)
self.subsample_reads() |
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def targets(self):
""" Using the data from the BLAST analyses, set the targets folder, and create the 'mapping file'. This is the genera-specific FASTA file that... |
logging.info('Performing analysis with {} targets folder'.format(self.analysistype))
for sample in self.runmetadata:
if sample.general.bestassemblyfile != 'NA':
sample[self.analysistype].targetpath = \
os.path.join(self.targetpath, 'genera', sample[self.a... |
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def subsample(self):
""" Subsample 1000 reads from the baited files """ |
# Create the threads for the analysis
logging.info('Subsampling FASTQ reads')
for _ in range(self.cpus):
threads = Thread(target=self.subsamplethreads, args=())
threads.setDaemon(True)
threads.start()
with progressbar(self.runmetadata.samples) as bar:... |
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def fasta(self):
""" Convert the subsampled reads to FASTA format using reformat.sh """ |
logging.info('Converting FASTQ files to FASTA format')
# Create the threads for the analysis
for _ in range(self.cpus):
threads = Thread(target=self.fastathreads, args=())
threads.setDaemon(True)
threads.start()
with progressbar(self.runmetadata.sampl... |
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def blast(self):
""" Run BLAST analyses of the subsampled FASTQ reads against the NCBI 16S reference database """ |
logging.info('BLASTing FASTA files against {} database'.format(self.analysistype))
for _ in range(self.cpus):
threads = Thread(target=self.blastthreads, args=())
threads.setDaemon(True)
threads.start()
with progressbar(self.runmetadata.samples) as bar:
... |
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def blastparse(self):
""" Parse the blast results, and store necessary data in dictionaries in sample object """ |
logging.info('Parsing BLAST results')
# Load the NCBI 16S reference database as a dictionary
for sample in self.runmetadata.samples:
if sample.general.bestassemblyfile != 'NA':
# Load the NCBI 16S reference database as a dictionary
dbrecords = SeqIO.t... |
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| def load_json(json_object):
''' Load json from file or file name '''
content = None
if isinstance(json_object, str) and os.path.exists(json_object):
with open_(json_object) as f:
try:
content = json.load(f)
except Exception as e:
debug.log("Warning: Content of '%... |
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def sort2groups(array, gpat=['_R1','_R2']):
""" Sort an array of strings to groups by patterns """ |
groups = [REGroup(gp) for gp in gpat]
unmatched = []
for item in array:
matched = False
for m in groups:
if m.match(item):
matched = True
break
if not matched: unmatched.append(item)
return [sorted(m.list) for m in groups], sorted(unmatched) |
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def sort_and_distribute(array, splits=2):
""" Sort an array of strings to groups by alphabetically continuous distribution """ |
if not isinstance(array, (list,tuple)): raise TypeError("array must be a list")
if not isinstance(splits, int): raise TypeError("splits must be an integer")
remaining = sorted(array)
if sys.version_info < (3, 0):
myrange = xrange(splits)
else:
myrange = range(splits)
groups = [[] for i in... |
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def file_zipper(root_dir):
""" This function will zip the files created in the runroot directory and subdirectories """ |
# FINDING AND ZIPPING UNZIPPED FILES
for root, dirs, files in os.walk(root_dir, topdown=False):
if root != "":
if root[-1] != '/': root += '/'
for current_file in files:
filepath = "%s/%s"%(root, current_file)
try:
file_size = os.path.getsize(filepat... |
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def file_unzipper(directory):
""" This function will unzip all files in the runroot directory and subdirectories """ |
debug.log("Unzipping directory (%s)..."%directory)
#FINDING AND UNZIPPING ZIPPED FILES
for root, dirs, files in os.walk(directory, topdown=False):
if root != "":
orig_dir = os.getcwd()
os.chdir(directory)
Popen('gunzip -q -f *.gz > /dev/null 2>&1', shell=True).wait()
... |
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def move_file(src, dst):
""" this function will simply move the file from the source path to the dest path given as input """ |
# Sanity checkpoint
src = re.sub('[^\w/\-\.\*]', '', src)
dst = re.sub('[^\w/\-\.\*]', '', dst)
if len(re.sub('[\W]', '', src)) < 5 or len(re.sub('[\W]', '', dst)) < 5:
debug.log("Error: Moving file failed. Provided paths are invalid! src='%s' dst='%s'"%(src, dst))
else:
# Check destination
... |
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def log(self, *lst):
""" Print list of strings to the predefined logfile if debug is set. and sets the caught_error message if an error is found """ |
self.print2file(self.logfile, self.debug, True, *lst)
if 'Error' in '\n'.join([str(x) for x in lst]):
self.caught_error = '\n'.join([str(x) for x in lst]) |
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def log_no_newline(self, msg):
""" print the message to the predefined log file without newline """ |
self.print2file(self.logfile, False, False, msg) |
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def graceful_exit(self, msg):
""" This function Tries to update the MSQL database before exiting. """ |
# Print stored errors to stderr
if self.caught_error:
self.print2file(self.stderr, False, False, self.caught_error)
# Kill process with error message
self.log(msg)
sys.exit(1) |
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def match(self, s):
""" Matches the string to the stored regular expression, and stores all groups in mathches. Returns False on negative match. """ |
self.matches = self.re.search(s)
return self.matches |
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def reporter(self):
""" Create the MASH report """ |
logging.info('Creating {} report'.format(self.analysistype))
make_path(self.reportpath)
header = 'Strain,ReferenceGenus,ReferenceFile,ReferenceGenomeMashDistance,Pvalue,NumMatchingHashes\n'
data = ''
for sample in self.metadata:
try:
data += '{},{},{}... |
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def edges(self):
""" Return the edge characters of this node. """ |
edge_str = ctypes.create_string_buffer(MAX_CHARS)
cgaddag.gdg_edges(self.gdg, self.node, edge_str)
return [char for char in edge_str.value.decode("ascii")] |
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def letter_set(self):
""" Return the letter set of this node. """ |
end_str = ctypes.create_string_buffer(MAX_CHARS)
cgaddag.gdg_letter_set(self.gdg, self.node, end_str)
return [char for char in end_str.value.decode("ascii")] |
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def is_end(self, char):
""" Return `True` if this `char` is part of this node's letter set, `False` otherwise. """ |
char = char.lower()
return bool(cgaddag.gdg_is_end(self.gdg, self.node, char.encode("ascii"))) |
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def follow(self, chars):
""" Traverse the GADDAG to the node at the end of the given characters. Args: chars: An string of characters to traverse in the GADDAG. ... |
chars = chars.lower()
node = self.node
for char in chars:
node = cgaddag.gdg_follow_edge(self.gdg, node, char.encode("ascii"))
if not node:
raise KeyError(char)
return Node(self.gdg, node) |
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def read(alias_name, allow_none=False):
"""Get the raw docker link value. Get the raw environment variable for the docker link Args: alias_name: The environment ... |
warnings.warn('Will be removed in v1.0', DeprecationWarning, stacklevel=2)
return core.read('{0}_PORT'.format(alias_name), default=None, allow_none=allow_none) |
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def isset(alias_name):
"""Return a boolean if the docker link is set or not and is a valid looking docker link value. Args: alias_name: The link alias name """ |
warnings.warn('Will be removed in v1.0', DeprecationWarning, stacklevel=2)
raw_value = read(alias_name, allow_none=True)
if raw_value:
if re.compile(r'.+://.+:\d+').match(raw_value):
return True
else:
warnings.warn('"{0}_PORT={1}" does not look like a docker link.'.f... |
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def protocol(alias_name, default=None, allow_none=False):
"""Get the protocol from the docker link alias or return the default. Args: alias_name: The docker link... |
warnings.warn('Will be removed in v1.0', DeprecationWarning, stacklevel=2)
try:
return _split_docker_link(alias_name)[0]
except KeyError as err:
if default or allow_none:
return default
else:
raise err |
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def port(alias_name, default=None, allow_none=False):
"""Get the port from the docker link alias or return the default. Args: alias_name: The docker link alias d... |
warnings.warn('Will be removed in v1.0', DeprecationWarning, stacklevel=2)
try:
return int(_split_docker_link(alias_name)[2])
except KeyError as err:
if default or allow_none:
return default
else:
raise err |
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def attributer(self):
""" Parses the 16S target files to link accession numbers stored in the .fai and metadata files to the genera stored in the target file """ |
from Bio import SeqIO
import operator
for sample in self.runmetadata.samples:
# Load the records from the target file into a dictionary
record_dict = SeqIO.to_dict(SeqIO.parse(sample[self.analysistype].baitfile, "fasta"))
sample[self.analysistype].classificat... |
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def spawn_server_api(api_name, app, api_spec, error_callback, decorator):
"""Take a a Flask app and a swagger file in YAML format describing a REST API, and popu... |
def mycallback(endpoint):
handler_func = get_function(endpoint.handler_server)
# Generate api endpoint around that handler
handler_wrapper = _generate_handler_wrapper(api_name, api_spec, endpoint, handler_func, error_callback, decorator)
# Bind handler to the API path
log... |
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def _responsify(api_spec, error, status):
"""Take a bravado-core model representing an error, and return a Flask Response with the given error code and error ins... |
result_json = api_spec.model_to_json(error)
r = jsonify(result_json)
r.status_code = status
return r |
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def format_escape( foreground=None, background=None, bold=False, faint=False, italic=False, underline=False, blink=False, inverted=False ):
"""Returns the ANSI e... |
fg_format = None
if isinstance( foreground, int ):
fg_format = ANSI_FORMAT_FOREGROUND_XTERM_CMD.format( foreground )
else:
fg_rgba = colour.normalise_rgba( foreground )
if fg_rgba[3] != 0:
fg_format = ANSI_FORMAT_FOREGROUND_CMD.format( *fg_rgba[:3] )
bg_format = Non... |
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def format_string( string, foreground=None, background=None, reset=True, bold=False, faint=False, italic=False, underline=False, blink=False, inverted=False ):
"... |
colour_format = format_escape( foreground, background, bold, faint,
italic, underline, blink, inverted )
reset_format = '' if not reset else ANSI_FORMAT_RESET
return '{}{}{}'.format( colour_format, string, reset_format ) |
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def format_pixels( top, bottom, reset=True, repeat=1 ):
"""Return the ANSI escape sequence to render two vertically-stacked pixels as a single monospace characte... |
top_src = None
if isinstance( top, int ):
top_src = top
else:
top_rgba = colour.normalise_rgba( top )
if top_rgba[3] != 0:
top_src = top_rgba
bottom_src = None
if isinstance( bottom, int ):
bottom_src = bottom
else:
bottom_rgba = colour.norma... |
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def format_image_iter( data_fetch, x_start=0, y_start=0, width=32, height=32, frame=0, columns=1, downsample=1 ):
"""Return the ANSI escape sequence to render a ... |
frames = []
try:
frame_iter = iter( frame )
frames = [f for f in frame_iter]
except TypeError:
frames = [frame]
rows = math.ceil( len( frames )/columns )
for r in range( rows ):
for y in range( 0, height, 2*downsample ):
result = []
for c in ... |
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def update_buffer_with_value( self, value, buffer, parent=None ):
"""Write a Python object into a byte array, using the field definition. value Input Python obje... |
assert common.is_bytes( buffer )
self.validate( value, parent )
return |
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def get_end_offset( self, value, parent=None, index=None ):
"""Return the end offset of the Field's data. Useful for chainloading. value Input Python object to p... |
return self.get_start_offset( value, parent, index ) + self.get_size( value, parent, index ) |
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| def nonalpha_split(string):
'''Split 'string' along any punctuation or whitespace.'''
return re.findall(r'[%s]+|[^%s]+' % (A, A), string, flags=FLAGS) |
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| def extract_words(string):
'''Extract all alphabetic syllabified forms from 'string'.'''
return re.findall(r'[%s]+[%s\.]*[%s]+' % (A, A, A), string, flags=FLAGS) |
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def init_threads(t=None, s=None):
"""Should define dummyThread class and dummySignal class""" |
global THREAD, SIGNAL
THREAD = t or dummyThread
SIGNAL = s or dummySignal |
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def thread_with_callback(on_error, on_done, requete_with_callback):
""" Return a thread emiting `state_changed` between each sub-requests. :param on_error: callb... |
class C(THREAD):
error = SIGNAL(str)
done = SIGNAL(object)
state_changed = SIGNAL(int, int)
def __del__(self):
self.wait()
def run(self):
try:
r = requete_with_callback(self.state_changed.emit)
except (ConnexionError, S... |
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def build_parser(parser: argparse.ArgumentParser) -> None: """Build a parser for CLI arguments and options.""" |
parser.add_argument(
'--delimiter',
help='a delimiter for the samples (teeth) in the key',
default=' ',
)
parser.add_argument(
'--encoding',
help='the encoding of the population file',
default='utf-8',
)
parser.add_argument(
'--nsamples', '-n'... |
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def default_parser() -> argparse.ArgumentParser: """Create a parser for CLI arguments and options.""" |
parser = argparse.ArgumentParser(
prog=CONSOLE_SCRIPT,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
)
build_parser(parser)
return parser |
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def key( seq: Sequence, tooth: Callable[[Sequence], str] = ( lambda seq: str(random.SystemRandom().choice(seq)).strip() ), nteeth: int = 6, delimiter: str = ' ', ... |
return delimiter.join(tooth(seq) for _ in range(nteeth)) |
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def main(argv: Sequence[str] = SYS_ARGV) -> int: """Execute CLI commands.""" |
args = default_parser().parse_args(argv)
try:
seq = POPULATIONS[args.population] # type: Sequence
except KeyError:
try:
with open(args.population, 'r', encoding=args.encoding) as file_:
seq = list(file_)
except (OSError, UnicodeError) as ex:
... |
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def apt_add_repository_from_apt_string(apt_string, apt_file):
""" adds a new repository file for apt """ |
apt_file_path = '/etc/apt/sources.list.d/%s' % apt_file
if not file_contains(apt_file_path, apt_string.lower(), use_sudo=True):
file_append(apt_file_path, apt_string.lower(), use_sudo=True)
with hide('running', 'stdout'):
sudo("DEBIAN_FRONTEND=noninteractive apt-get update") |
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def arch():
""" returns the current cpu archictecture """ |
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
warn_only=True, capture=True):
result = sudo('rpm -E %dist').strip()
return result |
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def disable_openssh_rdns(distribution):
""" Set 'UseDNS no' in openssh config to disable rDNS lookups On each request for a new channel openssh defaults to an rD... |
log_green('Disabling openssh reverse dns lookups')
openssh_config_file = '/etc/ssh/sshd_config'
dns_config = 'UseDNS no'
if not file_contains(openssh_config_file, dns_config, use_sudo=True):
file_append(openssh_config_file, dns_config, use_sudo=True)
service_name = 'sshd'
if 'ub... |
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def connect_to_ec2(region, access_key_id, secret_access_key):
""" returns a connection object to AWS EC2 """ |
conn = boto.ec2.connect_to_region(region,
aws_access_key_id=access_key_id,
aws_secret_access_key=secret_access_key)
return conn |
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def connect_to_rackspace(region, access_key_id, secret_access_key):
""" returns a connection object to Rackspace """ |
pyrax.set_setting('identity_type', 'rackspace')
pyrax.set_default_region(region)
pyrax.set_credentials(access_key_id, secret_access_key)
nova = pyrax.connect_to_cloudservers(region=region)
return nova |
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def create_gce_image(zone, project, instance_name, name, description):
""" Shuts down the instance and creates and image from the disk. Assumes that the disk nam... |
disk_name = instance_name
try:
down_gce(instance_name=instance_name, project=project, zone=zone)
except HttpError as e:
if e.resp.status == 404:
log_yellow("the instance {} is already down".format(instance_name))
else:
raise e
body = {
"rawDisk"... |
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def create_image(cloud, **kwargs):
""" proxy call for ec2, rackspace create ami backend functions """ |
if cloud == 'ec2':
return create_ami(**kwargs)
if cloud == 'rackspace':
return create_rackspace_image(**kwargs)
if cloud == 'gce':
return create_gce_image(**kwargs) |
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def create_server(cloud, **kwargs):
""" Create a new instance """ |
if cloud == 'ec2':
_create_server_ec2(**kwargs)
elif cloud == 'rackspace':
_create_server_rackspace(**kwargs)
elif cloud == 'gce':
_create_server_gce(**kwargs)
else:
raise ValueError("Unknown cloud type: {}".format(cloud)) |
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def gce_wait_until_done(operation):
""" Perform a GCE operation, blocking until the operation completes. This function will then poll the operation until it reac... |
operation_name = operation['name']
if 'zone' in operation:
zone_url_parts = operation['zone'].split('/')
project = zone_url_parts[-3]
zone = zone_url_parts[-1]
def get_zone_operation():
return _get_gce_compute().zoneOperations().get(
project=project,... |
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def startup_gce_instance(instance_name, project, zone, username, machine_type, image, public_key, disk_name=None):
""" For now, jclouds is broken for GCE and we ... |
log_green("Started...")
log_yellow("...Creating GCE Jenkins Slave Instance...")
instance_config = get_gce_instance_config(
instance_name, project, zone, machine_type, image,
username, public_key, disk_name
)
operation = _get_gce_compute().instances().insert(
project=project,... |
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def _create_server_ec2(region, access_key_id, secret_access_key, disk_name, disk_size, ami, key_pair, instance_type, username, tags={}, security_groups=None):
""... |
conn = connect_to_ec2(region, access_key_id, secret_access_key)
log_green("Started...")
log_yellow("...Creating EC2 instance...")
# we need a larger boot device to store our cached images
ebs_volume = EBSBlockDeviceType()
ebs_volume.size = disk_size
bdm = BlockDeviceMapping()
bdm[disk... |
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def enable_marathon_basic_authentication(principal, password):
""" configures marathon to start with authentication """ |
upstart_file = '/etc/init/marathon.conf'
with hide('running', 'stdout'):
sudo('echo -n "{}" > /etc/marathon-mesos.credentials'.format(password))
boot_args = ' '.join(['exec',
'/usr/bin/marathon',
'--http_credentials',
'"{... |
<SYSTEM_TASK:>
Solve the following problem using Python, implementing the functions described below, one line at a time
<END_TASK>
<USER_TASK:>
Description:
def enable_mesos_basic_authentication(principal, password):
""" enables and adds a new authorized principal """ |
restart = False
secrets_file = '/etc/mesos/secrets'
secrets_entry = '%s %s' % (principal, password)
if not file_contains(filename=secrets_file,
text=secrets_entry, use_sudo=True):
file_append(filename=secrets_file, text=secrets_entry, use_sudo=True)
file_attribs... |
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