_id stringlengths 2 7 | title stringlengths 1 88 | partition stringclasses 3
values | text stringlengths 75 19.8k | language stringclasses 1
value | meta_information dict |
|---|---|---|---|---|---|
q272500 | delete | test | def delete(self, name):
'''delete an image from Google Storage.
Parameters
==========
name: the name of the file (or image) to delete
'''
bot.debug("DELETE %s" % name)
for file_object in files:
if isinstance(file_object, dict):
if "kind" in file_object:
... | python | {
"resource": ""
} |
q272501 | destroy | test | def destroy(self, name):
'''destroy an instance, meaning take down the instance and stop the build.
Parameters
==========
name: the name of the instance to stop building.
'''
instances = self._get_instances()
project = self._get_project()
zone = self._get_zone()
found = Fa... | python | {
"resource": ""
} |
q272502 | get_subparsers | test | def get_subparsers(parser):
'''get_subparser will get a dictionary of subparsers, to help with printing help
'''
actions = [action for action in parser._actions
if isinstance(action, argparse._SubParsersAction)]
subparsers = dict()
for action in actions:
# get all subparser... | python | {
"resource": ""
} |
q272503 | RobotNamer.generate | test | def generate(self, delim='-', length=4, chars='0123456789'):
'''
Generate a robot name. Inspiration from Haikunator, but much more
poorly implemented ;)
Parameters
==========
delim: Delimiter
length: TokenLength
chars: TokenChars
'''
... | python | {
"resource": ""
} |
q272504 | get_tmpdir | test | def get_tmpdir(requested_tmpdir=None, prefix="", create=True):
'''get a temporary directory for an operation. If SREGISTRY_TMPDIR
is set, return that. Otherwise, return the output of tempfile.mkdtemp
Parameters
==========
requested_tmpdir: an optional requested temporary directory, firs... | python | {
"resource": ""
} |
q272505 | extract_tar | test | def extract_tar(archive, output_folder, handle_whiteout=False):
'''extract a tar archive to a specified output folder
Parameters
==========
archive: the archive file to extract
output_folder: the output folder to extract to
handle_whiteout: use docker2oci variation to handle... | python | {
"resource": ""
} |
q272506 | _extract_tar | test | def _extract_tar(archive, output_folder):
'''use blob2oci to handle whiteout files for extraction. Credit for this
script goes to docker2oci by Olivier Freyermouth, and see script
folder for license.
Parameters
==========
archive: the archive to extract
output_folder the o... | python | {
"resource": ""
} |
q272507 | get_file_hash | test | def get_file_hash(filename):
'''find the SHA256 hash string of a file
'''
hasher = hashlib.sha256()
with open(filename, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
hasher.update(chunk)
return hasher.hexdigest() | python | {
"resource": ""
} |
q272508 | read_file | test | def read_file(filename, mode="r", readlines=True):
'''write_file will open a file, "filename" and write content, "content"
and properly close the file
'''
with open(filename, mode) as filey:
if readlines is True:
content = filey.readlines()
else:
content = file... | python | {
"resource": ""
} |
q272509 | read_json | test | def read_json(filename, mode='r'):
'''read_json reads in a json file and returns
the data structure as dict.
'''
with open(filename, mode) as filey:
data = json.load(filey)
return data | python | {
"resource": ""
} |
q272510 | clean_up | test | def clean_up(files):
'''clean up will delete a list of files, only if they exist
'''
if not isinstance(files, list):
files = [files]
for f in files:
if os.path.exists(f):
bot.verbose3("Cleaning up %s" % f)
os.remove(f) | python | {
"resource": ""
} |
q272511 | push | test | def push(self, path, name, tag=None):
'''push an image to an S3 endpoint'''
path = os.path.abspath(path)
image = os.path.basename(path)
bot.debug("PUSH %s" % path)
if not os.path.exists(path):
bot.error('%s does not exist.' %path)
sys.exit(1)
# Extract the metadata
names =... | python | {
"resource": ""
} |
q272512 | get_or_create_collection | test | def get_or_create_collection(self, name):
'''get a collection if it exists. If it doesn't exist, create it first.
Parameters
==========
name: the collection name, usually parsed from get_image_names()['name']
'''
from sregistry.database.models import Collection
collection = self.get_collec... | python | {
"resource": ""
} |
q272513 | get_collection | test | def get_collection(self, name):
'''get a collection, if it exists, otherwise return None.
'''
from sregistry.database.models import Collection
return Collection.query.filter(Collection.name == name).first() | python | {
"resource": ""
} |
q272514 | get_container | test | def get_container(self, name, collection_id, tag="latest", version=None):
'''get a container, otherwise return None.
'''
from sregistry.database.models import Container
if version is None:
container = Container.query.filter_by(collection_id = collection_id,
... | python | {
"resource": ""
} |
q272515 | images | test | def images(self, query=None):
'''List local images in the database, optionally with a query.
Paramters
=========
query: a string to search for in the container or collection name|tag|uri
'''
from sregistry.database.models import Collection, Container
rows = []
if query is not... | python | {
"resource": ""
} |
q272516 | inspect | test | def inspect(self, name):
'''Inspect a local image in the database, which typically includes the
basic fields in the model.
'''
print(name)
container = self.get(name)
if container is not None:
collection = container.collection.name
fields = container.__dict__.copy()
fi... | python | {
"resource": ""
} |
q272517 | rename | test | def rename(self, image_name, path):
'''rename performs a move, but ensures the path is maintained in storage
Parameters
==========
image_name: the image name (uri) to rename to.
path: the name to rename (basename is taken)
'''
container = self.get(image_name, quiet=True)
i... | python | {
"resource": ""
} |
q272518 | mv | test | def mv(self, image_name, path):
'''Move an image from it's current location to a new path.
Removing the image from organized storage is not the recommended approach
however is still a function wanted by some.
Parameters
==========
image_name: the parsed image name.
path: t... | python | {
"resource": ""
} |
q272519 | rmi | test | def rmi(self, image_name):
'''Remove an image from the database and filesystem.
'''
container = self.rm(image_name, delete=True)
if container is not None:
bot.info("[rmi] %s" % container) | python | {
"resource": ""
} |
q272520 | add | test | def add(self, image_path=None,
image_uri=None,
image_name=None,
url=None,
metadata=None,
save=True,
copy=False):
'''get or create a container, including the collection to add it to.
This function can be used from a file on the... | python | {
"resource": ""
} |
q272521 | push | test | def push(self, path, name, tag=None):
'''push an image to Singularity Registry'''
path = os.path.abspath(path)
image = os.path.basename(path)
bot.debug("PUSH %s" % path)
if not os.path.exists(path):
bot.error('%s does not exist.' %path)
sys.exit(1)
# Interaction with a registr... | python | {
"resource": ""
} |
q272522 | parse_header | test | def parse_header(recipe, header="from", remove_header=True):
'''take a recipe, and return the complete header, line. If
remove_header is True, only return the value.
Parameters
==========
recipe: the recipe file
headers: the header key to find and parse
remove_header: if t... | python | {
"resource": ""
} |
q272523 | find_single_recipe | test | def find_single_recipe(filename, pattern="Singularity", manifest=None):
'''find_single_recipe will parse a single file, and if valid,
return an updated manifest
Parameters
==========
filename: the filename to assess for a recipe
pattern: a default pattern to search for
man... | python | {
"resource": ""
} |
q272524 | create_build_package | test | def create_build_package(package_files):
'''given a list of files, copy them to a temporary folder,
compress into a .tar.gz, and rename based on the file hash.
Return the full path to the .tar.gz in the temporary folder.
Parameters
==========
package_files: a list of files to inc... | python | {
"resource": ""
} |
q272525 | run_build | test | def run_build(self, config, bucket, names):
'''run a build, meaning creating a build. Retry if there is failure
'''
project = self._get_project()
# prefix, message, color
bot.custom('PROJECT', project, "CYAN")
bot.custom('BUILD ', config['steps'][0]['name'], "CYAN")
response ... | python | {
"resource": ""
} |
q272526 | update_blob_metadata | test | def update_blob_metadata(blob, response, config, bucket, names):
'''a specific function to take a blob, along with a SUCCESS response
from Google build, the original config, and update the blob
metadata with the artifact file name, dependencies, and image hash.
'''
manifest = os.path.basenam... | python | {
"resource": ""
} |
q272527 | format_container_name | test | def format_container_name(name, special_characters=None):
'''format_container_name will take a name supplied by the user,
remove all special characters (except for those defined by "special-characters"
and return the new image name.
'''
if special_characters is None:
special_characters = []
... | python | {
"resource": ""
} |
q272528 | SRegistryMessage.useColor | test | def useColor(self):
'''useColor will determine if color should be added
to a print. Will check if being run in a terminal, and
if has support for asci'''
COLORIZE = get_user_color_preference()
if COLORIZE is not None:
return COLORIZE
streams = [self.errorStrea... | python | {
"resource": ""
} |
q272529 | SRegistryMessage.emitError | test | def emitError(self, level):
'''determine if a level should print to
stderr, includes all levels but INFO and QUIET'''
if level in [ABORT,
ERROR,
WARNING,
VERBOSE,
VERBOSE1,
VERBOSE2,
... | python | {
"resource": ""
} |
q272530 | SRegistryMessage.write | test | def write(self, stream, message):
'''write will write a message to a stream,
first checking the encoding
'''
if isinstance(message, bytes):
message = message.decode('utf-8')
stream.write(message) | python | {
"resource": ""
} |
q272531 | SRegistryMessage.table | test | def table(self, rows, col_width=2):
'''table will print a table of entries. If the rows is
a dictionary, the keys are interpreted as column names. if
not, a numbered list is used.
'''
labels = [str(x) for x in range(1,len(rows)+1)]
if isinstance(rows, dict):
... | python | {
"resource": ""
} |
q272532 | push | test | def push(self, path, name, tag=None):
'''push an image to Globus endpoint. In this case, the name is the
globus endpoint id and path.
--name <endpointid>:/path/for/image
'''
# Split the name into endpoint and rest
endpoint, remote = self._parse_endpoint_name(name)
path = os.path.a... | python | {
"resource": ""
} |
q272533 | get_template | test | def get_template(name):
'''return a default template for some function in sregistry
If there is no template, None is returned.
Parameters
==========
name: the name of the template to retrieve
'''
name = name.lower()
templates = dict()
templates['tarinfo'] = {"gid": 0,
... | python | {
"resource": ""
} |
q272534 | get_manifest | test | def get_manifest(self, repo_name, tag):
'''return the image manifest via the aws client, saved in self.manifest
'''
image = None
repo = self.aws.describe_images(repositoryName=repo_name)
if 'imageDetails' in repo:
for contender in repo.get('imageDetails'):
if tag in contender['i... | python | {
"resource": ""
} |
q272535 | get_build_template | test | def get_build_template(name=None, manager='apt'):
'''get a particular build template, by default we return templates
that are based on package managers.
Parameters
==========
name: the full path of the template file to use.
manager: the package manager to use in the template (yum... | python | {
"resource": ""
} |
q272536 | Client._update_secrets | test | def _update_secrets(self):
'''update secrets will take a secrets credential file
either located at .sregistry or the environment variable
SREGISTRY_CLIENT_SECRETS and update the current client
secrets as well as the associated API base. This is where you
should do an... | python | {
"resource": ""
} |
q272537 | _make_repr | test | def _make_repr(class_name, *args, **kwargs):
"""
Generate a repr string.
Positional arguments should be the positional arguments used to
construct the class. Keyword arguments should consist of tuples of
the attribute value and default. If the value is the default, then
it won't be rendered in ... | python | {
"resource": ""
} |
q272538 | s3errors | test | def s3errors(path):
"""Translate S3 errors to FSErrors."""
try:
yield
except ClientError as error:
_error = error.response.get("Error", {})
error_code = _error.get("Code", None)
response_meta = error.response.get("ResponseMetadata", {})
http_status = response_meta.get... | python | {
"resource": ""
} |
q272539 | S3File.factory | test | def factory(cls, filename, mode, on_close):
"""Create a S3File backed with a temporary file."""
_temp_file = tempfile.TemporaryFile()
proxy = cls(_temp_file, filename, mode, on_close=on_close)
return proxy | python | {
"resource": ""
} |
q272540 | gravatar_url | test | def gravatar_url(user_or_email, size=GRAVATAR_DEFAULT_SIZE):
""" Builds a gravatar url from an user or email """
if hasattr(user_or_email, 'email'):
email = user_or_email.email
else:
email = user_or_email
try:
return escape(get_gravatar_url(email=email, size=size))
except:
... | python | {
"resource": ""
} |
q272541 | get_gravatar_url | test | def get_gravatar_url(email, size=GRAVATAR_DEFAULT_SIZE, default=GRAVATAR_DEFAULT_IMAGE,
rating=GRAVATAR_DEFAULT_RATING, secure=GRAVATAR_DEFAULT_SECURE):
"""
Builds a url to a gravatar from an email address.
:param email: The email to fetch the gravatar for
:param size: The size (in pixels) of t... | python | {
"resource": ""
} |
q272542 | has_gravatar | test | def has_gravatar(email):
"""
Returns True if the user has a gravatar, False if otherwise
"""
# Request a 404 response if the gravatar does not exist
url = get_gravatar_url(email, default=GRAVATAR_DEFAULT_IMAGE_404)
# Verify an OK response was received
try:
request = Request(url)
... | python | {
"resource": ""
} |
q272543 | get_gravatar_profile_url | test | def get_gravatar_profile_url(email, secure=GRAVATAR_DEFAULT_SECURE):
"""
Builds a url to a gravatar profile from an email address.
:param email: The email to fetch the gravatar for
:param secure: If True use https, otherwise plain http
"""
if secure:
url_base = GRAVATAR_SECURE_URL
e... | python | {
"resource": ""
} |
q272544 | chimera_blocks | test | def chimera_blocks(M=16, N=16, L=4):
"""
Generator for blocks for a chimera block quotient
"""
for x in xrange(M):
for y in xrange(N):
for u in (0, 1):
yield tuple((x, y, u, k) for k in xrange(L)) | python | {
"resource": ""
} |
q272545 | chimera_block_quotient | test | def chimera_block_quotient(G, blocks):
"""
Extract the blocks from a graph, and returns a
block-quotient graph according to the acceptability
functions block_good and eblock_good
Inputs:
G: a networkx graph
blocks: a tuple of tuples
"""
from networkx import Graph
from i... | python | {
"resource": ""
} |
q272546 | enumerate_resonance_smiles | test | def enumerate_resonance_smiles(smiles):
"""Return a set of resonance forms as SMILES strings, given a SMILES string.
:param smiles: A SMILES string.
:returns: A set containing SMILES strings for every possible resonance form.
:rtype: set of strings.
"""
mol = Chem.MolFromSmiles(smiles)
#Che... | python | {
"resource": ""
} |
q272547 | ResonanceEnumerator.enumerate | test | def enumerate(self, mol):
"""Enumerate all possible resonance forms and return them as a list.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: A list of all possible resonance forms of the molecule.
:rtype: list of rdkit.Chem.rdchem.Mol
"""
... | python | {
"resource": ""
} |
q272548 | Normalizer.normalize | test | def normalize(self, mol):
"""Apply a series of Normalization transforms to correct functional groups and recombine charges.
A series of transforms are applied to the molecule. For each Normalization, the transform is applied repeatedly
until no further changes occur. If any changes occurred, we... | python | {
"resource": ""
} |
q272549 | Normalizer._apply_transform | test | def _apply_transform(self, mol, rule):
"""Repeatedly apply normalization transform to molecule until no changes occur.
It is possible for multiple products to be produced when a rule is applied. The rule is applied repeatedly to
each of the products, until no further changes occur or after 20 a... | python | {
"resource": ""
} |
q272550 | TautomerCanonicalizer.canonicalize | test | def canonicalize(self, mol):
"""Return a canonical tautomer by enumerating and scoring all possible tautomers.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:return: The canonical tautomer.
:rtype: rdkit.Chem.rdchem.Mol
"""
# TODO: Overload the... | python | {
"resource": ""
} |
q272551 | validate_smiles | test | def validate_smiles(smiles):
"""Return log messages for a given SMILES string using the default validations.
Note: This is a convenience function for quickly validating a single SMILES string. It is more efficient to use
the :class:`~molvs.validate.Validator` class directly when working with many molecules... | python | {
"resource": ""
} |
q272552 | MetalDisconnector.disconnect | test | def disconnect(self, mol):
"""Break covalent bonds between metals and organic atoms under certain conditions.
The algorithm works as follows:
- Disconnect N, O, F from any metal.
- Disconnect other non-metals from transition metals + Al (but not Hg, Ga, Ge, In, Sn, As, Tl, Pb, Bi, Po).... | python | {
"resource": ""
} |
q272553 | standardize_smiles | test | def standardize_smiles(smiles):
"""Return a standardized canonical SMILES string given a SMILES string.
Note: This is a convenience function for quickly standardizing a single SMILES string. It is more efficient to use
the :class:`~molvs.standardize.Standardizer` class directly when working with many molec... | python | {
"resource": ""
} |
q272554 | enumerate_tautomers_smiles | test | def enumerate_tautomers_smiles(smiles):
"""Return a set of tautomers as SMILES strings, given a SMILES string.
:param smiles: A SMILES string.
:returns: A set containing SMILES strings for every possible tautomer.
:rtype: set of strings.
"""
# Skip sanitize as standardize does this anyway
m... | python | {
"resource": ""
} |
q272555 | canonicalize_tautomer_smiles | test | def canonicalize_tautomer_smiles(smiles):
"""Return a standardized canonical tautomer SMILES string given a SMILES string.
Note: This is a convenience function for quickly standardizing and finding the canonical tautomer for a single
SMILES string. It is more efficient to use the :class:`~molvs.standardize... | python | {
"resource": ""
} |
q272556 | Standardizer.standardize | test | def standardize(self, mol):
"""Return a standardized version the given molecule.
The standardization process consists of the following stages: RDKit
:py:func:`~rdkit.Chem.rdmolops.RemoveHs`, RDKit :py:func:`~rdkit.Chem.rdmolops.SanitizeMol`,
:class:`~molvs.metal.MetalDisconnector`, :cla... | python | {
"resource": ""
} |
q272557 | Standardizer.tautomer_parent | test | def tautomer_parent(self, mol, skip_standardize=False):
"""Return the tautomer parent of a given molecule.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True if mol has already been standardized.
:returns: The tautomer pare... | python | {
"resource": ""
} |
q272558 | Standardizer.fragment_parent | test | def fragment_parent(self, mol, skip_standardize=False):
"""Return the fragment parent of a given molecule.
The fragment parent is the largest organic covalent unit in the molecule.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Se... | python | {
"resource": ""
} |
q272559 | Standardizer.stereo_parent | test | def stereo_parent(self, mol, skip_standardize=False):
"""Return the stereo parent of a given molecule.
The stereo parent has all stereochemistry information removed from tetrahedral centers and double bonds.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:para... | python | {
"resource": ""
} |
q272560 | Standardizer.isotope_parent | test | def isotope_parent(self, mol, skip_standardize=False):
"""Return the isotope parent of a given molecule.
The isotope parent has all atoms replaced with the most abundant isotope for that element.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_... | python | {
"resource": ""
} |
q272561 | Standardizer.charge_parent | test | def charge_parent(self, mol, skip_standardize=False):
"""Return the charge parent of a given molecule.
The charge parent is the uncharged version of the fragment parent.
:param mol: The input molecule.
:type mol: rdkit.Chem.rdchem.Mol
:param bool skip_standardize: Set to True i... | python | {
"resource": ""
} |
q272562 | Standardizer.super_parent | test | def super_parent(self, mol, skip_standardize=False):
"""Return the super parent of a given molecule.
THe super parent is fragment, charge, isotope, stereochemistry and tautomer insensitive. From the input
molecule, the largest fragment is taken. This is uncharged and then isotope and stereochem... | python | {
"resource": ""
} |
q272563 | main | test | def main():
"""Main function for molvs command line interface."""
# Root options
parser = MolvsParser(epilog='use "molvs <command> -h" to show help for a specific command')
subparsers = parser.add_subparsers(title='Available commands')
# Options common to all commands
common_parser = MolvsPar... | python | {
"resource": ""
} |
q272564 | FragmentRemover.remove | test | def remove(self, mol):
"""Return the molecule with specified fragments removed.
:param mol: The molecule to remove fragments from.
:type mol: rdkit.Chem.rdchem.Mol
:return: The molecule with fragments removed.
:rtype: rdkit.Chem.rdchem.Mol
"""
log.debug('Running ... | python | {
"resource": ""
} |
q272565 | LargestFragmentChooser.choose | test | def choose(self, mol):
"""Return the largest covalent unit.
The largest fragment is determined by number of atoms (including hydrogens). Ties are broken by taking the
fragment with the higher molecular weight, and then by taking the first alphabetically by SMILES if needed.
:param mol:... | python | {
"resource": ""
} |
q272566 | integrate_ivp | test | def integrate_ivp(u0=1.0, v0=0.0, mu=1.0, tend=10.0, dt0=1e-8, nt=0,
nsteps=600, t0=0.0, atol=1e-8, rtol=1e-8, plot=False,
savefig='None', method='bdf', dpi=100, verbose=False):
"""
Example program integrating an IVP problem of van der Pol oscillator
"""
f, j = get_f_... | python | {
"resource": ""
} |
q272567 | GitHub_LLNL_Stats.get_stats | test | def get_stats(self, username='', password='', organization='llnl',
force=True, repo_type='public'):
"""
Retrieves the statistics from the given organization with the given
credentials. Will not retreive data if file exists and force hasn't been
set to True. This is to save GH API... | python | {
"resource": ""
} |
q272568 | GitHub_LLNL_Stats.get_mems_of_org | test | def get_mems_of_org(self):
"""
Retrieves the number of members of the organization.
"""
print 'Getting members.'
counter = 0
for member in self.org_retrieved.iter_members():
self.members_json[member.id] = member.to_json()
counter += 1
retur... | python | {
"resource": ""
} |
q272569 | GitHub_LLNL_Stats.get_teams_of_org | test | def get_teams_of_org(self):
"""
Retrieves the number of teams of the organization.
"""
print 'Getting teams.'
counter = 0
for team in self.org_retrieved.iter_teams():
self.teams_json[team.id] = team.to_json()
counter += 1
return counter | python | {
"resource": ""
} |
q272570 | GitHub_LLNL_Stats.repos | test | def repos(self, repo_type='public', organization='llnl'):
"""
Retrieves info about the repos of the current organization.
"""
print 'Getting repos.'
for repo in self.org_retrieved.iter_repos(type=repo_type):
#JSON
json = repo.to_json()
self.rep... | python | {
"resource": ""
} |
q272571 | GitHub_LLNL_Stats.get_total_contributors | test | def get_total_contributors(self, repo):
"""
Retrieves the number of contributors to a repo in the organization.
Also adds to unique contributor list.
"""
repo_contributors = 0
for contributor in repo.iter_contributors():
repo_contributors += 1
self... | python | {
"resource": ""
} |
q272572 | GitHub_LLNL_Stats.get_pull_reqs | test | def get_pull_reqs(self, repo):
"""
Retrieves the number of pull requests on a repo in the organization.
"""
pull_reqs_open = 0
pull_reqs_closed = 0
for pull_request in repo.iter_pulls(state='all'):
self.pull_requests_json[repo.name].append(pull_request.to_json... | python | {
"resource": ""
} |
q272573 | GitHub_LLNL_Stats.get_issues | test | def get_issues(self, repo, organization='llnl'):
"""
Retrieves the number of closed issues.
"""
#JSON
path = ('../github-data/' + organization + '/' + repo.name + '/issues')
is_only_today = False
if not os.path.exists(path): #no previous path, get all issues
... | python | {
"resource": ""
} |
q272574 | GitHub_LLNL_Stats.get_readme | test | def get_readme(self, repo):
"""
Checks to see if the given repo has a ReadMe. MD means it has a correct
Readme recognized by GitHub.
"""
readme_contents = repo.readme()
if readme_contents is not None:
self.total_readmes += 1
return 'MD'
if ... | python | {
"resource": ""
} |
q272575 | GitHub_LLNL_Stats.get_license | test | def get_license(self, repo):
"""
Checks to see if the given repo has a top level LICENSE file.
"""
if self.search_limit >= 28:
print 'Hit search limit. Sleeping for 60 sec.'
time.sleep(60)
self.search_limit = 0
self.search_limit += 1
se... | python | {
"resource": ""
} |
q272576 | GitHub_LLNL_Stats.get_commits | test | def get_commits(self, repo, organization='llnl'):
"""
Retrieves the number of commits to a repo in the organization. If it is
the first time getting commits for a repo, it will get all commits and
save them to JSON. If there are previous commits saved, it will only get
commits th... | python | {
"resource": ""
} |
q272577 | GitHub_LLNL_Stats.write_org_json | test | def write_org_json(self, date=(datetime.date.today()),
organization='llnl',dict_to_write={}, path_ending_type='',
is_list=False):
"""
Writes stats from the organization to JSON.
"""
path = ('../github-data/' + organization + '-org/'
+ path_ending_type + '/' + ... | python | {
"resource": ""
} |
q272578 | GitHub_LLNL_Stats.write_totals | test | def write_totals(self, file_path='', date=str(datetime.date.today()),
organization='N/A', members=0, teams=0):
"""
Updates the total.csv file with current data.
"""
total_exists = os.path.isfile(file_path)
with open(file_path, 'a') as out_total:
if not total_... | python | {
"resource": ""
} |
q272579 | GitHub_LLNL_Stats.write_languages | test | def write_languages(self, file_path='',date=str(datetime.date.today())):
"""
Updates languages.csv file with current data.
"""
self.remove_date(file_path=file_path, date=date)
languages_exists = os.path.isfile(file_path)
with open(file_path, 'a') as out_languages:
... | python | {
"resource": ""
} |
q272580 | GitHub_LLNL_Stats.checkDir | test | def checkDir(self, file_path=''):
"""
Checks if a directory exists. If not, it creates one with the specified
file_path.
"""
if not os.path.exists(os.path.dirname(file_path)):
try:
os.makedirs(os.path.dirname(file_path))
except OSError as e... | python | {
"resource": ""
} |
q272581 | GitHub_LLNL_Stats.remove_date | test | def remove_date(self, file_path='', date=str(datetime.date.today())):
"""
Removes all rows of the associated date from the given csv file.
Defaults to today.
"""
languages_exists = os.path.isfile(file_path)
if languages_exists:
with open(file_path, 'rb') as in... | python | {
"resource": ""
} |
q272582 | gov_orgs | test | def gov_orgs():
"""
Returns a list of the names of US Government GitHub organizations
Based on: https://government.github.com/community/
Exmample return:
{'llnl', '18f', 'gsa', 'dhs-ncats', 'spack', ...}
"""
us_gov_github_orgs = set()
gov_orgs = requests.get('https://government.gi... | python | {
"resource": ""
} |
q272583 | create_enterprise_session | test | def create_enterprise_session(url, token=None):
"""
Create a github3.py session for a GitHub Enterprise instance
If token is not provided, will attempt to use the GITHUB_API_TOKEN
environment variable if present.
"""
gh_session = github3.enterprise_login(url=url, token=token)
if gh_sessio... | python | {
"resource": ""
} |
q272584 | _check_api_limits | test | def _check_api_limits(gh_session, api_required=250, sleep_time=15):
"""
Simplified check for API limits
If necessary, spin in place waiting for API to reset before returning.
See: https://developer.github.com/v3/#rate-limiting
"""
api_rates = gh_session.rate_limit()
api_remaining = api_ra... | python | {
"resource": ""
} |
q272585 | connect | test | def connect(url='https://github.com', token=None):
"""
Create a GitHub session for making requests
"""
gh_session = None
if url == 'https://github.com':
gh_session = create_session(token)
else:
gh_session = create_enterprise_session(url, token)
if gh_session is None:
... | python | {
"resource": ""
} |
q272586 | query_repos | test | def query_repos(gh_session, orgs=None, repos=None, public_only=True):
"""
Yields GitHub3.py repo objects for provided orgs and repo names
If orgs and repos are BOTH empty, execute special mode of getting ALL
repositories from the GitHub Server.
If public_only is True, will return only those repos ... | python | {
"resource": ""
} |
q272587 | GitHub_Stargazers.get_org | test | def get_org(self, organization_name=''):
"""
Retrieves an organization via given org name. If given
empty string, prompts user for an org name.
"""
self.organization_name = organization_name
if(organization_name == ''):
self.organization_name = raw_input('Orga... | python | {
"resource": ""
} |
q272588 | GitHub_Stargazers.write_to_file | test | def write_to_file(self, file_path='', date=(datetime.date.today()),
organization='llnl'):
"""
Writes stargazers data to file.
"""
with open(file_path, 'w+') as out:
out.write('date,organization,stargazers\n')
sorted_stargazers = sorted(self.stargazers)#sor... | python | {
"resource": ""
} |
q272589 | Project.from_gitlab | test | def from_gitlab(klass, repository, labor_hours=True):
"""
Create CodeGovProject object from GitLab Repository
"""
if not isinstance(repository, gitlab.v4.objects.Project):
raise TypeError('Repository must be a gitlab Repository object')
project = klass()
log... | python | {
"resource": ""
} |
q272590 | Project.from_doecode | test | def from_doecode(klass, record):
"""
Create CodeGovProject object from DOE CODE record
Handles crafting Code.gov Project
"""
if not isinstance(record, dict):
raise TypeError('`record` must be a dict')
project = klass()
# -- REQUIRED FIELDS --
... | python | {
"resource": ""
} |
q272591 | _license_obj | test | def _license_obj(license):
"""
A helper function to look up license object information
Use names from: https://api.github.com/licenses
"""
obj = None
if license in ('MIT', 'MIT License'):
obj = {
'URL': 'https://api.github.com/licenses/mit',
'name': 'MIT'
... | python | {
"resource": ""
} |
q272592 | GitHub_Traffic.get_traffic | test | def get_traffic(self):
"""
Retrieves the traffic for the repositories of the given organization.
"""
print 'Getting traffic.'
#Uses the developer API. Note this could change.
headers = {'Accept': 'application/vnd.github.spiderman-preview', 'Authorization': 'token ' + self... | python | {
"resource": ""
} |
q272593 | GitHub_Traffic.get_releases | test | def get_releases(self, url='', headers={}, repo_name=''):
"""
Retrieves the releases for the given repo in JSON.
"""
url_releases = (url + '/releases')
r = requests.get(url_releases, headers=headers)
self.releases_json[repo_name] = r.json() | python | {
"resource": ""
} |
q272594 | GitHub_Traffic.get_referrers | test | def get_referrers(self, url='', headers={}, repo_name=''):
"""
Retrieves the total referrers and unique referrers of all repos in json
and then stores it in a dict.
"""
#JSON
url_referrers = (url + '/traffic/popular/referrers')
r1 = requests.get(url_referrers, hea... | python | {
"resource": ""
} |
q272595 | GitHub_Traffic.get_data | test | def get_data(self, url='',headers={}, date=str(datetime.date.today()),
dict_to_store={}, type='', repo_name=''):
"""
Retrieves data from json and stores it in the supplied dict. Accepts
'clones' or 'views' as type.
"""
#JSON
url = (url + '/traffic/' + type)
... | python | {
"resource": ""
} |
q272596 | GitHub_Traffic.write_json | test | def write_json(self, date=(datetime.date.today()),
organization='llnl',dict_to_write={}, path_ending_type=''):
"""
Writes all traffic data to file in JSON form.
"""
for repo in dict_to_write:
if len(dict_to_write[repo]) != 0:#don't need to write out empty lists
... | python | {
"resource": ""
} |
q272597 | GitHub_Traffic.write_to_file | test | def write_to_file(self, referrers_file_path='', views_file_path='',
clones_file_path='', date=(datetime.date.today()), organization='llnl',
views_row_count=0, clones_row_count=0):
"""
Writes all traffic data to file.
"""
self.write_referrers_to_file(file_path=referrers_fi... | python | {
"resource": ""
} |
q272598 | GitHub_Traffic.check_data_redundancy | test | def check_data_redundancy(self, file_path='', dict_to_check={}):
"""
Checks the given csv file against the json data scraped for the given
dict. It will remove all data retrieved that has already been recorded
so we don't write redundant data to file. Returns count of rows from
f... | python | {
"resource": ""
} |
q272599 | GitHub_Traffic.write_data_to_file | test | def write_data_to_file(self, file_path='', date=str(datetime.date.today()),
organization='llnl',dict_to_write={}, name='', row_count=0):
"""
Writes given dict to file.
"""
exists = os.path.isfile(file_path)
with open(file_path, 'a') as out:
if not exists:
... | python | {
"resource": ""
} |
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