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value | url stringlengths 87 315 | code_tokens listlengths 19 28.4k | sha stringlengths 40 40 |
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train | User.sync | Sync this model with latest data on the saltant server.
Note that in addition to returning the updated object, it also
updates the existing object.
Returns:
:class:`saltant.models.user.User`:
This user instance after syncing. | saltant/models/user.py | def sync(self):
"""Sync this model with latest data on the saltant server.
Note that in addition to returning the updated object, it also
updates the existing object.
Returns:
:class:`saltant.models.user.User`:
This user instance after syncing.
"""
... | def sync(self):
"""Sync this model with latest data on the saltant server.
Note that in addition to returning the updated object, it also
updates the existing object.
Returns:
:class:`saltant.models.user.User`:
This user instance after syncing.
"""
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train | Block.serialised | Tuple containing the contents of the Block. | mrcrowbar/blocks.py | def serialised( self ):
"""Tuple containing the contents of the Block."""
klass = self.__class__
return ((klass.__module__, klass.__name__), tuple( (name, field.serialise( self._field_data[name], parent=self ) ) for name, field in klass._fields.items())) | def serialised( self ):
"""Tuple containing the contents of the Block."""
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train | Block.clone_data | Clone data from another Block.
source
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"""Clone data from another Block.
source
Block instance to copy from.
"""
klass = self.__class__
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train | Block.import_data | Import data from a byte array.
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"""Import data from a byte array.
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Byte array to import from.
"""
klass = self.__class__
if raw_buffer:
assert common.is_bytes( raw_buffer )
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"""Import data from a byte array.
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Byte array to import from.
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train | Block.export_data | Export data to a byte array. | mrcrowbar/blocks.py | def export_data( self ):
"""Export data to a byte array."""
klass = self.__class__
output = bytearray( b'\x00'*self.get_size() )
# prevalidate all data before export.
# this is important to ensure that any dependent fields
# are updated beforehand, e.g. a count referenc... | def export_data( self ):
"""Export data to a byte array."""
klass = self.__class__
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train | Block.update_deps | Update dependencies on all the fields on this Block instance. | mrcrowbar/blocks.py | def update_deps( self ):
"""Update dependencies on all the fields on this Block instance."""
klass = self.__class__
for name in klass._fields:
self.update_deps_on_field( name )
return | def update_deps( self ):
"""Update dependencies on all the fields on this Block instance."""
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train | Block.validate | Validate all the fields on this Block instance. | mrcrowbar/blocks.py | def validate( self ):
"""Validate all the fields on this Block instance."""
klass = self.__class__
for name in klass._fields:
self.validate_field( name )
return | def validate( self ):
"""Validate all the fields on this Block instance."""
klass = self.__class__
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train | Block.get_size | Get the projected size (in bytes) of the exported data from this Block instance. | mrcrowbar/blocks.py | def get_size( self ):
"""Get the projected size (in bytes) of the exported data from this Block instance."""
klass = self.__class__
size = 0
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size = max( size, klass._fields[name].get_end_offset( self._field_data[name], parent=self ) )
for ch... | def get_size( self ):
"""Get the projected size (in bytes) of the exported data from this Block instance."""
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train | GADDAG.save | Save the GADDAG to file.
Args:
path: path to save the GADDAG to.
compressed: compress the saved GADDAG using gzip.
exist_ok: overwrite existing file at `path`. | gaddag/gaddag.py | def save(self, path, compressed=True, exist_ok=False):
"""
Save the GADDAG to file.
Args:
path: path to save the GADDAG to.
compressed: compress the saved GADDAG using gzip.
exist_ok: overwrite existing file at `path`.
"""
path = os.path.expan... | def save(self, path, compressed=True, exist_ok=False):
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Save the GADDAG to file.
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path: path to save the GADDAG to.
compressed: compress the saved GADDAG using gzip.
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train | GADDAG.load | Load a GADDAG from file, replacing the words currently in this GADDAG.
Args:
path: path to saved GADDAG to be loaded. | gaddag/gaddag.py | def load(self, path):
"""
Load a GADDAG from file, replacing the words currently in this GADDAG.
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path: path to saved GADDAG to be loaded.
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train | GADDAG.starts_with | Find all words starting with a prefix.
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Returns:
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Find all words starting with a prefix.
Args:
prefix: A prefix to be searched for.
Returns:
A list of all words found.
"""
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Find all words starting with a prefix.
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A list of all words found.
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train | GADDAG.contains | Find all words containing a substring.
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Returns:
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Find all words containing a substring.
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sub: A substring to be searched for.
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A list of all words found.
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Find all words containing a substring.
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sub: A substring to be searched for.
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A list of all words found.
"""
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train | GADDAG.ends_with | Find all words ending with a suffix.
Args:
suffix: A suffix to be searched for.
Returns:
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Find all words ending with a suffix.
Args:
suffix: A suffix to be searched for.
Returns:
A list of all words found.
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Find all words ending with a suffix.
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A list of all words found.
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train | GADDAG.add_word | Add a word to the GADDAG.
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Add a word to the GADDAG.
Args:
word: A word to be added to the GADDAG.
"""
word = word.lower()
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Add a word to the GADDAG.
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word: A word to be added to the GADDAG.
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:param source - application context - where did it come from?
:param title - brief description - what kind of event happened?
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""" Similar to format, but takes additional reserved params to promote logging best-practices
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train | ContainerTaskType.put | Updates this task type on the saltant server.
Returns:
:class:`saltant.models.container_task_type.ContainerTaskType`:
A task type model instance representing the task type
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Returns:
:class:`saltant.models.container_task_type.ContainerTaskType`:
A task type model instance representing the task type
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"""Updates this task type on the saltant server.
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:class:`saltant.models.container_task_type.ContainerTaskType`:
A task type model instance representing the task type
just updated.
"""
return self.manager.put(
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train | ContainerTaskTypeManager.create | Create a container task type.
Args:
name (str): The name of the task.
command_to_run (str): The command to run to execute the task.
container_image (str): The container name and tag. For
example, ubuntu:14.04 for Docker; and docker://ubuntu:14:04
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container_type,
description="",
logs_path="",
results_path="",
environment_variables=None,
required_arguments=None,
required_arguments_default_values=None,
extra_data_... | def create(
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container_type,
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logs_path="",
results_path="",
environment_variables=None,
required_arguments=None,
required_arguments_default_values=None,
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train | ContainerTaskTypeManager.put | Updates a task type on the saltant server.
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id (int): The ID of the task type.
name (str): The name of the task type.
description (str): The description of the task type.
command_to_run (str): The command to run to execute the task.
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train | _strtobool | Convert a string representation of truth to true (1) or false (0).
True values are 'y', 'yes', 't', 'true', 'on', and '1'; false values
are 'n', 'no', 'f', 'false', 'off', '0' and ''. Raises ValueError if
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"""Convert a string representation of truth to true (1) or false (0).
True values are 'y', 'yes', 't', 'true', 'on', and '1'; false values
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"""
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train | _str_to_list | Convert a string to a list with sanitization. | envitro/core.py | def _str_to_list(value, separator):
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train | write | Write a raw env value.
A ``None`` value clears the environment variable.
Args:
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value: The value to write | envitro/core.py | def write(name, value):
"""Write a raw env value.
A ``None`` value clears the environment variable.
Args:
name: The environment variable name
value: The value to write
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train | includeme | this function adds some configuration for the application | pyramid_urireferencer/__init__.py | def includeme(config):
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config.add_view_deriver(protected_resources.protected_view)
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Gets the Referencer from config and adds it to the registry.
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Get the referencer class
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train | PyHeaderSheet.write | :param args: tuple(value, style), tuple(value, style)
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:param args: value, value
:param kwargs: header=value, header=value | pyheaderfile/basefile.py | def write(self, *args, **kwargs):
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Function for taking a Unicode scalar value representing a Hangul syllable and decomposing it into a tuple
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train | apply_T1 | There is a syllable boundary in front of every CV-sequence. | finnsyll/prev/v05.py | def apply_T1(word):
'''There is a syllable boundary in front of every CV-sequence.'''
# split consonants and vowels: 'balloon' -> ['b', 'a', 'll', 'oo', 'n']
WORD = [w for w in re.split('([ieAyOauo]+)', word) if w]
count = 0
for i, v in enumerate(WORD):
if i == 0 and is_consonant(v[0]):
... | def apply_T1(word):
'''There is a syllable boundary in front of every CV-sequence.'''
# split consonants and vowels: 'balloon' -> ['b', 'a', 'll', 'oo', 'n']
WORD = [w for w in re.split('([ieAyOauo]+)', word) if w]
count = 0
for i, v in enumerate(WORD):
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train | extended_cigar | Convert mutation annotations to extended cigar format
https://github.com/lh3/minimap2#the-cs-optional-tag
USAGE:
>>> template = 'CGATCGATAAATAGAGTAG---GAATAGCA'
>>> query = 'CGATCG---AATAGAGTAGGTCGAATtGCA'
>>> extended_cigar(template, query) == ':6-ata:10+gtc:4*at:3'
True | cgecore/alignment.py | def extended_cigar(aligned_template, aligned_query):
''' Convert mutation annotations to extended cigar format
https://github.com/lh3/minimap2#the-cs-optional-tag
USAGE:
>>> template = 'CGATCGATAAATAGAGTAG---GAATAGCA'
>>> query = 'CGATCG---AATAGAGTAGGTCGAATtGCA'
>>> extended_cigar(tem... | def extended_cigar(aligned_template, aligned_query):
''' Convert mutation annotations to extended cigar format
https://github.com/lh3/minimap2#the-cs-optional-tag
USAGE:
>>> template = 'CGATCGATAAATAGAGTAG---GAATAGCA'
>>> query = 'CGATCG---AATAGAGTAGGTCGAATtGCA'
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train | cigar2query | Generate query sequence from the template and extended cigar annotation
USAGE:
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>>> cigar = ':6-ata:10+gtc:4*at:3'
>>> cigar2query(template, cigar) == 'CGATCGAATAGAGTAGGTCGAATtGCA'.upper()
True | cgecore/alignment.py | def cigar2query(template, cigar):
''' Generate query sequence from the template and extended cigar annotation
USAGE:
>>> template = 'CGATCGATAAATAGAGTAGGAATAGCA'
>>> cigar = ':6-ata:10+gtc:4*at:3'
>>> cigar2query(template, cigar) == 'CGATCGAATAGAGTAGGTCGAATtGCA'.upper()
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'''
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USAGE:
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>>> cigar = ':6-ata:10+gtc:4*at:3'
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train | Blaster | BLAST wrapper method, that takes a simple input and produces a overview
list of the hits to templates, and their alignments
Usage
>>> import os, subprocess, collections
>>> from Bio.Blast import NCBIXML
>>> from Bio import SeqIO
>>> from string import maketrans
>>> inputfile = 't... | cgecore/alignment.py | def Blaster(inputfile, databases, db_path, out_path='.', min_cov=0.6,
threshold=0.9, blast='blastn', cut_off=True):
''' BLAST wrapper method, that takes a simple input and produces a overview
list of the hits to templates, and their alignments
Usage
>>> import os, subprocess, collections
... | def Blaster(inputfile, databases, db_path, out_path='.', min_cov=0.6,
threshold=0.9, blast='blastn', cut_off=True):
''' BLAST wrapper method, that takes a simple input and produces a overview
list of the hits to templates, and their alignments
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train | compare_results | Function for comparing hits and saving only the best hit | cgecore/alignment.py | def compare_results(save, best_hsp, tmp_results, tmp_gene_split):
''' Function for comparing hits and saving only the best hit '''
# Get data for comparison
hit_id = best_hsp['hit_id']
new_start_query = best_hsp['query_start']
new_end_query = best_hsp['query_end']
new_start_sbjct = int(best_hsp['sbjct... | def compare_results(save, best_hsp, tmp_results, tmp_gene_split):
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# Get data for comparison
hit_id = best_hsp['hit_id']
new_start_query = best_hsp['query_start']
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train | calculate_new_length | Function for calcualting new length if the gene is split on several
contigs | cgecore/alignment.py | 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... | def calculate_new_length(gene_split, gene_results, hit):
''' Function for calcualting new length if the gene is split on several
contigs
'''
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first = 1
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train | stream_to_packet | 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 remaining
data, or ``None`` | modpypes/app.py | 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 remaining
data, or ``None``
"""
if len(data) < 6:
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# unpack the length
pktlen = struct.unpack(">H", ... | def stream_to_packet(data):
"""
Chop a stream of data into MODBUS packets.
:param data: stream of data
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data, or ``None``
"""
if len(data) < 6:
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Handy for JSON serialization. We can optionally handle instances,
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To handle cyclical data structures we could track the actual objects
visited in a set, but not all objects are... | qg/core/jsonutils.py | def to_primitive(value, convert_instances=False, convert_datetime=True,
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"""Convert a complex object into primitives.
Handy for JSON serialization. We can optionally handle instances,
but since this is a recursive function, we could have cyclical
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"""Convert a complex object into primitives.
Handy for JSON serialization. We can optionally handle instances,
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train | get_vowel | Return the firstmost vowel in 'syll'. | finnsyll/phonology.py | def get_vowel(syll):
'''Return the firstmost vowel in 'syll'.'''
return re.search(r'([ieaouäöy]{1})', syll, flags=FLAGS).group(1).upper() | def get_vowel(syll):
'''Return the firstmost vowel in 'syll'.'''
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train | is_light | Return True if 'syll' is light. | finnsyll/phonology.py | def is_light(syll):
'''Return True if 'syll' is light.'''
return re.match(r'(^|[^ieaouäöy]+)[ieaouäöy]{1}$', syll, flags=FLAGS) | def is_light(syll):
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train | stress | Assign primary and secondary stress to 'syllabified_simplex_word'. | finnsyll/phonology.py | 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):
... | 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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train | sonseq | Return True if 'word' does not violate sonority sequencing. | finnsyll/phonology.py | def sonseq(word):
'''Return True if 'word' does not violate sonority sequencing.'''
parts = re.split(r'([ieaouäöy]+)', word, flags=re.I | re.U)
onset, coda = parts[0], parts[-1]
# simplex onset Finnish complex onset
if len(onset) <= 1 or onset.lower() in ONSETS:
# simplex coda ... | def sonseq(word):
'''Return True if 'word' does not violate sonority sequencing.'''
parts = re.split(r'([ieaouäöy]+)', word, flags=re.I | re.U)
onset, coda = parts[0], parts[-1]
# simplex onset Finnish complex onset
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train | harmonic | Return True if the word's vowels agree in frontness/backness. | finnsyll/phonology.py | def harmonic(word):
'''Return True if the word's vowels agree in frontness/backness.'''
depth = {'ä': 0, 'ö': 0, 'y': 0, 'a': 1, 'o': 1, 'u': 1}
vowels = filter(lambda ch: is_front(ch) or is_back(ch), word)
depths = (depth[x.lower()] for x in vowels)
return len(set(depths)) < 2 | def harmonic(word):
'''Return True if the word's vowels agree in frontness/backness.'''
depth = {'ä': 0, 'ö': 0, 'y': 0, 'a': 1, 'o': 1, 'u': 1}
vowels = filter(lambda ch: is_front(ch) or is_back(ch), word)
depths = (depth[x.lower()] for x in vowels)
return len(set(depths)) < 2 | [
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train | ExecutableTaskType.put | Updates this task type on the saltant server.
Returns:
:class:`saltant.models.container_task_type.ExecutableTaskType`:
An executable task type model instance representing the task type
just updated. | saltant/models/executable_task_type.py | def put(self):
"""Updates this task type on the saltant server.
Returns:
:class:`saltant.models.container_task_type.ExecutableTaskType`:
An executable task type model instance representing the task type
just updated.
"""
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name (str): The name of the task.
command_to_run (str): The command to run to execute the task.
description (str, optional): The description of the task type.
environment_variables (list, optional): The environment
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train | ExecutableTaskTypeManager.put | Updates a task type on the saltant server.
Args:
id (int): The ID of the task type.
name (str): The name of the task type.
description (str): The description of the task type.
command_to_run (str): The command to run to execute the task.
environment_v... | saltant/models/executable_task_type.py | def put(
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environment_variables,
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required_arguments_default_values,
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train | Reports.reporter | Creates a report of the genesippr results
:param analysistype: The variable to use when accessing attributes in the metadata object | sipprverse_reporter/reports.py | def reporter(self, analysistype='genesippr'):
"""
Creates a report of the genesippr results
:param analysistype: The variable to use when accessing attributes in the metadata object
"""
logging.info('Creating {} report'.format(analysistype))
# Create a dictionary to link ... | def reporter(self, analysistype='genesippr'):
"""
Creates a report of the genesippr results
:param analysistype: The variable to use when accessing attributes in the metadata object
"""
logging.info('Creating {} report'.format(analysistype))
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train | Reports.genusspecific | Creates simplified genus-specific reports. Instead of the % ID and the fold coverage, a simple +/- scheme is
used for presence/absence
:param analysistype: The variable to use when accessing attributes in the metadata object | sipprverse_reporter/reports.py | def genusspecific(self, analysistype='genesippr'):
"""
Creates simplified genus-specific reports. Instead of the % ID and the fold coverage, a simple +/- scheme is
used for presence/absence
:param analysistype: The variable to use when accessing attributes in the metadata object
... | def genusspecific(self, analysistype='genesippr'):
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Creates simplified genus-specific reports. Instead of the % ID and the fold coverage, a simple +/- scheme is
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:param analysistype: The variable to use when accessing attributes in the metadata object
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train | Reports.gdcsreporter | Creates a report of the GDCS results
:param analysistype: The variable to use when accessing attributes in the metadata object | sipprverse_reporter/reports.py | def gdcsreporter(self, analysistype='GDCS'):
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Creates a report of the GDCS results
:param analysistype: The variable to use when accessing attributes in the metadata object
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logging.info('Creating {} report'.format(analysistype))
# Initialise list to store all the G... | def gdcsreporter(self, analysistype='GDCS'):
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Creates a report of the GDCS results
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train | Reports.gdcs_fai | GDCS analyses need to use the .fai file supplied in the targets folder rather than the one created following
reverse baiting
:param sample: sample object
:param analysistype: current analysis being performed | sipprverse_reporter/reports.py | def gdcs_fai(sample, analysistype='GDCS'):
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GDCS analyses need to use the .fai file supplied in the targets folder rather than the one created following
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:param sample: sample object
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GDCS analyses need to use the .fai file supplied in the targets folder rather than the one created following
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train | Reports.sixteensreporter | Creates a report of the results
:param analysistype: The variable to use when accessing attributes in the metadata object | sipprverse_reporter/reports.py | def sixteensreporter(self, analysistype='sixteens_full'):
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Creates a report of the results
:param analysistype: The variable to use when accessing attributes in the metadata object
"""
# Create the path in which the reports are stored
make_path(self.reportpath)
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Creates a report of the results
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"""
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train | Reports.confindr_reporter | Creates a final report of all the ConFindr results | sipprverse_reporter/reports.py | def confindr_reporter(self, analysistype='confindr'):
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Creates a final report of all the ConFindr results
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# Initialise the data strings
data = 'Strain,Genus,NumContamSNVs,ContamStatus,PercentContam,PercentContamSTD\n'
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Creates a final report of all the ConFindr results
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train | Reports.methodreporter | Create final reports collating results from all the individual iterations through the method pipeline | sipprverse_reporter/reports.py | 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.repor... | def methodreporter(self):
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Create final reports collating results from all the individual iterations through the method pipeline
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train | ReportImage.main | Run the methods required to create the genesippr report summary image | sipprverse_reporter/reports.py | def main(self):
"""
Run the methods required to create the genesippr report summary image
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self.dataframe_setup()
self.figure_populate(self.outputfolder,
self.image_report,
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... | def main(self):
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Run the methods required to create the genesippr report summary image
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train | ReportImage.data_sanitise | Format the data to be consistent with heatmaps
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:param header: class of the data - certain categories have specific formatting requirements
:return: the formatted output string | sipprverse_reporter/reports.py | def data_sanitise(self, inputstring, header=None):
"""
Format the data to be consistent with heatmaps
:param inputstring: string containing data to be formatted
:param header: class of the data - certain categories have specific formatting requirements
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Format the data to be consistent with heatmaps
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train | ReportImage.dataframe_setup | Set-up a report to store the desired header: sanitized string combinations | sipprverse_reporter/reports.py | def dataframe_setup(self):
"""
Set-up a report to store the desired header: sanitized string combinations
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# Initialise a dictionary to store the sanitized headers and strings
genesippr_dict = dict()
# Try to open all the reports - use pandas to extract the results fro... | def dataframe_setup(self):
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Set-up a report to store the desired header: sanitized string combinations
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train | ReportImage.figure_populate | Create the report image from the summary report created in self.dataframesetup
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:param csv: Name of the report file from which data are to be extracted
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"""
Create the report image from the summary report created in self.dataframesetup
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Create the report image from the summary report created in self.dataframesetup
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train | add_usr_local_bin_to_path | adds /usr/local/bin to $PATH | bookshelf/api_v2/os_helpers.py | def add_usr_local_bin_to_path(log=False):
""" adds /usr/local/bin to $PATH """
if log:
bookshelf2.logging_helpers.log_green('inserts /usr/local/bin into PATH')
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""" adds /usr/local/bin to $PATH """
if log:
bookshelf2.logging_helpers.log_green('inserts /usr/local/bin into PATH')
with settings(hide('warnings', 'running', 'stdout', 'stderr'),
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train | dir_attribs | cuisine dir_attribs doesn't do sudo, so we implement our own
Updates the mode/owner/group for the given remote directory. | bookshelf/api_v2/os_helpers.py | def dir_attribs(location, mode=None, owner=None,
group=None, recursive=False, use_sudo=False):
""" cuisine dir_attribs doesn't do sudo, so we implement our own
Updates the mode/owner/group for the given remote directory."""
args = ''
if recursive:
args = args + ' -R '
if... | def dir_attribs(location, mode=None, owner=None,
group=None, recursive=False, use_sudo=False):
""" cuisine dir_attribs doesn't do sudo, so we implement our own
Updates the mode/owner/group for the given remote directory."""
args = ''
if recursive:
args = args + ' -R '
if... | [
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train | dir_ensure | cuisine dir_ensure doesn't do sudo, so we implement our own
Ensures that there is a remote directory at the given location,
optionally updating its mode/owner/group.
If we are not updating the owner/group then this can be done as a single
ssh call, so use that method, otherwise set owner/group after cre... | bookshelf/api_v2/os_helpers.py | def dir_ensure(location, recursive=False, mode=None,
owner=None, group=None, use_sudo=False):
""" cuisine dir_ensure doesn't do sudo, so we implement our own
Ensures that there is a remote directory at the given location,
optionally updating its mode/owner/group.
If we are not updating th... | def dir_ensure(location, recursive=False, mode=None,
owner=None, group=None, use_sudo=False):
""" cuisine dir_ensure doesn't do sudo, so we implement our own
Ensures that there is a remote directory at the given location,
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train | dir_exists | Tells if there is a remote directory at the given location. | bookshelf/api_v2/os_helpers.py | 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... | def dir_exists(location, use_sudo=False):
"""Tells if there is a remote directory at the given location."""
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if use_sudo:
# convert return code 0 to True
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train | disable_env_reset_on_sudo | updates /etc/sudoers so that users from %wheel keep their
environment when executing a sudo call | bookshelf/api_v2/os_helpers.py | def disable_env_reset_on_sudo(log=False):
""" updates /etc/sudoers so that users from %wheel keep their
environment when executing a sudo call
"""
if log:
bookshelf2.logging_helpers.log_green('disabling env reset on sudo')
file_append('/etc/sudoers',
'Defaults:%wheel !en... | def disable_env_reset_on_sudo(log=False):
""" updates /etc/sudoers so that users from %wheel keep their
environment when executing a sudo call
"""
if log:
bookshelf2.logging_helpers.log_green('disabling env reset on sudo')
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train | disable_requiretty_on_sudoers | allow sudo calls through ssh without a tty | bookshelf/api_v2/os_helpers.py | 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',
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return True | 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',
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train | file_attribs | Updates the mode/owner/group for the remote file at the given
location. | bookshelf/api_v2/os_helpers.py | def file_attribs(location,
mode=None,
owner=None,
group=None,
use_sudo=False,
recursive=True):
"""Updates the mode/owner/group for the remote file at the given
location."""
return dir_attribs(location=location,
... | def file_attribs(location,
mode=None,
owner=None,
group=None,
use_sudo=False,
recursive=True):
"""Updates the mode/owner/group for the remote file at the given
location."""
return dir_attribs(location=location,
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train | os_release | returns /etc/os-release in a dictionary | bookshelf/api_v2/os_helpers.py | def os_release():
""" returns /etc/os-release in a dictionary """
with settings(hide('warnings', 'running', 'stderr'),
warn_only=True, capture=True):
release = {}
data = run('cat /etc/os-release')
for line in data.split('\n'):
if not line:
c... | def os_release():
""" returns /etc/os-release in a dictionary """
with settings(hide('warnings', 'running', 'stderr'),
warn_only=True, capture=True):
release = {}
data = run('cat /etc/os-release')
for line in data.split('\n'):
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train | linux_distribution | returns the linux distribution in lower case | bookshelf/api_v2/os_helpers.py | 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']) | def linux_distribution():
""" returns the linux distribution in lower case """
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warn_only=True, capture=True):
data = os_release()
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train | lsb_release | returns /etc/lsb-release in a dictionary | bookshelf/api_v2/os_helpers.py | def lsb_release():
""" returns /etc/lsb-release in a dictionary """
with settings(hide('warnings', 'running'), capture=True):
_lsb_release = {}
data = sudo('cat /etc/lsb-release')
for line in data.split('\n'):
if not line:
continue
parts = line.sp... | def lsb_release():
""" returns /etc/lsb-release in a dictionary """
with settings(hide('warnings', 'running'), capture=True):
_lsb_release = {}
data = sudo('cat /etc/lsb-release')
for line in data.split('\n'):
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train | restart_service | restarts a service | bookshelf/api_v2/os_helpers.py | def restart_service(service, log=False):
""" restarts a service """
with settings():
if log:
bookshelf2.logging_helpers.log_yellow(
'stoping service %s' % service)
sudo('service %s stop' % service)
if log:
bookshelf2.logging_helpers.log_yellow(
... | def restart_service(service, log=False):
""" restarts a service """
with settings():
if log:
bookshelf2.logging_helpers.log_yellow(
'stoping service %s' % service)
sudo('service %s stop' % service)
if log:
bookshelf2.logging_helpers.log_yellow(
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train | systemd | manipulates systemd services | bookshelf/api_v2/os_helpers.py | 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:... | 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):
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train | install_os_updates | installs OS updates | bookshelf/api_v2/os_helpers.py | 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(... | 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")
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train | Stats.ansi_format | Return a human readable ANSI-terminal printout of the stats.
width
Custom width for the graph (in characters).
height
Custom height for the graph (in characters). | mrcrowbar/statistics.py | def ansi_format( self, width=64, height=12 ):
"""Return a human readable ANSI-terminal printout of the stats.
width
Custom width for the graph (in characters).
height
Custom height for the graph (in characters).
"""
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Custom width for the graph (in characters).
height
Custom height for the graph (in characters).
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Returns:
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whitelist just updated. | saltant/models/task_whitelist.py | def put(self):
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Returns:
:class:`saltant.models.task_whitelist.TaskWhitelist`:
A task whitelist model instance representing the task
whitelist just updated.
"""
return self.manager.put(
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:class:`saltant.models.task_whitelist.TaskWhitelist`:
A task whitelist model instance representing the task
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"""
return self.manager.put(
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name (str): The name of the task whitelist.
description (str, optional): A description of the task whitelist.
whitelisted_container_task_types (list, optional): A list of
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"""Create a task whitelist.
Args:
name (str): The name of the task whitelist.
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whitelisted_executable_task_types=None,
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"""Create a task whitelist.
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name (str): The name of the task whitelist.
description (str, optional): A desc... | [
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name (str, optional): The name of the task whitelist.
description (str, optional): A description of the task whitelist.
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Args:
id (int): The ID of the task whitelist.
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id (int): The ID of the task whitelist.
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Logging threshold, as defined in the logging module of the Python
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"""
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"""Returns the differences between two byte strings in tabular hexadecimal/ASCII format.
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train | BitReader.set_offset | Set the current read offset (in bytes) for the instance. | mrcrowbar/utils.py | def set_offset( self, offset ):
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"""Set the current read offset (in bytes) for the instance."""
assert offset in range( len( self.buffer ) )
self.pos = offset
self._fill_buffer() | [
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] | moralrecordings/mrcrowbar | python | https://github.com/moralrecordings/mrcrowbar/blob/b1ed882c4555552e7656b2d84aca543184577fa3/mrcrowbar/utils.py#L538-L542 | [
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