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projectshift/shift-boiler | boiler/user/models.py | User.password_link_expired | def password_link_expired(self, now=None):
""" Check if password link expired """
if not now: now = datetime.datetime.utcnow()
return self.password_link_expires < now | python | def password_link_expired(self, now=None):
""" Check if password link expired """
if not now: now = datetime.datetime.utcnow()
return self.password_link_expires < now | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/user/models.py#L346-L349 | train |
projectshift/shift-boiler | boiler/user/models.py | User.add_role | def add_role(self, role):
"""
Add role to user
Role must be valid and saved first, otherwise will
raise an exception.
"""
schema = RoleSchema()
ok = schema.process(role)
if not ok or not role.id:
err = 'Role must be valid and saved before adding to user'
raise x.UserException(err)
self.__roles.append(role) | python | def add_role(self, role):
"""
Add role to user
Role must be valid and saved first, otherwise will
raise an exception.
"""
schema = RoleSchema()
ok = schema.process(role)
if not ok or not role.id:
err = 'Role must be valid and saved before adding to user'
raise x.UserException(err)
self.__roles.append(role) | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/user/models.py#L363-L375 | train |
projectshift/shift-boiler | boiler/user/models.py | User.has_role | def has_role(self, role_or_handle):
""" Checks if user has role """
if not isinstance(role_or_handle, str):
return role_or_handle in self.roles
has_role = False
for role in self.roles:
if role.handle == role_or_handle:
has_role = True
break
return has_role | python | def has_role(self, role_or_handle):
""" Checks if user has role """
if not isinstance(role_or_handle, str):
return role_or_handle in self.roles
has_role = False
for role in self.roles:
if role.handle == role_or_handle:
has_role = True
break
return has_role | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/user/models.py#L382-L393 | train |
ronhanson/python-tbx | fabfile/git.py | push | def push(remote='origin', branch='master'):
"""git push commit"""
print(cyan("Pulling changes from repo ( %s / %s)..." % (remote, branch)))
local("git push %s %s" % (remote, branch)) | python | def push(remote='origin', branch='master'):
"""git push commit"""
print(cyan("Pulling changes from repo ( %s / %s)..." % (remote, branch)))
local("git push %s %s" % (remote, branch)) | [
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| 87f72ae0cadecafbcd144f1e930181fba77f6b83 | https://github.com/ronhanson/python-tbx/blob/87f72ae0cadecafbcd144f1e930181fba77f6b83/fabfile/git.py#L7-L10 | train |
ronhanson/python-tbx | fabfile/git.py | pull | def pull(remote='origin', branch='master'):
"""git pull commit"""
print(cyan("Pulling changes from repo ( %s / %s)..." % (remote, branch)))
local("git pull %s %s" % (remote, branch)) | python | def pull(remote='origin', branch='master'):
"""git pull commit"""
print(cyan("Pulling changes from repo ( %s / %s)..." % (remote, branch)))
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| 87f72ae0cadecafbcd144f1e930181fba77f6b83 | https://github.com/ronhanson/python-tbx/blob/87f72ae0cadecafbcd144f1e930181fba77f6b83/fabfile/git.py#L14-L17 | train |
ronhanson/python-tbx | fabfile/git.py | sync | def sync(remote='origin', branch='master'):
"""git pull and push commit"""
pull(branch, remote)
push(branch, remote)
print(cyan("Git Synced!")) | python | def sync(remote='origin', branch='master'):
"""git pull and push commit"""
pull(branch, remote)
push(branch, remote)
print(cyan("Git Synced!")) | [
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| 87f72ae0cadecafbcd144f1e930181fba77f6b83 | https://github.com/ronhanson/python-tbx/blob/87f72ae0cadecafbcd144f1e930181fba77f6b83/fabfile/git.py#L21-L25 | train |
ZEDGR/pychal | challonge/attachments.py | update | def update(tournament, match, attachment, **params):
"""Update the attributes of a match attachment."""
api.fetch(
"PUT",
"tournaments/%s/matches/%s/attachments/%s" % (tournament, match, attachment),
"match_attachment",
**params) | python | def update(tournament, match, attachment, **params):
"""Update the attributes of a match attachment."""
api.fetch(
"PUT",
"tournaments/%s/matches/%s/attachments/%s" % (tournament, match, attachment),
"match_attachment",
**params) | [
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| 3600fa9e0557a2a14eb1ad0c0711d28dad3693d7 | https://github.com/ZEDGR/pychal/blob/3600fa9e0557a2a14eb1ad0c0711d28dad3693d7/challonge/attachments.py#L27-L33 | train |
MacHu-GWU/sqlalchemy_mate-project | sqlalchemy_mate/crud/selecting.py | count_row | def count_row(engine, table):
"""
Return number of rows in a table.
Example::
>>> count_row(engine, table_user)
3
**中文文档**
返回一个表中的行数。
"""
return engine.execute(select([func.count()]).select_from(table)).fetchone()[0] | python | def count_row(engine, table):
"""
Return number of rows in a table.
Example::
>>> count_row(engine, table_user)
3
**中文文档**
返回一个表中的行数。
"""
return engine.execute(select([func.count()]).select_from(table)).fetchone()[0] | [
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| 946754744c8870f083fd7b4339fca15d1d6128b2 | https://github.com/MacHu-GWU/sqlalchemy_mate-project/blob/946754744c8870f083fd7b4339fca15d1d6128b2/sqlalchemy_mate/crud/selecting.py#L10-L23 | train |
projectshift/shift-boiler | boiler/user/util/oauth_providers.py | OauthProviders.get_providers | def get_providers(self):
"""
Get OAuth providers
Returns a dictionary of oauth applications ready to be registered with
flask oauth extension at application bootstrap.
"""
if self.providers:
return self.providers
providers = dict()
for provider in self.config:
configurator = provider.lower() + '_config'
if not hasattr(self, configurator):
err = 'Provider [{}] not recognized'.format(provider)
raise ValueError(err)
provider_config = self.config[provider]
configurator = getattr(self, configurator)
providers[provider] = configurator(
id=provider_config.get('id'),
secret=provider_config.get('secret'),
scope=provider_config.get('scope'),
offline=provider_config.get('offline')
)
self.providers = providers
return self.providers | python | def get_providers(self):
"""
Get OAuth providers
Returns a dictionary of oauth applications ready to be registered with
flask oauth extension at application bootstrap.
"""
if self.providers:
return self.providers
providers = dict()
for provider in self.config:
configurator = provider.lower() + '_config'
if not hasattr(self, configurator):
err = 'Provider [{}] not recognized'.format(provider)
raise ValueError(err)
provider_config = self.config[provider]
configurator = getattr(self, configurator)
providers[provider] = configurator(
id=provider_config.get('id'),
secret=provider_config.get('secret'),
scope=provider_config.get('scope'),
offline=provider_config.get('offline')
)
self.providers = providers
return self.providers | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/user/util/oauth_providers.py#L21-L47 | train |
projectshift/shift-boiler | boiler/user/util/oauth_providers.py | OauthProviders.token_getter | def token_getter(provider, token=None):
""" Generic token getter for all the providers """
session_key = provider + '_token'
if token is None:
token = session.get(session_key)
return token | python | def token_getter(provider, token=None):
""" Generic token getter for all the providers """
session_key = provider + '_token'
if token is None:
token = session.get(session_key)
return token | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/user/util/oauth_providers.py#L50-L55 | train |
projectshift/shift-boiler | boiler/user/util/oauth_providers.py | OauthProviders.register_token_getter | def register_token_getter(self, provider):
""" Register callback to retrieve token from session """
app = oauth.remote_apps[provider]
decorator = getattr(app, 'tokengetter')
def getter(token=None):
return self.token_getter(provider, token)
decorator(getter) | python | def register_token_getter(self, provider):
""" Register callback to retrieve token from session """
app = oauth.remote_apps[provider]
decorator = getattr(app, 'tokengetter')
def getter(token=None):
return self.token_getter(provider, token)
decorator(getter) | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/user/util/oauth_providers.py#L57-L65 | train |
projectshift/shift-boiler | boiler/user/util/oauth_providers.py | OauthProviders.vkontakte_config | def vkontakte_config(self, id, secret, scope=None, offline=False, **_):
""" Get config dictionary for vkontakte oauth """
if scope is None: scope = 'email,offline'
if offline: scope += ',offline'
token_params = dict(scope=scope)
config = dict(
request_token_url=None,
access_token_url='https://oauth.vk.com/access_token',
authorize_url='https://oauth.vk.com/authorize',
base_url='https://api.vk.com/method/',
consumer_key=id,
consumer_secret=secret,
request_token_params=token_params
)
return config | python | def vkontakte_config(self, id, secret, scope=None, offline=False, **_):
""" Get config dictionary for vkontakte oauth """
if scope is None: scope = 'email,offline'
if offline: scope += ',offline'
token_params = dict(scope=scope)
config = dict(
request_token_url=None,
access_token_url='https://oauth.vk.com/access_token',
authorize_url='https://oauth.vk.com/authorize',
base_url='https://api.vk.com/method/',
consumer_key=id,
consumer_secret=secret,
request_token_params=token_params
)
return config | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/user/util/oauth_providers.py#L87-L102 | train |
projectshift/shift-boiler | boiler/user/util/oauth_providers.py | OauthProviders.instagram_config | def instagram_config(self, id, secret, scope=None, **_):
""" Get config dictionary for instagram oauth """
scope = scope if scope else 'basic'
token_params = dict(scope=scope)
config = dict(
# request_token_url=None,
access_token_url='/oauth/access_token/',
authorize_url='/oauth/authorize/',
base_url='https://api.instagram.com/',
consumer_key=id,
consumer_secret=secret,
request_token_params=token_params
)
return config | python | def instagram_config(self, id, secret, scope=None, **_):
""" Get config dictionary for instagram oauth """
scope = scope if scope else 'basic'
token_params = dict(scope=scope)
config = dict(
# request_token_url=None,
access_token_url='/oauth/access_token/',
authorize_url='/oauth/authorize/',
base_url='https://api.instagram.com/',
consumer_key=id,
consumer_secret=secret,
request_token_params=token_params
)
return config | [
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| Get config dictionary for instagram oauth | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/user/util/oauth_providers.py#L123-L137 | train |
Kortemme-Lab/klab | klab/bio/relatrix.py | ResidueRelatrix.convert | def convert(self, chain_id, residue_id, from_scheme, to_scheme):
'''The API conversion function. This converts between the different residue ID schemes.'''
# At the cost of three function calls, we ignore the case of the scheme parameters to be more user-friendly.
from_scheme = from_scheme.lower()
to_scheme = to_scheme.lower()
assert(from_scheme in ResidueRelatrix.schemes)
assert(to_scheme in ResidueRelatrix.schemes)
return self._convert(chain_id, residue_id, from_scheme, to_scheme) | python | def convert(self, chain_id, residue_id, from_scheme, to_scheme):
'''The API conversion function. This converts between the different residue ID schemes.'''
# At the cost of three function calls, we ignore the case of the scheme parameters to be more user-friendly.
from_scheme = from_scheme.lower()
to_scheme = to_scheme.lower()
assert(from_scheme in ResidueRelatrix.schemes)
assert(to_scheme in ResidueRelatrix.schemes)
return self._convert(chain_id, residue_id, from_scheme, to_scheme) | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/relatrix.py#L143-L151 | train |
Kortemme-Lab/klab | klab/bio/relatrix.py | ResidueRelatrix._convert | def _convert(self, chain_id, residue_id, from_scheme, to_scheme):
'''The actual 'private' conversion function.'''
# There are 12 valid combinations but rather than write them all out explicitly, we will use recursion, sacrificing speed for brevity
if from_scheme == 'rosetta':
atom_id = self.rosetta_to_atom_sequence_maps.get(chain_id, {})[residue_id]
if to_scheme == 'atom':
return atom_id
else:
return self._convert(chain_id, atom_id, 'atom', to_scheme)
if from_scheme == 'atom':
if to_scheme == 'rosetta':
return self.atom_to_rosetta_sequence_maps.get(chain_id, {})[residue_id]
else:
seqres_id = self.atom_to_seqres_sequence_maps.get(chain_id, {})[residue_id]
if to_scheme == 'seqres':
return seqres_id
return self.convert(chain_id, seqres_id, 'seqres', to_scheme)
if from_scheme == 'seqres':
if to_scheme == 'uniparc':
return self.seqres_to_uniparc_sequence_maps.get(chain_id, {})[residue_id]
else:
atom_id = self.seqres_to_atom_sequence_maps.get(chain_id, {})[residue_id]
if to_scheme == 'atom':
return atom_id
return self.convert(chain_id, atom_id, 'atom', to_scheme)
if from_scheme == 'uniparc':
seqres_id = self.uniparc_to_seqres_sequence_maps.get(chain_id, {})[residue_id]
if to_scheme == 'seqres':
return seqres_id
else:
return self._convert(chain_id, seqres_id, 'seqres', to_scheme)
raise Exception("We should never reach this line.") | python | def _convert(self, chain_id, residue_id, from_scheme, to_scheme):
'''The actual 'private' conversion function.'''
# There are 12 valid combinations but rather than write them all out explicitly, we will use recursion, sacrificing speed for brevity
if from_scheme == 'rosetta':
atom_id = self.rosetta_to_atom_sequence_maps.get(chain_id, {})[residue_id]
if to_scheme == 'atom':
return atom_id
else:
return self._convert(chain_id, atom_id, 'atom', to_scheme)
if from_scheme == 'atom':
if to_scheme == 'rosetta':
return self.atom_to_rosetta_sequence_maps.get(chain_id, {})[residue_id]
else:
seqres_id = self.atom_to_seqres_sequence_maps.get(chain_id, {})[residue_id]
if to_scheme == 'seqres':
return seqres_id
return self.convert(chain_id, seqres_id, 'seqres', to_scheme)
if from_scheme == 'seqres':
if to_scheme == 'uniparc':
return self.seqres_to_uniparc_sequence_maps.get(chain_id, {})[residue_id]
else:
atom_id = self.seqres_to_atom_sequence_maps.get(chain_id, {})[residue_id]
if to_scheme == 'atom':
return atom_id
return self.convert(chain_id, atom_id, 'atom', to_scheme)
if from_scheme == 'uniparc':
seqres_id = self.uniparc_to_seqres_sequence_maps.get(chain_id, {})[residue_id]
if to_scheme == 'seqres':
return seqres_id
else:
return self._convert(chain_id, seqres_id, 'seqres', to_scheme)
raise Exception("We should never reach this line.") | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/relatrix.py#L153-L186 | train |
Kortemme-Lab/klab | klab/bio/relatrix.py | ResidueRelatrix.convert_from_rosetta | def convert_from_rosetta(self, residue_id, to_scheme):
'''A simpler conversion function to convert from Rosetta numbering without requiring the chain identifier.'''
assert(type(residue_id) == types.IntType)
# Find the chain_id associated with the residue_id
# Scan *all* sequences without breaking out to make sure that we do not have any duplicate maps
chain_id = None
for c, sequence in self.rosetta_sequences.iteritems():
for id, r in sequence:
if r.ResidueID == residue_id:
assert(chain_id == None)
chain_id = c
if chain_id:
return self.convert(chain_id, residue_id, 'rosetta', to_scheme)
else:
return None | python | def convert_from_rosetta(self, residue_id, to_scheme):
'''A simpler conversion function to convert from Rosetta numbering without requiring the chain identifier.'''
assert(type(residue_id) == types.IntType)
# Find the chain_id associated with the residue_id
# Scan *all* sequences without breaking out to make sure that we do not have any duplicate maps
chain_id = None
for c, sequence in self.rosetta_sequences.iteritems():
for id, r in sequence:
if r.ResidueID == residue_id:
assert(chain_id == None)
chain_id = c
if chain_id:
return self.convert(chain_id, residue_id, 'rosetta', to_scheme)
else:
return None | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/relatrix.py#L189-L206 | train |
Kortemme-Lab/klab | klab/bio/relatrix.py | ResidueRelatrix._validate | def _validate(self):
'''Validate the mappings.'''
self._validate_fasta_vs_seqres()
self._validate_mapping_signature()
self._validate_id_types()
self._validate_residue_types() | python | def _validate(self):
'''Validate the mappings.'''
self._validate_fasta_vs_seqres()
self._validate_mapping_signature()
self._validate_id_types()
self._validate_residue_types() | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/relatrix.py#L210-L216 | train |
Kortemme-Lab/klab | klab/bio/relatrix.py | ResidueRelatrix._validate_id_types | def _validate_id_types(self):
'''Check that the ID types are integers for Rosetta, SEQRES, and UniParc sequences and 6-character PDB IDs for the ATOM sequences.'''
for sequences in [self.uniparc_sequences, self.fasta_sequences, self.seqres_sequences, self.rosetta_sequences]:
for chain_id, sequence in sequences.iteritems():
sequence_id_types = set(map(type, sequence.ids()))
if sequence_id_types:
assert(len(sequence_id_types) == 1)
assert(sequence_id_types.pop() == types.IntType)
for chain_id, sequence in self.atom_sequences.iteritems():
sequence_id_types = set(map(type, sequence.ids()))
assert(len(sequence_id_types) == 1)
sequence_id_type = sequence_id_types.pop()
assert(sequence_id_type == types.StringType or sequence_id_type == types.UnicodeType) | python | def _validate_id_types(self):
'''Check that the ID types are integers for Rosetta, SEQRES, and UniParc sequences and 6-character PDB IDs for the ATOM sequences.'''
for sequences in [self.uniparc_sequences, self.fasta_sequences, self.seqres_sequences, self.rosetta_sequences]:
for chain_id, sequence in sequences.iteritems():
sequence_id_types = set(map(type, sequence.ids()))
if sequence_id_types:
assert(len(sequence_id_types) == 1)
assert(sequence_id_types.pop() == types.IntType)
for chain_id, sequence in self.atom_sequences.iteritems():
sequence_id_types = set(map(type, sequence.ids()))
assert(len(sequence_id_types) == 1)
sequence_id_type = sequence_id_types.pop()
assert(sequence_id_type == types.StringType or sequence_id_type == types.UnicodeType) | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/relatrix.py#L303-L317 | train |
Kortemme-Lab/klab | klab/bio/relatrix.py | ResidueRelatrix._validate_residue_types | def _validate_residue_types(self):
'''Make sure all the residue types map through translation.'''
for chain_id, sequence_map in self.rosetta_to_atom_sequence_maps.iteritems():
rosetta_sequence = self.rosetta_sequences[chain_id]
atom_sequence = self.atom_sequences[chain_id]
for rosetta_id, atom_id, _ in sequence_map:
assert(rosetta_sequence[rosetta_id].ResidueAA == atom_sequence[atom_id].ResidueAA)
for chain_id, sequence_map in self.atom_to_seqres_sequence_maps.iteritems():
atom_sequence = self.atom_sequences[chain_id]
seqres_sequence = self.seqres_sequences[chain_id]
for atom_id, seqres_id, _ in sorted(sequence_map):
assert(atom_sequence[atom_id].ResidueAA == seqres_sequence[seqres_id].ResidueAA)
for chain_id, sequence_map in self.seqres_to_uniparc_sequence_maps.iteritems():
if self.pdb_chain_to_uniparc_chain_mapping.get(chain_id):
seqres_sequence = self.seqres_sequences[chain_id]
uniparc_sequence = self.uniparc_sequences[self.pdb_chain_to_uniparc_chain_mapping[chain_id]]
for seqres_id, uniparc_id_resid_pair, substitution_match in sequence_map:
uniparc_id = uniparc_id_resid_pair[1]
# Some of the matches may not be identical but all the '*' Clustal Omega matches should be identical
if substitution_match and substitution_match.clustal == 1:
assert(seqres_sequence[seqres_id].ResidueAA == uniparc_sequence[uniparc_id].ResidueAA) | python | def _validate_residue_types(self):
'''Make sure all the residue types map through translation.'''
for chain_id, sequence_map in self.rosetta_to_atom_sequence_maps.iteritems():
rosetta_sequence = self.rosetta_sequences[chain_id]
atom_sequence = self.atom_sequences[chain_id]
for rosetta_id, atom_id, _ in sequence_map:
assert(rosetta_sequence[rosetta_id].ResidueAA == atom_sequence[atom_id].ResidueAA)
for chain_id, sequence_map in self.atom_to_seqres_sequence_maps.iteritems():
atom_sequence = self.atom_sequences[chain_id]
seqres_sequence = self.seqres_sequences[chain_id]
for atom_id, seqres_id, _ in sorted(sequence_map):
assert(atom_sequence[atom_id].ResidueAA == seqres_sequence[seqres_id].ResidueAA)
for chain_id, sequence_map in self.seqres_to_uniparc_sequence_maps.iteritems():
if self.pdb_chain_to_uniparc_chain_mapping.get(chain_id):
seqres_sequence = self.seqres_sequences[chain_id]
uniparc_sequence = self.uniparc_sequences[self.pdb_chain_to_uniparc_chain_mapping[chain_id]]
for seqres_id, uniparc_id_resid_pair, substitution_match in sequence_map:
uniparc_id = uniparc_id_resid_pair[1]
# Some of the matches may not be identical but all the '*' Clustal Omega matches should be identical
if substitution_match and substitution_match.clustal == 1:
assert(seqres_sequence[seqres_id].ResidueAA == uniparc_sequence[uniparc_id].ResidueAA) | [
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| Make sure all the residue types map through translation. | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/relatrix.py#L320-L343 | train |
Kortemme-Lab/klab | klab/bio/relatrix.py | ResidueRelatrix._create_sequences | def _create_sequences(self):
'''Get all of the Sequences - Rosetta, ATOM, SEQRES, FASTA, UniParc.'''
# Create the Rosetta sequences and the maps from the Rosetta sequences to the ATOM sequences
try:
self.pdb.construct_pdb_to_rosetta_residue_map(self.rosetta_scripts_path, rosetta_database_path = self.rosetta_database_path, cache_dir = self.cache_dir)
except PDBMissingMainchainAtomsException:
self.pdb_to_rosetta_residue_map_error = True
# Get all the Sequences
if self.pdb_id not in do_not_use_the_sequence_aligner:
self.uniparc_sequences = self.PDB_UniParc_SA.uniparc_sequences
else:
self.uniparc_sequences = self.sifts.get_uniparc_sequences()
self.fasta_sequences = self.FASTA.get_sequences(self.pdb_id)
self.seqres_sequences = self.pdb.seqres_sequences
self.atom_sequences = self.pdb.atom_sequences
if self.pdb_to_rosetta_residue_map_error:
self.rosetta_sequences = {}
for c in self.atom_sequences.keys():
self.rosetta_sequences[c] = Sequence()
else:
self.rosetta_sequences = self.pdb.rosetta_sequences
# Update the chain types for the UniParc sequences
uniparc_pdb_chain_mapping = {}
if self.pdb_id not in do_not_use_the_sequence_aligner:
for pdb_chain_id, matches in self.PDB_UniParc_SA.clustal_matches.iteritems():
if matches:
# we are not guaranteed to have a match e.g. the short chain J in 1A2C, chimeras, etc.
uniparc_chain_id = matches.keys()[0]
assert(len(matches) == 1)
uniparc_pdb_chain_mapping[uniparc_chain_id] = uniparc_pdb_chain_mapping.get(uniparc_chain_id, [])
uniparc_pdb_chain_mapping[uniparc_chain_id].append(pdb_chain_id)
else:
for pdb_chain_id, uniparc_chain_ids in self.sifts.get_pdb_chain_to_uniparc_id_map().iteritems():
for uniparc_chain_id in uniparc_chain_ids:
uniparc_pdb_chain_mapping[uniparc_chain_id] = uniparc_pdb_chain_mapping.get(uniparc_chain_id, [])
uniparc_pdb_chain_mapping[uniparc_chain_id].append(pdb_chain_id)
for uniparc_chain_id, pdb_chain_ids in uniparc_pdb_chain_mapping.iteritems():
sequence_type = set([self.seqres_sequences[p].sequence_type for p in pdb_chain_ids])
assert(len(sequence_type) == 1)
sequence_type = sequence_type.pop()
assert(self.uniparc_sequences[uniparc_chain_id].sequence_type == None)
self.uniparc_sequences[uniparc_chain_id].set_type(sequence_type)
for p in pdb_chain_ids:
self.pdb_chain_to_uniparc_chain_mapping[p] = uniparc_chain_id
# Update the chain types for the FASTA sequences
for chain_id, sequence in self.seqres_sequences.iteritems():
self.fasta_sequences[chain_id].set_type(sequence.sequence_type) | python | def _create_sequences(self):
'''Get all of the Sequences - Rosetta, ATOM, SEQRES, FASTA, UniParc.'''
# Create the Rosetta sequences and the maps from the Rosetta sequences to the ATOM sequences
try:
self.pdb.construct_pdb_to_rosetta_residue_map(self.rosetta_scripts_path, rosetta_database_path = self.rosetta_database_path, cache_dir = self.cache_dir)
except PDBMissingMainchainAtomsException:
self.pdb_to_rosetta_residue_map_error = True
# Get all the Sequences
if self.pdb_id not in do_not_use_the_sequence_aligner:
self.uniparc_sequences = self.PDB_UniParc_SA.uniparc_sequences
else:
self.uniparc_sequences = self.sifts.get_uniparc_sequences()
self.fasta_sequences = self.FASTA.get_sequences(self.pdb_id)
self.seqres_sequences = self.pdb.seqres_sequences
self.atom_sequences = self.pdb.atom_sequences
if self.pdb_to_rosetta_residue_map_error:
self.rosetta_sequences = {}
for c in self.atom_sequences.keys():
self.rosetta_sequences[c] = Sequence()
else:
self.rosetta_sequences = self.pdb.rosetta_sequences
# Update the chain types for the UniParc sequences
uniparc_pdb_chain_mapping = {}
if self.pdb_id not in do_not_use_the_sequence_aligner:
for pdb_chain_id, matches in self.PDB_UniParc_SA.clustal_matches.iteritems():
if matches:
# we are not guaranteed to have a match e.g. the short chain J in 1A2C, chimeras, etc.
uniparc_chain_id = matches.keys()[0]
assert(len(matches) == 1)
uniparc_pdb_chain_mapping[uniparc_chain_id] = uniparc_pdb_chain_mapping.get(uniparc_chain_id, [])
uniparc_pdb_chain_mapping[uniparc_chain_id].append(pdb_chain_id)
else:
for pdb_chain_id, uniparc_chain_ids in self.sifts.get_pdb_chain_to_uniparc_id_map().iteritems():
for uniparc_chain_id in uniparc_chain_ids:
uniparc_pdb_chain_mapping[uniparc_chain_id] = uniparc_pdb_chain_mapping.get(uniparc_chain_id, [])
uniparc_pdb_chain_mapping[uniparc_chain_id].append(pdb_chain_id)
for uniparc_chain_id, pdb_chain_ids in uniparc_pdb_chain_mapping.iteritems():
sequence_type = set([self.seqres_sequences[p].sequence_type for p in pdb_chain_ids])
assert(len(sequence_type) == 1)
sequence_type = sequence_type.pop()
assert(self.uniparc_sequences[uniparc_chain_id].sequence_type == None)
self.uniparc_sequences[uniparc_chain_id].set_type(sequence_type)
for p in pdb_chain_ids:
self.pdb_chain_to_uniparc_chain_mapping[p] = uniparc_chain_id
# Update the chain types for the FASTA sequences
for chain_id, sequence in self.seqres_sequences.iteritems():
self.fasta_sequences[chain_id].set_type(sequence.sequence_type) | [
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| Get all of the Sequences - Rosetta, ATOM, SEQRES, FASTA, UniParc. | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/relatrix.py#L505-L558 | train |
kkinder/NdbSearchableBase | NdbSearchableBase/SearchableModel.py | SearchableModel.search | def search(cls,
query_string,
options=None,
enable_facet_discovery=False,
return_facets=None,
facet_options=None,
facet_refinements=None,
deadline=None,
**kwargs):
"""
Searches the index. Conveniently searches only for documents that belong to instances of this class.
:param query_string: The query to match against documents in the index. See search.Query() for details.
:param options: A QueryOptions describing post-processing of search results.
:param enable_facet_discovery: discovery top relevent facets to this search query and return them.
:param return_facets: An iterable of FacetRequest or basestring as facet name to
return specific facet with the result.
:param facet_options: A FacetOption describing processing of facets.
:param facet_refinements: An iterable of FacetRefinement objects or refinement
token strings used to filter out search results based on a facet value.
refinements for different facets will be conjunction and refinements for
the same facet will be disjunction.
:param deadline: Deadline for RPC call in seconds; if None use the default.
:param kwargs: A SearchResults containing a list of documents matched, number returned
and number matched by the query.
:return: A SearchResults containing a list of documents matched, number returned
and number matched by the query.
:raises: QueryError: If the query string is not parseable.
TypeError: If any of the parameters have invalid types, or an unknown
attribute is passed.
ValueError: If any of the parameters have invalid values (e.g., a
negative deadline).
"""
search_class = cls.search_get_class_names()[-1]
query_string += ' ' + 'class_name:%s' % (search_class,)
q = search.Query(
query_string=query_string,
options=options,
enable_facet_discovery=enable_facet_discovery,
return_facets=return_facets,
facet_options=facet_options,
facet_refinements=facet_refinements
)
index = cls.search_get_index()
return index.search(q, deadline=deadline, **kwargs) | python | def search(cls,
query_string,
options=None,
enable_facet_discovery=False,
return_facets=None,
facet_options=None,
facet_refinements=None,
deadline=None,
**kwargs):
"""
Searches the index. Conveniently searches only for documents that belong to instances of this class.
:param query_string: The query to match against documents in the index. See search.Query() for details.
:param options: A QueryOptions describing post-processing of search results.
:param enable_facet_discovery: discovery top relevent facets to this search query and return them.
:param return_facets: An iterable of FacetRequest or basestring as facet name to
return specific facet with the result.
:param facet_options: A FacetOption describing processing of facets.
:param facet_refinements: An iterable of FacetRefinement objects or refinement
token strings used to filter out search results based on a facet value.
refinements for different facets will be conjunction and refinements for
the same facet will be disjunction.
:param deadline: Deadline for RPC call in seconds; if None use the default.
:param kwargs: A SearchResults containing a list of documents matched, number returned
and number matched by the query.
:return: A SearchResults containing a list of documents matched, number returned
and number matched by the query.
:raises: QueryError: If the query string is not parseable.
TypeError: If any of the parameters have invalid types, or an unknown
attribute is passed.
ValueError: If any of the parameters have invalid values (e.g., a
negative deadline).
"""
search_class = cls.search_get_class_names()[-1]
query_string += ' ' + 'class_name:%s' % (search_class,)
q = search.Query(
query_string=query_string,
options=options,
enable_facet_discovery=enable_facet_discovery,
return_facets=return_facets,
facet_options=facet_options,
facet_refinements=facet_refinements
)
index = cls.search_get_index()
return index.search(q, deadline=deadline, **kwargs) | [
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| 4f999336b464704a0929cec135c1f09fb1ddfb7c | https://github.com/kkinder/NdbSearchableBase/blob/4f999336b464704a0929cec135c1f09fb1ddfb7c/NdbSearchableBase/SearchableModel.py#L49-L94 | train |
kkinder/NdbSearchableBase | NdbSearchableBase/SearchableModel.py | SearchableModel.search_update_index | def search_update_index(self):
"""
Updates the search index for this instance.
This happens automatically on put.
"""
doc_id = self.search_get_document_id(self.key)
fields = [search.AtomField('class_name', name) for name in self.search_get_class_names()]
index = self.search_get_index()
if self.searchable_fields is None:
searchable_fields = []
for field, prop in self._properties.items():
if field == 'class':
continue
for class_, field_type in SEARCHABLE_PROPERTY_TYPES.items():
if isinstance(prop, class_):
searchable_fields.append(field)
else:
searchable_fields = self.searchable_fields
for f in set(searchable_fields):
prop = self._properties[f]
value = getattr(self, f)
field = None
field_found = False
for class_, field_type in SEARCHABLE_PROPERTY_TYPES.items():
if isinstance(prop, class_):
field_found = True
if value is not None:
if isinstance(value, list) or isinstance(value, tuple) or isinstance(value, set):
for v in value:
field = field_type(name=f, value=v)
elif isinstance(value, ndb.Key):
field = field_type(name=f, value=value.urlsafe())
else:
field = field_type(name=f, value=value)
if not field_found:
raise ValueError('Cannot find field type for %r on %r' % (prop, self.__class__))
if field is not None:
fields.append(field)
document = search.Document(doc_id, fields=fields)
index.put(document) | python | def search_update_index(self):
"""
Updates the search index for this instance.
This happens automatically on put.
"""
doc_id = self.search_get_document_id(self.key)
fields = [search.AtomField('class_name', name) for name in self.search_get_class_names()]
index = self.search_get_index()
if self.searchable_fields is None:
searchable_fields = []
for field, prop in self._properties.items():
if field == 'class':
continue
for class_, field_type in SEARCHABLE_PROPERTY_TYPES.items():
if isinstance(prop, class_):
searchable_fields.append(field)
else:
searchable_fields = self.searchable_fields
for f in set(searchable_fields):
prop = self._properties[f]
value = getattr(self, f)
field = None
field_found = False
for class_, field_type in SEARCHABLE_PROPERTY_TYPES.items():
if isinstance(prop, class_):
field_found = True
if value is not None:
if isinstance(value, list) or isinstance(value, tuple) or isinstance(value, set):
for v in value:
field = field_type(name=f, value=v)
elif isinstance(value, ndb.Key):
field = field_type(name=f, value=value.urlsafe())
else:
field = field_type(name=f, value=value)
if not field_found:
raise ValueError('Cannot find field type for %r on %r' % (prop, self.__class__))
if field is not None:
fields.append(field)
document = search.Document(doc_id, fields=fields)
index.put(document) | [
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| 4f999336b464704a0929cec135c1f09fb1ddfb7c | https://github.com/kkinder/NdbSearchableBase/blob/4f999336b464704a0929cec135c1f09fb1ddfb7c/NdbSearchableBase/SearchableModel.py#L96-L143 | train |
kkinder/NdbSearchableBase | NdbSearchableBase/SearchableModel.py | SearchableModel.search_get_class_names | def search_get_class_names(cls):
"""
Returns class names for use in document indexing.
"""
if hasattr(cls, '_class_key'):
class_names = []
for n in cls._class_key():
class_names.append(n)
return class_names
else:
return [cls.__name__] | python | def search_get_class_names(cls):
"""
Returns class names for use in document indexing.
"""
if hasattr(cls, '_class_key'):
class_names = []
for n in cls._class_key():
class_names.append(n)
return class_names
else:
return [cls.__name__] | [
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| 4f999336b464704a0929cec135c1f09fb1ddfb7c | https://github.com/kkinder/NdbSearchableBase/blob/4f999336b464704a0929cec135c1f09fb1ddfb7c/NdbSearchableBase/SearchableModel.py#L146-L156 | train |
kkinder/NdbSearchableBase | NdbSearchableBase/SearchableModel.py | SearchableModel.from_urlsafe | def from_urlsafe(cls, urlsafe):
"""
Returns an instance of the model from a urlsafe string.
:param urlsafe: urlsafe key
:return: Instance of cls
"""
try:
key = ndb.Key(urlsafe=urlsafe)
except:
return None
obj = key.get()
if obj and isinstance(obj, cls):
return obj | python | def from_urlsafe(cls, urlsafe):
"""
Returns an instance of the model from a urlsafe string.
:param urlsafe: urlsafe key
:return: Instance of cls
"""
try:
key = ndb.Key(urlsafe=urlsafe)
except:
return None
obj = key.get()
if obj and isinstance(obj, cls):
return obj | [
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| 4f999336b464704a0929cec135c1f09fb1ddfb7c | https://github.com/kkinder/NdbSearchableBase/blob/4f999336b464704a0929cec135c1f09fb1ddfb7c/NdbSearchableBase/SearchableModel.py#L159-L172 | train |
kkinder/NdbSearchableBase | NdbSearchableBase/SearchableModel.py | SearchableModel.get_from_search_doc | def get_from_search_doc(cls, doc_id):
"""
Returns an instance of the model from a search document id.
:param doc_id: Search document id
:return: Instance of cls
"""
# If the document was passed instead of the doc_id, get the document.
if hasattr(doc_id, 'doc_id'):
doc_id = doc_id.doc_id
return cls.from_urlsafe(doc_id) | python | def get_from_search_doc(cls, doc_id):
"""
Returns an instance of the model from a search document id.
:param doc_id: Search document id
:return: Instance of cls
"""
# If the document was passed instead of the doc_id, get the document.
if hasattr(doc_id, 'doc_id'):
doc_id = doc_id.doc_id
return cls.from_urlsafe(doc_id) | [
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| 4f999336b464704a0929cec135c1f09fb1ddfb7c | https://github.com/kkinder/NdbSearchableBase/blob/4f999336b464704a0929cec135c1f09fb1ddfb7c/NdbSearchableBase/SearchableModel.py#L175-L185 | train |
kkinder/NdbSearchableBase | NdbSearchableBase/SearchableModel.py | SearchableModel._pre_delete_hook | def _pre_delete_hook(cls, key):
"""
Removes instance from index.
"""
if cls.searching_enabled:
doc_id = cls.search_get_document_id(key)
index = cls.search_get_index()
index.delete(doc_id) | python | def _pre_delete_hook(cls, key):
"""
Removes instance from index.
"""
if cls.searching_enabled:
doc_id = cls.search_get_document_id(key)
index = cls.search_get_index()
index.delete(doc_id) | [
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| 4f999336b464704a0929cec135c1f09fb1ddfb7c | https://github.com/kkinder/NdbSearchableBase/blob/4f999336b464704a0929cec135c1f09fb1ddfb7c/NdbSearchableBase/SearchableModel.py#L188-L195 | train |
adaptive-learning/proso-apps | proso/models/environment.py | Environment.process_answer | def process_answer(self, user, item, asked, answered, time, answer, response_time, guess, **kwargs):
"""
This method is used during the answer streaming and is called after the
predictive model for each answer.
Args:
user (int):
identifier of ther user answering the question
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identifier of the asked item
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"I don't know"
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time the answer took in milliseconds
time (datetime.datetime)
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probability of correct response in case of random answer
"""
pass | python | def process_answer(self, user, item, asked, answered, time, answer, response_time, guess, **kwargs):
"""
This method is used during the answer streaming and is called after the
predictive model for each answer.
Args:
user (int):
identifier of ther user answering the question
asked (int):
identifier of the asked item
answered (int):
identifier of the answered item or None if the user answered
"I don't know"
response_time (int)
time the answer took in milliseconds
time (datetime.datetime)
time when the user answered the question
guess (float):
probability of correct response in case of random answer
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| 8278c72e498d6ef8d392cc47b48473f4ec037142 | https://github.com/adaptive-learning/proso-apps/blob/8278c72e498d6ef8d392cc47b48473f4ec037142/proso/models/environment.py#L18-L38 | train |
Apstra/aeon-venos | pylib/aeon/nxos/autoload/guestshell.py | _guestshell._get_sz_info | def _get_sz_info(self):
"""
Obtains the current resource allocations, assumes that the
guestshell is in an 'Activated' state
"""
if 'None' == self._state:
return None
cmd = 'show virtual-service detail name guestshell+'
got = self.cli(cmd)
got = got['TABLE_detail']['ROW_detail']
sz_cpu = int(got['cpu_reservation'])
sz_disk = int(got['disk_reservation'])
sz_memory = int(got['memory_reservation'])
self.sz_has = _guestshell.Resources(
cpu=sz_cpu, memory=sz_memory, disk=sz_disk) | python | def _get_sz_info(self):
"""
Obtains the current resource allocations, assumes that the
guestshell is in an 'Activated' state
"""
if 'None' == self._state:
return None
cmd = 'show virtual-service detail name guestshell+'
got = self.cli(cmd)
got = got['TABLE_detail']['ROW_detail']
sz_cpu = int(got['cpu_reservation'])
sz_disk = int(got['disk_reservation'])
sz_memory = int(got['memory_reservation'])
self.sz_has = _guestshell.Resources(
cpu=sz_cpu, memory=sz_memory, disk=sz_disk) | [
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| 4d4f73d5904831ddc78c30922a8a226c90cf7d90 | https://github.com/Apstra/aeon-venos/blob/4d4f73d5904831ddc78c30922a8a226c90cf7d90/pylib/aeon/nxos/autoload/guestshell.py#L198-L215 | train |
assamite/creamas | creamas/image.py | fractal_dimension | def fractal_dimension(image):
'''Estimates the fractal dimension of an image with box counting.
Counts pixels with value 0 as empty and everything else as non-empty.
Input image has to be grayscale.
See, e.g `Wikipedia <https://en.wikipedia.org/wiki/Fractal_dimension>`_.
:param image: numpy.ndarray
:returns: estimation of fractal dimension
:rtype: float
'''
pixels = []
for i in range(image.shape[0]):
for j in range(image.shape[1]):
if image[i, j] > 0:
pixels.append((i, j))
lx = image.shape[1]
ly = image.shape[0]
pixels = np.array(pixels)
if len(pixels) < 2:
return 0
scales = np.logspace(1, 4, num=20, endpoint=False, base=2)
Ns = []
for scale in scales:
H, edges = np.histogramdd(pixels,
bins=(np.arange(0, lx, scale),
np.arange(0, ly, scale)))
H_sum = np.sum(H > 0)
if H_sum == 0:
H_sum = 1
Ns.append(H_sum)
coeffs = np.polyfit(np.log(scales), np.log(Ns), 1)
hausdorff_dim = -coeffs[0]
return hausdorff_dim | python | def fractal_dimension(image):
'''Estimates the fractal dimension of an image with box counting.
Counts pixels with value 0 as empty and everything else as non-empty.
Input image has to be grayscale.
See, e.g `Wikipedia <https://en.wikipedia.org/wiki/Fractal_dimension>`_.
:param image: numpy.ndarray
:returns: estimation of fractal dimension
:rtype: float
'''
pixels = []
for i in range(image.shape[0]):
for j in range(image.shape[1]):
if image[i, j] > 0:
pixels.append((i, j))
lx = image.shape[1]
ly = image.shape[0]
pixels = np.array(pixels)
if len(pixels) < 2:
return 0
scales = np.logspace(1, 4, num=20, endpoint=False, base=2)
Ns = []
for scale in scales:
H, edges = np.histogramdd(pixels,
bins=(np.arange(0, lx, scale),
np.arange(0, ly, scale)))
H_sum = np.sum(H > 0)
if H_sum == 0:
H_sum = 1
Ns.append(H_sum)
coeffs = np.polyfit(np.log(scales), np.log(Ns), 1)
hausdorff_dim = -coeffs[0]
return hausdorff_dim | [
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:rtype: float | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/image.py#L11-L46 | train |
assamite/creamas | creamas/image.py | channel_portion | def channel_portion(image, channel):
'''Estimates the amount of a color relative to other colors.
:param image: numpy.ndarray
:param channel: int
:returns: portion of a channel in an image
:rtype: float
'''
# Separate color channels
rgb = []
for i in range(3):
rgb.append(image[:, :, i].astype(int))
ch = rgb.pop(channel)
relative_values = ch - np.sum(rgb, axis=0) / 2
relative_values = np.maximum(np.zeros(ch.shape), relative_values)
return float(np.average(relative_values) / 255) | python | def channel_portion(image, channel):
'''Estimates the amount of a color relative to other colors.
:param image: numpy.ndarray
:param channel: int
:returns: portion of a channel in an image
:rtype: float
'''
# Separate color channels
rgb = []
for i in range(3):
rgb.append(image[:, :, i].astype(int))
ch = rgb.pop(channel)
relative_values = ch - np.sum(rgb, axis=0) / 2
relative_values = np.maximum(np.zeros(ch.shape), relative_values)
return float(np.average(relative_values) / 255) | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/image.py#L49-L67 | train |
assamite/creamas | creamas/image.py | intensity | def intensity(image):
'''Calculates the average intensity of the pixels in an image.
Accepts both RGB and grayscale images.
:param image: numpy.ndarray
:returns: image intensity
:rtype: float
'''
if len(image.shape) > 2:
# Convert to grayscale
image = cv2.cvtColor(image, cv2.COLOR_RGB2GRAY) / 255
elif issubclass(image.dtype.type, np.integer):
image /= 255
return float(np.sum(image) / np.prod(image.shape)) | python | def intensity(image):
'''Calculates the average intensity of the pixels in an image.
Accepts both RGB and grayscale images.
:param image: numpy.ndarray
:returns: image intensity
:rtype: float
'''
if len(image.shape) > 2:
# Convert to grayscale
image = cv2.cvtColor(image, cv2.COLOR_RGB2GRAY) / 255
elif issubclass(image.dtype.type, np.integer):
image /= 255
return float(np.sum(image) / np.prod(image.shape)) | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/image.py#L70-L83 | train |
Kortemme-Lab/klab | klab/cloning/dna.py | sliding_window | def sliding_window(sequence, win_size, step=1):
"""
Returns a generator that will iterate through
the defined chunks of input sequence. Input sequence
must be iterable.
Credit: http://scipher.wordpress.com/2010/12/02/simple-sliding-window-iterator-in-python/
https://github.com/xguse/scipherPyProj/blob/master/scipherSrc/defs/basicDefs.py
"""
# Verify the inputs
try:
it = iter(sequence)
except TypeError:
raise ValueError("sequence must be iterable.")
if not isinstance(win_size, int):
raise ValueError("type(win_size) must be int.")
if not isinstance(step, int):
raise ValueError("type(step) must be int.")
if step > win_size:
raise ValueError("step must not be larger than win_size.")
if win_size > len(sequence):
raise ValueError("win_size must not be larger than sequence length.")
# Pre-compute number of chunks to emit
num_chunks = ((len(sequence) - win_size) / step) + 1
# Do the work
for i in range(0, num_chunks * step, step):
yield sequence[i:i+win_size] | python | def sliding_window(sequence, win_size, step=1):
"""
Returns a generator that will iterate through
the defined chunks of input sequence. Input sequence
must be iterable.
Credit: http://scipher.wordpress.com/2010/12/02/simple-sliding-window-iterator-in-python/
https://github.com/xguse/scipherPyProj/blob/master/scipherSrc/defs/basicDefs.py
"""
# Verify the inputs
try:
it = iter(sequence)
except TypeError:
raise ValueError("sequence must be iterable.")
if not isinstance(win_size, int):
raise ValueError("type(win_size) must be int.")
if not isinstance(step, int):
raise ValueError("type(step) must be int.")
if step > win_size:
raise ValueError("step must not be larger than win_size.")
if win_size > len(sequence):
raise ValueError("win_size must not be larger than sequence length.")
# Pre-compute number of chunks to emit
num_chunks = ((len(sequence) - win_size) / step) + 1
# Do the work
for i in range(0, num_chunks * step, step):
yield sequence[i:i+win_size] | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/cloning/dna.py#L103-L132 | train |
Kortemme-Lab/klab | klab/cloning/dna.py | dna_to_re | def dna_to_re(seq):
"""
Return a compiled regular expression that will match anything described by
the input sequence. For example, a sequence that contains a 'N' matched
any base at that position.
"""
seq = seq.replace('K', '[GT]')
seq = seq.replace('M', '[AC]')
seq = seq.replace('R', '[AG]')
seq = seq.replace('Y', '[CT]')
seq = seq.replace('S', '[CG]')
seq = seq.replace('W', '[AT]')
seq = seq.replace('B', '[CGT]')
seq = seq.replace('V', '[ACG]')
seq = seq.replace('H', '[ACT]')
seq = seq.replace('D', '[AGT]')
seq = seq.replace('X', '[GATC]')
seq = seq.replace('N', '[GATC]')
return re.compile(seq) | python | def dna_to_re(seq):
"""
Return a compiled regular expression that will match anything described by
the input sequence. For example, a sequence that contains a 'N' matched
any base at that position.
"""
seq = seq.replace('K', '[GT]')
seq = seq.replace('M', '[AC]')
seq = seq.replace('R', '[AG]')
seq = seq.replace('Y', '[CT]')
seq = seq.replace('S', '[CG]')
seq = seq.replace('W', '[AT]')
seq = seq.replace('B', '[CGT]')
seq = seq.replace('V', '[ACG]')
seq = seq.replace('H', '[ACT]')
seq = seq.replace('D', '[AGT]')
seq = seq.replace('X', '[GATC]')
seq = seq.replace('N', '[GATC]')
return re.compile(seq) | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/cloning/dna.py#L139-L159 | train |
Kortemme-Lab/klab | klab/cloning/dna.py | case_highlight | def case_highlight(seq, subseq):
"""
Highlights all instances of subseq in seq by making them uppercase and
everything else lowercase.
"""
return re.subs(subseq.lower(), subseq.upper(), seq.lower()) | python | def case_highlight(seq, subseq):
"""
Highlights all instances of subseq in seq by making them uppercase and
everything else lowercase.
"""
return re.subs(subseq.lower(), subseq.upper(), seq.lower()) | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/cloning/dna.py#L161-L166 | train |
inveniosoftware/invenio-pidrelations | invenio_pidrelations/indexers.py | index_relations | def index_relations(sender, pid_type, json=None,
record=None, index=None, **kwargs):
"""Add relations to the indexed record."""
if not json:
json = {}
pid = PersistentIdentifier.query.filter(
PersistentIdentifier.object_uuid == record.id,
PersistentIdentifier.pid_type == pid_type,
).one_or_none()
relations = None
if pid:
relations = serialize_relations(pid)
if relations:
json['relations'] = relations
return json | python | def index_relations(sender, pid_type, json=None,
record=None, index=None, **kwargs):
"""Add relations to the indexed record."""
if not json:
json = {}
pid = PersistentIdentifier.query.filter(
PersistentIdentifier.object_uuid == record.id,
PersistentIdentifier.pid_type == pid_type,
).one_or_none()
relations = None
if pid:
relations = serialize_relations(pid)
if relations:
json['relations'] = relations
return json | [
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| a49f3725cf595b663c5b04814280b231f88bc333 | https://github.com/inveniosoftware/invenio-pidrelations/blob/a49f3725cf595b663c5b04814280b231f88bc333/invenio_pidrelations/indexers.py#L37-L51 | train |
inveniosoftware/invenio-pidrelations | invenio_pidrelations/indexers.py | index_siblings | def index_siblings(pid, include_pid=False, children=None,
neighbors_eager=False, eager=False, with_deposits=True):
"""Send sibling records of the passed pid for indexing.
Note: By default does not index the 'pid' itself,
only zero or more siblings.
:param pid: PID (recid) of whose siblings are to be indexed.
:param children: Overrides children with a fixed list of PID.
Children should contain the 'pid' itself if 'neighbors_eager' is to
be used, otherwise the last child is treated as the only neighbor.
:param eager: Index all siblings immediately.
:param include_pid: If True, will index also the provided 'pid'
(default:False).
:param neighbors_eager: Index the neighboring PIDs w.r.t. 'pid'
immediately, and the rest with a bulk_index (default: False)
:param with_deposits: Reindex also corresponding record's deposits.
"""
assert not (neighbors_eager and eager), \
"""Only one of the 'eager' and 'neighbors_eager' flags
can be set to True, not both"""
if children is None:
parent_pid = PIDNodeVersioning(pid=pid).parents.first()
children = PIDNodeVersioning(pid=parent_pid).children.all()
objid = str(pid.object_uuid)
children = [str(p.object_uuid) for p in children]
idx = children.index(objid) if objid in children else len(children)
# Split children (which can include the pid) into left and right siblings
# If 'pid' is not in children, idx is the length of list, so 'left'
# will be all children, and 'right' will be an empty list
# [X X X] X [X X X]
if include_pid:
# [X X X X] [X X X] Includes pid to the 'left' set
left = children[:idx + 1]
else:
# [X X X] X [X X X]
left = children[:idx]
right = children[idx + 1:]
if eager:
eager_uuids = left + right
bulk_uuids = []
elif neighbors_eager:
# neighbors are last of 'left' and first or 'right' siblings
# X X [X] X [X] X X
eager_uuids = left[-1:] + right[:1]
# all of the siblings, except the neighbours
# [X X] X X X [X X]
bulk_uuids = left[:-1] + right[1:]
else:
eager_uuids = []
bulk_uuids = left + right
def get_dep_uuids(rec_uuids):
"""Get corresponding deposit UUIDs from record's UUIDs."""
return [str(PersistentIdentifier.get(
'depid',
Record.get_record(id_)['_deposit']['id']).object_uuid)
for id_ in rec_uuids]
if with_deposits:
eager_uuids += get_dep_uuids(eager_uuids)
bulk_uuids += get_dep_uuids(bulk_uuids)
for id_ in eager_uuids:
RecordIndexer().index_by_id(id_)
if bulk_uuids:
RecordIndexer().bulk_index(bulk_uuids) | python | def index_siblings(pid, include_pid=False, children=None,
neighbors_eager=False, eager=False, with_deposits=True):
"""Send sibling records of the passed pid for indexing.
Note: By default does not index the 'pid' itself,
only zero or more siblings.
:param pid: PID (recid) of whose siblings are to be indexed.
:param children: Overrides children with a fixed list of PID.
Children should contain the 'pid' itself if 'neighbors_eager' is to
be used, otherwise the last child is treated as the only neighbor.
:param eager: Index all siblings immediately.
:param include_pid: If True, will index also the provided 'pid'
(default:False).
:param neighbors_eager: Index the neighboring PIDs w.r.t. 'pid'
immediately, and the rest with a bulk_index (default: False)
:param with_deposits: Reindex also corresponding record's deposits.
"""
assert not (neighbors_eager and eager), \
"""Only one of the 'eager' and 'neighbors_eager' flags
can be set to True, not both"""
if children is None:
parent_pid = PIDNodeVersioning(pid=pid).parents.first()
children = PIDNodeVersioning(pid=parent_pid).children.all()
objid = str(pid.object_uuid)
children = [str(p.object_uuid) for p in children]
idx = children.index(objid) if objid in children else len(children)
# Split children (which can include the pid) into left and right siblings
# If 'pid' is not in children, idx is the length of list, so 'left'
# will be all children, and 'right' will be an empty list
# [X X X] X [X X X]
if include_pid:
# [X X X X] [X X X] Includes pid to the 'left' set
left = children[:idx + 1]
else:
# [X X X] X [X X X]
left = children[:idx]
right = children[idx + 1:]
if eager:
eager_uuids = left + right
bulk_uuids = []
elif neighbors_eager:
# neighbors are last of 'left' and first or 'right' siblings
# X X [X] X [X] X X
eager_uuids = left[-1:] + right[:1]
# all of the siblings, except the neighbours
# [X X] X X X [X X]
bulk_uuids = left[:-1] + right[1:]
else:
eager_uuids = []
bulk_uuids = left + right
def get_dep_uuids(rec_uuids):
"""Get corresponding deposit UUIDs from record's UUIDs."""
return [str(PersistentIdentifier.get(
'depid',
Record.get_record(id_)['_deposit']['id']).object_uuid)
for id_ in rec_uuids]
if with_deposits:
eager_uuids += get_dep_uuids(eager_uuids)
bulk_uuids += get_dep_uuids(bulk_uuids)
for id_ in eager_uuids:
RecordIndexer().index_by_id(id_)
if bulk_uuids:
RecordIndexer().bulk_index(bulk_uuids) | [
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Note: By default does not index the 'pid' itself,
only zero or more siblings.
:param pid: PID (recid) of whose siblings are to be indexed.
:param children: Overrides children with a fixed list of PID.
Children should contain the 'pid' itself if 'neighbors_eager' is to
be used, otherwise the last child is treated as the only neighbor.
:param eager: Index all siblings immediately.
:param include_pid: If True, will index also the provided 'pid'
(default:False).
:param neighbors_eager: Index the neighboring PIDs w.r.t. 'pid'
immediately, and the rest with a bulk_index (default: False)
:param with_deposits: Reindex also corresponding record's deposits. | [
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| a49f3725cf595b663c5b04814280b231f88bc333 | https://github.com/inveniosoftware/invenio-pidrelations/blob/a49f3725cf595b663c5b04814280b231f88bc333/invenio_pidrelations/indexers.py#L54-L124 | train |
brunato/lograptor | lograptor/filemap.py | GlobDict.iter_paths | def iter_paths(self, pathnames=None, mapfunc=None):
"""
Special iteration on paths. Yields couples of path and items. If a expanded path
doesn't match with any files a couple with path and `None` is returned.
:param pathnames: Iterable with a set of pathnames. If is `None` uses the all \
the stored pathnames.
:param mapfunc: A mapping function for building the effective path from various \
wildcards (eg. time spec wildcards).
:return: Yields 2-tuples.
"""
pathnames = pathnames or self._pathnames
if self.recursive and not pathnames:
pathnames = ['.']
elif not pathnames:
yield []
if mapfunc is not None:
for mapped_paths in map(mapfunc, pathnames):
for path in mapped_paths:
if self.recursive and (os.path.isdir(path) or os.path.islink(path)):
for t in os.walk(path, followlinks=self.follow_symlinks):
for filename, values in self.iglob(os.path.join(t[0], '*')):
yield filename, values
else:
empty_glob = True
for filename, values in self.iglob(path):
yield filename, values
empty_glob = False
if empty_glob:
yield path, None
else:
for path in pathnames:
if self.recursive and (os.path.isdir(path) or os.path.islink(path)):
for t in os.walk(path, followlinks=self.follow_symlinks):
for filename, values in self.iglob(os.path.join(t[0], '*')):
yield filename, values
else:
empty_glob = True
for filename, values in self.iglob(path):
yield filename, values
empty_glob = False
if empty_glob:
yield path, None | python | def iter_paths(self, pathnames=None, mapfunc=None):
"""
Special iteration on paths. Yields couples of path and items. If a expanded path
doesn't match with any files a couple with path and `None` is returned.
:param pathnames: Iterable with a set of pathnames. If is `None` uses the all \
the stored pathnames.
:param mapfunc: A mapping function for building the effective path from various \
wildcards (eg. time spec wildcards).
:return: Yields 2-tuples.
"""
pathnames = pathnames or self._pathnames
if self.recursive and not pathnames:
pathnames = ['.']
elif not pathnames:
yield []
if mapfunc is not None:
for mapped_paths in map(mapfunc, pathnames):
for path in mapped_paths:
if self.recursive and (os.path.isdir(path) or os.path.islink(path)):
for t in os.walk(path, followlinks=self.follow_symlinks):
for filename, values in self.iglob(os.path.join(t[0], '*')):
yield filename, values
else:
empty_glob = True
for filename, values in self.iglob(path):
yield filename, values
empty_glob = False
if empty_glob:
yield path, None
else:
for path in pathnames:
if self.recursive and (os.path.isdir(path) or os.path.islink(path)):
for t in os.walk(path, followlinks=self.follow_symlinks):
for filename, values in self.iglob(os.path.join(t[0], '*')):
yield filename, values
else:
empty_glob = True
for filename, values in self.iglob(path):
yield filename, values
empty_glob = False
if empty_glob:
yield path, None | [
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| b1f09fe1b429ed15110610092704ef12d253f3c9 | https://github.com/brunato/lograptor/blob/b1f09fe1b429ed15110610092704ef12d253f3c9/lograptor/filemap.py#L111-L154 | train |
brunato/lograptor | lograptor/filemap.py | FileMap.check_stat | def check_stat(self, path):
"""
Checks logfile stat information for excluding files not in datetime period.
On Linux it's possible to checks only modification time, because file creation info
are not available, so it's possible to exclude only older files.
In Unix BSD systems and windows information about file creation date and times are available,
so is possible to exclude too newer files.
"""
statinfo = os.stat(path)
st_mtime = datetime.fromtimestamp(statinfo.st_mtime)
if platform.system() == 'Linux':
check = st_mtime >= self.start_dt
else:
st_ctime = datetime.fromtimestamp(statinfo.st_ctime)
check = st_mtime >= self.start_dt and st_ctime <= self.end_dt
if not check:
logger.info("file %r not in datetime period!", path)
return check | python | def check_stat(self, path):
"""
Checks logfile stat information for excluding files not in datetime period.
On Linux it's possible to checks only modification time, because file creation info
are not available, so it's possible to exclude only older files.
In Unix BSD systems and windows information about file creation date and times are available,
so is possible to exclude too newer files.
"""
statinfo = os.stat(path)
st_mtime = datetime.fromtimestamp(statinfo.st_mtime)
if platform.system() == 'Linux':
check = st_mtime >= self.start_dt
else:
st_ctime = datetime.fromtimestamp(statinfo.st_ctime)
check = st_mtime >= self.start_dt and st_ctime <= self.end_dt
if not check:
logger.info("file %r not in datetime period!", path)
return check | [
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| b1f09fe1b429ed15110610092704ef12d253f3c9 | https://github.com/brunato/lograptor/blob/b1f09fe1b429ed15110610092704ef12d253f3c9/lograptor/filemap.py#L192-L210 | train |
brunato/lograptor | lograptor/filemap.py | FileMap.add | def add(self, files, items):
"""
Add a list of files with a reference to a list of objects.
"""
if isinstance(files, (str, bytes)):
files = iter([files])
for pathname in files:
try:
values = self._filemap[pathname]
except KeyError:
self._filemap[pathname] = items
else:
values.extend(items) | python | def add(self, files, items):
"""
Add a list of files with a reference to a list of objects.
"""
if isinstance(files, (str, bytes)):
files = iter([files])
for pathname in files:
try:
values = self._filemap[pathname]
except KeyError:
self._filemap[pathname] = items
else:
values.extend(items) | [
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| b1f09fe1b429ed15110610092704ef12d253f3c9 | https://github.com/brunato/lograptor/blob/b1f09fe1b429ed15110610092704ef12d253f3c9/lograptor/filemap.py#L212-L224 | train |
berkeley-cocosci/Wallace | examples/rogers/experiment.py | RogersExperiment.recruit | def recruit(self):
"""Recruit more participants."""
participants = Participant.query.\
with_entities(Participant.status).all()
# if all networks are full, close recruitment,
if not self.networks(full=False):
print "All networks are full, closing recruitment."
self.recruiter().close_recruitment()
# if anyone is still working, don't recruit
elif [p for p in participants if p.status < 100]:
print "People are still participating: not recruiting."
# we only need to recruit if the current generation is complete
elif (len([p for p in participants if p.status == 101]) %
self.generation_size) == 0:
print "Recruiting another generation."
self.recruiter().recruit_participants(n=self.generation_size)
# otherwise do nothing
else:
print "not recruiting." | python | def recruit(self):
"""Recruit more participants."""
participants = Participant.query.\
with_entities(Participant.status).all()
# if all networks are full, close recruitment,
if not self.networks(full=False):
print "All networks are full, closing recruitment."
self.recruiter().close_recruitment()
# if anyone is still working, don't recruit
elif [p for p in participants if p.status < 100]:
print "People are still participating: not recruiting."
# we only need to recruit if the current generation is complete
elif (len([p for p in participants if p.status == 101]) %
self.generation_size) == 0:
print "Recruiting another generation."
self.recruiter().recruit_participants(n=self.generation_size)
# otherwise do nothing
else:
print "not recruiting." | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/examples/rogers/experiment.py#L106-L127 | train |
berkeley-cocosci/Wallace | examples/rogers/experiment.py | RogersExperiment.data_check | def data_check(self, participant):
"""Check a participants data."""
participant_id = participant.uniqueid
nodes = Node.query.filter_by(participant_id=participant_id).all()
if len(nodes) != self.experiment_repeats + self.practice_repeats:
print("Error: Participant has {} nodes. Data check failed"
.format(len(nodes)))
return False
nets = [n.network_id for n in nodes]
if len(nets) != len(set(nets)):
print "Error: Participant participated in the same network \
multiple times. Data check failed"
return False
if None in [n.fitness for n in nodes]:
print "Error: some of participants nodes are missing a fitness. \
Data check failed."
return False
if None in [n.score for n in nodes]:
print "Error: some of participants nodes are missing a score. \
Data check failed"
return False
return True | python | def data_check(self, participant):
"""Check a participants data."""
participant_id = participant.uniqueid
nodes = Node.query.filter_by(participant_id=participant_id).all()
if len(nodes) != self.experiment_repeats + self.practice_repeats:
print("Error: Participant has {} nodes. Data check failed"
.format(len(nodes)))
return False
nets = [n.network_id for n in nodes]
if len(nets) != len(set(nets)):
print "Error: Participant participated in the same network \
multiple times. Data check failed"
return False
if None in [n.fitness for n in nodes]:
print "Error: some of participants nodes are missing a fitness. \
Data check failed."
return False
if None in [n.score for n in nodes]:
print "Error: some of participants nodes are missing a score. \
Data check failed"
return False
return True | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/examples/rogers/experiment.py#L168-L194 | train |
berkeley-cocosci/Wallace | examples/rogers/experiment.py | RogersExperiment.add_node_to_network | def add_node_to_network(self, node, network):
"""Add participant's node to a network."""
network.add_node(node)
node.receive()
environment = network.nodes(type=Environment)[0]
environment.connect(whom=node)
gene = node.infos(type=LearningGene)[0].contents
if (gene == "social"):
prev_agents = RogersAgent.query\
.filter(and_(RogersAgent.failed == False,
RogersAgent.network_id == network.id,
RogersAgent.generation == node.generation - 1))\
.all()
parent = random.choice(prev_agents)
parent.connect(whom=node)
parent.transmit(what=Meme, to_whom=node)
elif (gene == "asocial"):
environment.transmit(to_whom=node)
else:
raise ValueError("{} has invalid learning gene value of {}"
.format(node, gene))
node.receive() | python | def add_node_to_network(self, node, network):
"""Add participant's node to a network."""
network.add_node(node)
node.receive()
environment = network.nodes(type=Environment)[0]
environment.connect(whom=node)
gene = node.infos(type=LearningGene)[0].contents
if (gene == "social"):
prev_agents = RogersAgent.query\
.filter(and_(RogersAgent.failed == False,
RogersAgent.network_id == network.id,
RogersAgent.generation == node.generation - 1))\
.all()
parent = random.choice(prev_agents)
parent.connect(whom=node)
parent.transmit(what=Meme, to_whom=node)
elif (gene == "asocial"):
environment.transmit(to_whom=node)
else:
raise ValueError("{} has invalid learning gene value of {}"
.format(node, gene))
node.receive() | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/examples/rogers/experiment.py#L196-L219 | train |
berkeley-cocosci/Wallace | examples/rogers/experiment.py | RogersEnvironment.create_state | def create_state(self, proportion):
"""Create an environmental state."""
if random.random() < 0.5:
proportion = 1 - proportion
State(origin=self, contents=proportion) | python | def create_state(self, proportion):
"""Create an environmental state."""
if random.random() < 0.5:
proportion = 1 - proportion
State(origin=self, contents=proportion) | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/examples/rogers/experiment.py#L363-L367 | train |
berkeley-cocosci/Wallace | examples/rogers/experiment.py | RogersEnvironment.step | def step(self):
"""Prompt the environment to change."""
current_state = max(self.infos(type=State),
key=attrgetter('creation_time'))
current_contents = float(current_state.contents)
new_contents = 1 - current_contents
info_out = State(origin=self, contents=new_contents)
transformations.Mutation(info_in=current_state, info_out=info_out) | python | def step(self):
"""Prompt the environment to change."""
current_state = max(self.infos(type=State),
key=attrgetter('creation_time'))
current_contents = float(current_state.contents)
new_contents = 1 - current_contents
info_out = State(origin=self, contents=new_contents)
transformations.Mutation(info_in=current_state, info_out=info_out) | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/examples/rogers/experiment.py#L369-L376 | train |
Kortemme-Lab/klab | klab/cluster/python_script_template.py | print_subprocess_output | def print_subprocess_output(subp):
'''Prints the stdout and stderr output.'''
if subp:
if subp.errorcode != 0:
print('<error errorcode="%s">' % str(subp.errorcode))
print(subp.stderr)
print("</error>")
print_tag('stdout', '\n%s\n' % subp.stdout)
else:
print_tag('success', '\n%s\n' % subp.stdout)
print_tag('warnings', '\n%s\n' % subp.stderr) | python | def print_subprocess_output(subp):
'''Prints the stdout and stderr output.'''
if subp:
if subp.errorcode != 0:
print('<error errorcode="%s">' % str(subp.errorcode))
print(subp.stderr)
print("</error>")
print_tag('stdout', '\n%s\n' % subp.stdout)
else:
print_tag('success', '\n%s\n' % subp.stdout)
print_tag('warnings', '\n%s\n' % subp.stderr) | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/cluster/python_script_template.py#L48-L58 | train |
Alveo/pyalveo | pyalveo/objects.py | ItemGroup.get_all | def get_all(self, force_download=False):
""" Retrieve the metadata for all items in this list from the server,
as Item objects
:rtype: List
:returns: a List of the corresponding Item objects
:type force_download: Boolean
:param force_download: True to download from the server
regardless of the cache's contents
:raises: APIError if the API request is not successful
"""
cl = self.client
return [cl.get_item(item, force_download) for item in self.item_urls] | python | def get_all(self, force_download=False):
""" Retrieve the metadata for all items in this list from the server,
as Item objects
:rtype: List
:returns: a List of the corresponding Item objects
:type force_download: Boolean
:param force_download: True to download from the server
regardless of the cache's contents
:raises: APIError if the API request is not successful
"""
cl = self.client
return [cl.get_item(item, force_download) for item in self.item_urls] | [
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L170-L185 | train |
Alveo/pyalveo | pyalveo/objects.py | ItemGroup.get_item | def get_item(self, item_index, force_download=False):
""" Retrieve the metadata for a specific item in this ItemGroup
:type item_index: int
:param item_index: the index of the item
:type force_download: Boolean
:param force_download: True to download from the server
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:rtype: Item
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return self.client.get_item(self.item_urls[item_index], force_download) | python | def get_item(self, item_index, force_download=False):
""" Retrieve the metadata for a specific item in this ItemGroup
:type item_index: int
:param item_index: the index of the item
:type force_download: Boolean
:param force_download: True to download from the server
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:raises: APIError if the API request is not successful
"""
return self.client.get_item(self.item_urls[item_index], force_download) | [
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L230-L246 | train |
Alveo/pyalveo | pyalveo/objects.py | ItemList.refresh | def refresh(self):
""" Update this ItemList by re-downloading it from the server
:rtype: ItemList
:returns: this ItemList, after the refresh
:raises: APIError if the API request is not successful
"""
refreshed = self.client.get_item_list(self.url())
self.item_urls = refreshed.urls()
self.list_name = refreshed.name()
return self | python | def refresh(self):
""" Update this ItemList by re-downloading it from the server
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:returns: this ItemList, after the refresh
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refreshed = self.client.get_item_list(self.url())
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L345-L358 | train |
Alveo/pyalveo | pyalveo/objects.py | ItemList.append | def append(self, items):
""" Add some items to this ItemList and save the changes to the server
:param items: the items to add, either as a List of Item objects, an
ItemList, a List of item URLs as Strings, a single item URL as a
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:rtype: String
:returns: the server success message
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""" Add some items to this ItemList and save the changes to the server
:param items: the items to add, either as a List of Item objects, an
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L361-L377 | train |
Alveo/pyalveo | pyalveo/objects.py | Item.get_document | def get_document(self, index=0):
""" Return the metadata for the specified document, as a
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:type index: int
:param index: the index of the document
:rtype: Document
:returns: the metadata for the specified document
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try:
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""" Return the metadata for the specified document, as a
Document object
:type index: int
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:rtype: Document
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L462-L478 | train |
Alveo/pyalveo | pyalveo/objects.py | Item.get_primary_text | def get_primary_text(self, force_download=False):
""" Retrieve the primary text for this item from the server
:type force_download: Boolean
:param force_download: True to download from the server
regardless of the cache's contents
:rtype: String
:returns: the primary text
:raises: APIError if the API request is not successful
"""
return self.client.get_primary_text(self.url(), force_download) | python | def get_primary_text(self, force_download=False):
""" Retrieve the primary text for this item from the server
:type force_download: Boolean
:param force_download: True to download from the server
regardless of the cache's contents
:rtype: String
:returns: the primary text
:raises: APIError if the API request is not successful
"""
return self.client.get_primary_text(self.url(), force_download) | [
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L481-L495 | train |
Alveo/pyalveo | pyalveo/objects.py | Item.get_annotations | def get_annotations(self, atype=None, label=None):
""" Retrieve the annotations for this item from the server
:type atype: String
:param atype: return only results with a matching Type field
:type label: String
:param label: return only results with a matching Label field
:rtype: String
:returns: the annotations as a JSON string
:raises: APIError if the API request is not successful
"""
return self.client.get_item_annotations(self.url(), atype, label) | python | def get_annotations(self, atype=None, label=None):
""" Retrieve the annotations for this item from the server
:type atype: String
:param atype: return only results with a matching Type field
:type label: String
:param label: return only results with a matching Label field
:rtype: String
:returns: the annotations as a JSON string
:raises: APIError if the API request is not successful
"""
return self.client.get_item_annotations(self.url(), atype, label) | [
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L498-L513 | train |
Alveo/pyalveo | pyalveo/objects.py | Document.get_content | def get_content(self, force_download=False):
""" Retrieve the content for this Document from the server
:type force_download: Boolean
:param force_download: True to download from the server
regardless of the cache's contents
:rtype: String
:returns: the content data
:raises: APIError if the API request is not successful
"""
return self.client.get_document(self.url(), force_download) | python | def get_content(self, force_download=False):
""" Retrieve the content for this Document from the server
:type force_download: Boolean
:param force_download: True to download from the server
regardless of the cache's contents
:rtype: String
:returns: the content data
:raises: APIError if the API request is not successful
"""
return self.client.get_document(self.url(), force_download) | [
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L702-L716 | train |
Alveo/pyalveo | pyalveo/objects.py | Document.download_content | def download_content(self, dir_path='', filename=None,
force_download=False):
""" Download the content for this document to a file
:type dir_path: String
:param dir_path: the path to which to write the data
:type filename: String
:param filename: filename to write to (if None, defaults to the document's
name, as specified by its metadata
:type force_download: Boolean
:param force_download: True to download from the server
regardless of the cache's contents
:rtype: String
:returns: the path to the downloaded file
:raises: APIError if the API request is not successful
"""
if filename is None:
filename = self.get_filename()
path = os.path.join(dir_path, filename)
data = self.client.get_document(self.url(), force_download)
with open(path, 'wb') as f:
f.write(data)
return path | python | def download_content(self, dir_path='', filename=None,
force_download=False):
""" Download the content for this document to a file
:type dir_path: String
:param dir_path: the path to which to write the data
:type filename: String
:param filename: filename to write to (if None, defaults to the document's
name, as specified by its metadata
:type force_download: Boolean
:param force_download: True to download from the server
regardless of the cache's contents
:rtype: String
:returns: the path to the downloaded file
:raises: APIError if the API request is not successful
"""
if filename is None:
filename = self.get_filename()
path = os.path.join(dir_path, filename)
data = self.client.get_document(self.url(), force_download)
with open(path, 'wb') as f:
f.write(data)
return path | [
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| 1e9eec22bc031bc9a08066f9966565a546e6242e | https://github.com/Alveo/pyalveo/blob/1e9eec22bc031bc9a08066f9966565a546e6242e/pyalveo/objects.py#L730-L756 | train |
peergradeio/flask-mongo-profiler | flask_mongo_profiler/contrib/flask_admin/formatters/polymorphic_relations.py | generic_ref_formatter | def generic_ref_formatter(view, context, model, name, lazy=False):
"""
For GenericReferenceField and LazyGenericReferenceField
See Also
--------
diff_formatter
"""
try:
if lazy:
rel_model = getattr(model, name).fetch()
else:
rel_model = getattr(model, name)
except (mongoengine.DoesNotExist, AttributeError) as e:
# custom_field_type_formatters seems to fix the issue of stale references
# crashing pages, since it intercepts the display of all ReferenceField's.
return Markup(
'<span class="label label-danger">Error</span> <small>%s</small>' % e
)
if rel_model is None:
return ''
try:
return Markup(
'<a href="%s">%s</a>'
% (
url_for(
# Flask-Admin creates URL's namespaced w/ model class name, lowercase.
'%s.details_view' % rel_model.__class__.__name__.lower(),
id=rel_model.id,
),
rel_model,
)
)
except werkzeug.routing.BuildError as e:
return Markup(
'<span class="label label-danger">Error</span> <small>%s</small>' % e
) | python | def generic_ref_formatter(view, context, model, name, lazy=False):
"""
For GenericReferenceField and LazyGenericReferenceField
See Also
--------
diff_formatter
"""
try:
if lazy:
rel_model = getattr(model, name).fetch()
else:
rel_model = getattr(model, name)
except (mongoengine.DoesNotExist, AttributeError) as e:
# custom_field_type_formatters seems to fix the issue of stale references
# crashing pages, since it intercepts the display of all ReferenceField's.
return Markup(
'<span class="label label-danger">Error</span> <small>%s</small>' % e
)
if rel_model is None:
return ''
try:
return Markup(
'<a href="%s">%s</a>'
% (
url_for(
# Flask-Admin creates URL's namespaced w/ model class name, lowercase.
'%s.details_view' % rel_model.__class__.__name__.lower(),
id=rel_model.id,
),
rel_model,
)
)
except werkzeug.routing.BuildError as e:
return Markup(
'<span class="label label-danger">Error</span> <small>%s</small>' % e
) | [
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| a267eeb49fea07c9a24fb370bd9d7a90ed313ccf | https://github.com/peergradeio/flask-mongo-profiler/blob/a267eeb49fea07c9a24fb370bd9d7a90ed313ccf/flask_mongo_profiler/contrib/flask_admin/formatters/polymorphic_relations.py#L27-L65 | train |
peergradeio/flask-mongo-profiler | flask_mongo_profiler/contrib/flask_admin/formatters/polymorphic_relations.py | generic_document_type_formatter | def generic_document_type_formatter(view, context, model, name):
"""Return AdminLog.document field wrapped in URL to its list view."""
_document_model = model.get('document').document_type
url = _document_model.get_admin_list_url()
return Markup('<a href="%s">%s</a>' % (url, _document_model.__name__)) | python | def generic_document_type_formatter(view, context, model, name):
"""Return AdminLog.document field wrapped in URL to its list view."""
_document_model = model.get('document').document_type
url = _document_model.get_admin_list_url()
return Markup('<a href="%s">%s</a>' % (url, _document_model.__name__)) | [
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| a267eeb49fea07c9a24fb370bd9d7a90ed313ccf | https://github.com/peergradeio/flask-mongo-profiler/blob/a267eeb49fea07c9a24fb370bd9d7a90ed313ccf/flask_mongo_profiler/contrib/flask_admin/formatters/polymorphic_relations.py#L77-L81 | train |
berkeley-cocosci/Wallace | wallace/custom.py | return_page | def return_page(page):
"""Return a rendered template."""
try:
hit_id = request.args['hit_id']
assignment_id = request.args['assignment_id']
worker_id = request.args['worker_id']
mode = request.args['mode']
return render_template(
page,
hit_id=hit_id,
assignment_id=assignment_id,
worker_id=worker_id,
mode=mode
)
except:
try:
participant_id = request.args['participant_id']
return render_template(page, participant_id=participant_id)
except:
return error_response(error_type="{} args missing".format(page)) | python | def return_page(page):
"""Return a rendered template."""
try:
hit_id = request.args['hit_id']
assignment_id = request.args['assignment_id']
worker_id = request.args['worker_id']
mode = request.args['mode']
return render_template(
page,
hit_id=hit_id,
assignment_id=assignment_id,
worker_id=worker_id,
mode=mode
)
except:
try:
participant_id = request.args['participant_id']
return render_template(page, participant_id=participant_id)
except:
return error_response(error_type="{} args missing".format(page)) | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/wallace/custom.py#L120-L139 | train |
berkeley-cocosci/Wallace | wallace/custom.py | quitter | def quitter():
"""Overide the psiTurk quitter route."""
exp = experiment(session)
exp.log("Quitter route was hit.")
return Response(
dumps({"status": "success"}),
status=200,
mimetype='application/json') | python | def quitter():
"""Overide the psiTurk quitter route."""
exp = experiment(session)
exp.log("Quitter route was hit.")
return Response(
dumps({"status": "success"}),
status=200,
mimetype='application/json') | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/wallace/custom.py#L228-L236 | train |
berkeley-cocosci/Wallace | wallace/custom.py | ad_address | def ad_address(mode, hit_id):
"""Get the address of the ad on AWS.
This is used at the end of the experiment to send participants
back to AWS where they can complete and submit the HIT.
"""
if mode == "debug":
address = '/complete'
elif mode in ["sandbox", "live"]:
username = os.getenv('psiturk_access_key_id',
config.get("psiTurk Access",
"psiturk_access_key_id"))
password = os.getenv('psiturk_secret_access_id',
config.get("psiTurk Access",
"psiturk_secret_access_id"))
try:
req = requests.get(
'https://api.psiturk.org/api/ad/lookup/' + hit_id,
auth=(username, password))
except:
raise ValueError('api_server_not_reachable')
else:
if req.status_code == 200:
hit_address = req.json()['ad_id']
else:
raise ValueError("something here")
if mode == "sandbox":
address = ('https://sandbox.ad.psiturk.org/complete/' +
str(hit_address))
elif mode == "live":
address = 'https://ad.psiturk.org/complete/' + str(hit_address)
else:
raise ValueError("Unknown mode: {}".format(mode))
return success_response(field="address",
data=address,
request_type="ad_address") | python | def ad_address(mode, hit_id):
"""Get the address of the ad on AWS.
This is used at the end of the experiment to send participants
back to AWS where they can complete and submit the HIT.
"""
if mode == "debug":
address = '/complete'
elif mode in ["sandbox", "live"]:
username = os.getenv('psiturk_access_key_id',
config.get("psiTurk Access",
"psiturk_access_key_id"))
password = os.getenv('psiturk_secret_access_id',
config.get("psiTurk Access",
"psiturk_secret_access_id"))
try:
req = requests.get(
'https://api.psiturk.org/api/ad/lookup/' + hit_id,
auth=(username, password))
except:
raise ValueError('api_server_not_reachable')
else:
if req.status_code == 200:
hit_address = req.json()['ad_id']
else:
raise ValueError("something here")
if mode == "sandbox":
address = ('https://sandbox.ad.psiturk.org/complete/' +
str(hit_address))
elif mode == "live":
address = 'https://ad.psiturk.org/complete/' + str(hit_address)
else:
raise ValueError("Unknown mode: {}".format(mode))
return success_response(field="address",
data=address,
request_type="ad_address") | [
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This is used at the end of the experiment to send participants
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/wallace/custom.py#L248-L283 | train |
berkeley-cocosci/Wallace | wallace/custom.py | connect | def connect(node_id, other_node_id):
"""Connect to another node.
The ids of both nodes must be speficied in the url.
You can also pass direction (to/from/both) as an argument.
"""
exp = experiment(session)
# get the parameters
direction = request_parameter(parameter="direction", default="to")
if type(direction == Response):
return direction
# check the nodes exist
node = models.Node.query.get(node_id)
if node is None:
return error_response(error_type="/node/connect, node does not exist")
other_node = models.Node.query.get(other_node_id)
if other_node is None:
return error_response(
error_type="/node/connect, other node does not exist",
participant=node.participant)
# execute the request
try:
vectors = node.connect(whom=other_node, direction=direction)
for v in vectors:
assign_properties(v)
# ping the experiment
exp.vector_post_request(
node=node,
vectors=vectors)
session.commit()
except:
return error_response(error_type="/vector POST server error",
status=403,
participant=node.participant)
return success_response(field="vectors",
data=[v.__json__() for v in vectors],
request_type="vector post") | python | def connect(node_id, other_node_id):
"""Connect to another node.
The ids of both nodes must be speficied in the url.
You can also pass direction (to/from/both) as an argument.
"""
exp = experiment(session)
# get the parameters
direction = request_parameter(parameter="direction", default="to")
if type(direction == Response):
return direction
# check the nodes exist
node = models.Node.query.get(node_id)
if node is None:
return error_response(error_type="/node/connect, node does not exist")
other_node = models.Node.query.get(other_node_id)
if other_node is None:
return error_response(
error_type="/node/connect, other node does not exist",
participant=node.participant)
# execute the request
try:
vectors = node.connect(whom=other_node, direction=direction)
for v in vectors:
assign_properties(v)
# ping the experiment
exp.vector_post_request(
node=node,
vectors=vectors)
session.commit()
except:
return error_response(error_type="/vector POST server error",
status=403,
participant=node.participant)
return success_response(field="vectors",
data=[v.__json__() for v in vectors],
request_type="vector post") | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/wallace/custom.py#L649-L692 | train |
berkeley-cocosci/Wallace | wallace/custom.py | get_info | def get_info(node_id, info_id):
"""Get a specific info.
Both the node and info id must be specified in the url.
"""
exp = experiment(session)
# check the node exists
node = models.Node.query.get(node_id)
if node is None:
return error_response(error_type="/info, node does not exist")
# execute the experiment method:
info = models.Info.query.get(info_id)
if info is None:
return error_response(error_type="/info GET, info does not exist",
participant=node.participant)
elif (info.origin_id != node.id and
info.id not in
[t.info_id for t in node.transmissions(direction="incoming",
status="received")]):
return error_response(error_type="/info GET, forbidden info",
status=403,
participant=node.participant)
try:
# ping the experiment
exp.info_get_request(node=node, infos=info)
session.commit()
except:
return error_response(error_type="/info GET server error",
status=403,
participant=node.participant)
# return the data
return success_response(field="info",
data=info.__json__(),
request_type="info get") | python | def get_info(node_id, info_id):
"""Get a specific info.
Both the node and info id must be specified in the url.
"""
exp = experiment(session)
# check the node exists
node = models.Node.query.get(node_id)
if node is None:
return error_response(error_type="/info, node does not exist")
# execute the experiment method:
info = models.Info.query.get(info_id)
if info is None:
return error_response(error_type="/info GET, info does not exist",
participant=node.participant)
elif (info.origin_id != node.id and
info.id not in
[t.info_id for t in node.transmissions(direction="incoming",
status="received")]):
return error_response(error_type="/info GET, forbidden info",
status=403,
participant=node.participant)
try:
# ping the experiment
exp.info_get_request(node=node, infos=info)
session.commit()
except:
return error_response(error_type="/info GET server error",
status=403,
participant=node.participant)
# return the data
return success_response(field="info",
data=info.__json__(),
request_type="info get") | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/wallace/custom.py#L696-L733 | train |
berkeley-cocosci/Wallace | wallace/custom.py | transformation_post | def transformation_post(node_id, info_in_id, info_out_id):
"""Transform an info.
The ids of the node, info in and info out must all be in the url.
You can also pass transformation_type.
"""
exp = experiment(session)
# Get the parameters.
transformation_type = request_parameter(parameter="transformation_type",
parameter_type="known_class",
default=models.Transformation)
if type(transformation_type) == Response:
return transformation_type
# Check that the node etc. exists.
node = models.Node.query.get(node_id)
if node is None:
return error_response(
error_type="/transformation POST, node does not exist")
info_in = models.Info.query.get(info_in_id)
if info_in is None:
return error_response(
error_type="/transformation POST, info_in does not exist",
participant=node.participant)
info_out = models.Info.query.get(info_out_id)
if info_out is None:
return error_response(
error_type="/transformation POST, info_out does not exist",
participant=node.participant)
try:
# execute the request
transformation = transformation_type(info_in=info_in,
info_out=info_out)
assign_properties(transformation)
session.commit()
# ping the experiment
exp.transformation_post_request(node=node,
transformation=transformation)
session.commit()
except:
return error_response(error_type="/tranaformation POST failed",
participant=node.participant)
# return the data
return success_response(field="transformation",
data=transformation.__json__(),
request_type="transformation post") | python | def transformation_post(node_id, info_in_id, info_out_id):
"""Transform an info.
The ids of the node, info in and info out must all be in the url.
You can also pass transformation_type.
"""
exp = experiment(session)
# Get the parameters.
transformation_type = request_parameter(parameter="transformation_type",
parameter_type="known_class",
default=models.Transformation)
if type(transformation_type) == Response:
return transformation_type
# Check that the node etc. exists.
node = models.Node.query.get(node_id)
if node is None:
return error_response(
error_type="/transformation POST, node does not exist")
info_in = models.Info.query.get(info_in_id)
if info_in is None:
return error_response(
error_type="/transformation POST, info_in does not exist",
participant=node.participant)
info_out = models.Info.query.get(info_out_id)
if info_out is None:
return error_response(
error_type="/transformation POST, info_out does not exist",
participant=node.participant)
try:
# execute the request
transformation = transformation_type(info_in=info_in,
info_out=info_out)
assign_properties(transformation)
session.commit()
# ping the experiment
exp.transformation_post_request(node=node,
transformation=transformation)
session.commit()
except:
return error_response(error_type="/tranaformation POST failed",
participant=node.participant)
# return the data
return success_response(field="transformation",
data=transformation.__json__(),
request_type="transformation post") | [
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The ids of the node, info in and info out must all be in the url.
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/wallace/custom.py#L1053-L1104 | train |
berkeley-cocosci/Wallace | wallace/custom.py | api_notifications | def api_notifications():
"""Receive MTurk REST notifications."""
event_type = request.values['Event.1.EventType']
assignment_id = request.values['Event.1.AssignmentId']
# Add the notification to the queue.
db.logger.debug('rq: Queueing %s with id: %s for worker_function',
event_type, assignment_id)
q.enqueue(worker_function, event_type, assignment_id, None)
db.logger.debug('rq: Submitted Queue Length: %d (%s)', len(q),
', '.join(q.job_ids))
return success_response(request_type="notification") | python | def api_notifications():
"""Receive MTurk REST notifications."""
event_type = request.values['Event.1.EventType']
assignment_id = request.values['Event.1.AssignmentId']
# Add the notification to the queue.
db.logger.debug('rq: Queueing %s with id: %s for worker_function',
event_type, assignment_id)
q.enqueue(worker_function, event_type, assignment_id, None)
db.logger.debug('rq: Submitted Queue Length: %d (%s)', len(q),
', '.join(q.job_ids))
return success_response(request_type="notification") | [
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| 3650c0bc3b0804d0adb1d178c5eba9992babb1b0 | https://github.com/berkeley-cocosci/Wallace/blob/3650c0bc3b0804d0adb1d178c5eba9992babb1b0/wallace/custom.py#L1108-L1120 | train |
uogbuji/versa | tools/py/writer/rdfs.py | process | def process(source, target, rdfsonly, base=None, logger=logging):
'''
Prepare a statement into a triple ready for rdflib graph
'''
for link in source.match():
s, p, o = link[:3]
#SKip docheader statements
if s == (base or '') + '@docheader': continue
if p in RESOURCE_MAPPING: p = RESOURCE_MAPPING[p]
if o in RESOURCE_MAPPING: o = RESOURCE_MAPPING[o]
if p == VERSA_BASEIRI + 'refines':
tlinks = list(source.match(s, TYPE_REL))
if tlinks:
if tlinks[0][TARGET] == VERSA_BASEIRI + 'Resource':
p = I(RDFS_NAMESPACE + 'subClassOf')
elif tlinks[0][TARGET] == VERSA_BASEIRI + 'Property':
p = I(RDFS_NAMESPACE + 'subPropertyOf')
if p == VERSA_BASEIRI + 'properties':
suri = I(iri.absolutize(s, base)) if base else s
target.add((URIRef(o), URIRef(RDFS_NAMESPACE + 'domain'), URIRef(suri)))
continue
if p == VERSA_BASEIRI + 'value':
if o not in ['Literal', 'IRI']:
ouri = I(iri.absolutize(o, base)) if base else o
target.add((URIRef(s), URIRef(RDFS_NAMESPACE + 'range'), URIRef(ouri)))
continue
s = URIRef(s)
#Translate v:type to rdf:type
p = RDF.type if p == TYPE_REL else URIRef(p)
o = URIRef(o) if isinstance(o, I) else Literal(o)
if not rdfsonly or p.startswith(RDF_NAMESPACE) or p.startswith(RDFS_NAMESPACE):
target.add((s, p, o))
return | python | def process(source, target, rdfsonly, base=None, logger=logging):
'''
Prepare a statement into a triple ready for rdflib graph
'''
for link in source.match():
s, p, o = link[:3]
#SKip docheader statements
if s == (base or '') + '@docheader': continue
if p in RESOURCE_MAPPING: p = RESOURCE_MAPPING[p]
if o in RESOURCE_MAPPING: o = RESOURCE_MAPPING[o]
if p == VERSA_BASEIRI + 'refines':
tlinks = list(source.match(s, TYPE_REL))
if tlinks:
if tlinks[0][TARGET] == VERSA_BASEIRI + 'Resource':
p = I(RDFS_NAMESPACE + 'subClassOf')
elif tlinks[0][TARGET] == VERSA_BASEIRI + 'Property':
p = I(RDFS_NAMESPACE + 'subPropertyOf')
if p == VERSA_BASEIRI + 'properties':
suri = I(iri.absolutize(s, base)) if base else s
target.add((URIRef(o), URIRef(RDFS_NAMESPACE + 'domain'), URIRef(suri)))
continue
if p == VERSA_BASEIRI + 'value':
if o not in ['Literal', 'IRI']:
ouri = I(iri.absolutize(o, base)) if base else o
target.add((URIRef(s), URIRef(RDFS_NAMESPACE + 'range'), URIRef(ouri)))
continue
s = URIRef(s)
#Translate v:type to rdf:type
p = RDF.type if p == TYPE_REL else URIRef(p)
o = URIRef(o) if isinstance(o, I) else Literal(o)
if not rdfsonly or p.startswith(RDF_NAMESPACE) or p.startswith(RDFS_NAMESPACE):
target.add((s, p, o))
return | [
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| f092ffc7ed363a5b170890955168500f32de0dd5 | https://github.com/uogbuji/versa/blob/f092ffc7ed363a5b170890955168500f32de0dd5/tools/py/writer/rdfs.py#L50-L83 | train |
uogbuji/versa | tools/py/writer/rdfs.py | write | def write(models, base=None, graph=None, rdfsonly=False, prefixes=None, logger=logging):
'''
See the command line help
'''
prefixes = prefixes or {}
g = graph or rdflib.Graph()
#g.bind('bf', BFNS)
#g.bind('bfc', BFCNS)
#g.bind('bfd', BFDNS)
g.bind('v', VNS)
for k, v in prefixes.items():
g.bind(k, v)
for m in models:
base_out = m.base
process(m, g, rdfsonly, base=base_out, logger=logger)
return g | python | def write(models, base=None, graph=None, rdfsonly=False, prefixes=None, logger=logging):
'''
See the command line help
'''
prefixes = prefixes or {}
g = graph or rdflib.Graph()
#g.bind('bf', BFNS)
#g.bind('bfc', BFCNS)
#g.bind('bfd', BFDNS)
g.bind('v', VNS)
for k, v in prefixes.items():
g.bind(k, v)
for m in models:
base_out = m.base
process(m, g, rdfsonly, base=base_out, logger=logger)
return g | [
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| f092ffc7ed363a5b170890955168500f32de0dd5 | https://github.com/uogbuji/versa/blob/f092ffc7ed363a5b170890955168500f32de0dd5/tools/py/writer/rdfs.py#L86-L101 | train |
projectshift/shift-boiler | boiler/feature/routing.py | routing_feature | def routing_feature(app):
"""
Add routing feature
Allows to define application routes un urls.py file and use lazy views.
Additionally enables regular exceptions in route definitions
"""
# enable regex routes
app.url_map.converters['regex'] = RegexConverter
urls = app.name.rsplit('.', 1)[0] + '.urls.urls'
# important issue ahead
# see: https://github.com/projectshift/shift-boiler/issues/11
try:
urls = import_string(urls)
except ImportError as e:
err = 'Failed to import {}. If it exists, check that it does not '
err += 'import something non-existent itself! '
err += 'Try to manually import it to debug.'
raise ImportError(err.format(urls))
# add routes now
for route in urls.keys():
route_options = urls[route]
route_options['rule'] = route
app.add_url_rule(**route_options) | python | def routing_feature(app):
"""
Add routing feature
Allows to define application routes un urls.py file and use lazy views.
Additionally enables regular exceptions in route definitions
"""
# enable regex routes
app.url_map.converters['regex'] = RegexConverter
urls = app.name.rsplit('.', 1)[0] + '.urls.urls'
# important issue ahead
# see: https://github.com/projectshift/shift-boiler/issues/11
try:
urls = import_string(urls)
except ImportError as e:
err = 'Failed to import {}. If it exists, check that it does not '
err += 'import something non-existent itself! '
err += 'Try to manually import it to debug.'
raise ImportError(err.format(urls))
# add routes now
for route in urls.keys():
route_options = urls[route]
route_options['rule'] = route
app.add_url_rule(**route_options) | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/feature/routing.py#L5-L30 | train |
rosshamish/undoredo | undoredo.py | undoable | def undoable(method):
"""
Decorator undoable allows an instance method to be undone.
It does this by wrapping the method call as a Command, then calling self.do() on the command.
Classes which use this decorator should implement a do() method like such:
def do(self, command):
return self.undo_manager.do(command)
"""
def undoable_method(self, *args):
return self.do(Command(self, method, *args))
return undoable_method | python | def undoable(method):
"""
Decorator undoable allows an instance method to be undone.
It does this by wrapping the method call as a Command, then calling self.do() on the command.
Classes which use this decorator should implement a do() method like such:
def do(self, command):
return self.undo_manager.do(command)
"""
def undoable_method(self, *args):
return self.do(Command(self, method, *args))
return undoable_method | [
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| 634941181a74477b7ebafa43d9900e6f21fd0458 | https://github.com/rosshamish/undoredo/blob/634941181a74477b7ebafa43d9900e6f21fd0458/undoredo.py#L105-L118 | train |
projectshift/shift-boiler | boiler/migrations/config.py | MigrationsConfig.get_template_directory | def get_template_directory(self):
"""
Get path to migrations templates
This will get used when you run the db init command
"""
dir = os.path.join(os.path.dirname(__file__), 'templates')
return dir | python | def get_template_directory(self):
"""
Get path to migrations templates
This will get used when you run the db init command
"""
dir = os.path.join(os.path.dirname(__file__), 'templates')
return dir | [
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| 8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b | https://github.com/projectshift/shift-boiler/blob/8e6f3a3e4b9493fb6c8bd16bed160ede153bfb0b/boiler/migrations/config.py#L23-L29 | train |
CodersOfTheNight/oshino | oshino/agents/__init__.py | Agent.pull_metrics | async def pull_metrics(self, event_fn, loop=None):
"""
Method called by core.
Should not be overwritten.
"""
if self.lazy and not self.ready:
return None
logger = self.get_logger()
ts = timer()
logger.trace("Waiting for process event")
result = await self.process(event_fn)
td = int(timer() - ts)
logger.trace("It took: {}ms".format(td))
self._last_run = current_ts()
return result | python | async def pull_metrics(self, event_fn, loop=None):
"""
Method called by core.
Should not be overwritten.
"""
if self.lazy and not self.ready:
return None
logger = self.get_logger()
ts = timer()
logger.trace("Waiting for process event")
result = await self.process(event_fn)
td = int(timer() - ts)
logger.trace("It took: {}ms".format(td))
self._last_run = current_ts()
return result | [
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| 00f7e151e3ce1f3a7f43b353b695c4dba83c7f28 | https://github.com/CodersOfTheNight/oshino/blob/00f7e151e3ce1f3a7f43b353b695c4dba83c7f28/oshino/agents/__init__.py#L40-L55 | train |
CodersOfTheNight/oshino | oshino/agents/__init__.py | Agent.ready | def ready(self):
"""
Function used when agent is `lazy`.
It is being processed only when `ready` condition is satisfied
"""
logger = self.get_logger()
now = current_ts()
logger.trace("Current time: {0}".format(now))
logger.trace("Last Run: {0}".format(self._last_run))
delta = (now - self._last_run)
logger.trace("Delta: {0}, Interval: {1}"
.format(delta, self.interval * 1000))
return delta > self.interval * 1000 | python | def ready(self):
"""
Function used when agent is `lazy`.
It is being processed only when `ready` condition is satisfied
"""
logger = self.get_logger()
now = current_ts()
logger.trace("Current time: {0}".format(now))
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delta = (now - self._last_run)
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return delta > self.interval * 1000 | [
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| 00f7e151e3ce1f3a7f43b353b695c4dba83c7f28 | https://github.com/CodersOfTheNight/oshino/blob/00f7e151e3ce1f3a7f43b353b695c4dba83c7f28/oshino/agents/__init__.py#L66-L78 | train |
mardix/Mocha | mocha/contrib/auth/__init__.py | UserModel.create_jwt | def create_jwt(self, expires_in=None):
"""
Create a secure timed JWT token that can be passed. It save the user id,
which later will be used to retrieve the data
:param user: AuthUser, the user's object
:param expires_in: - time in second for the token to expire
:return: string
"""
s = utils.sign_jwt(data={"id": self.user.id},
secret_key=get_jwt_secret(),
salt=get_jwt_salt(),
expires_in=expires_in or get_jwt_ttl())
return s | python | def create_jwt(self, expires_in=None):
"""
Create a secure timed JWT token that can be passed. It save the user id,
which later will be used to retrieve the data
:param user: AuthUser, the user's object
:param expires_in: - time in second for the token to expire
:return: string
"""
s = utils.sign_jwt(data={"id": self.user.id},
secret_key=get_jwt_secret(),
salt=get_jwt_salt(),
expires_in=expires_in or get_jwt_ttl())
return s | [
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| Create a secure timed JWT token that can be passed. It save the user id,
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:param user: AuthUser, the user's object
:param expires_in: - time in second for the token to expire
:return: string | [
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| bce481cb31a0972061dd99bc548701411dcb9de3 | https://github.com/mardix/Mocha/blob/bce481cb31a0972061dd99bc548701411dcb9de3/mocha/contrib/auth/__init__.py#L449-L462 | train |
Kortemme-Lab/klab | klab/comms/mail.py | MailServer.sendgmail | def sendgmail(self, subject, recipients, plaintext, htmltext=None, cc=None, debug=False, useMIMEMultipart=True, gmail_account = '[email protected]', pw_filepath = None):
'''For this function to work, the password for the gmail user must be colocated with this file or passed in.'''
smtpserver = smtplib.SMTP("smtp.gmail.com", 587)
smtpserver.ehlo()
smtpserver.starttls()
smtpserver.ehlo
gmail_account = '[email protected]'
if pw_filepath:
smtpserver.login(gmail_account, read_file(pw_filepath))
else:
smtpserver.login(gmail_account, read_file('pw'))
for recipient in recipients:
if htmltext:
msg = MIMEText(htmltext, 'html')
msg['From'] = gmail_account
msg['To'] = recipient
msg['Subject'] = subject
smtpserver.sendmail(gmail_account, recipient, msg.as_string())
else:
header = 'To:' + recipient + '\n' + 'From: ' + gmail_account + '\n' + 'Subject:' + subject + '\n'
msg = header + '\n ' + plaintext + '\n\n'
smtpserver.sendmail(gmail_account, recipient, msg)
smtpserver.close() | python | def sendgmail(self, subject, recipients, plaintext, htmltext=None, cc=None, debug=False, useMIMEMultipart=True, gmail_account = '[email protected]', pw_filepath = None):
'''For this function to work, the password for the gmail user must be colocated with this file or passed in.'''
smtpserver = smtplib.SMTP("smtp.gmail.com", 587)
smtpserver.ehlo()
smtpserver.starttls()
smtpserver.ehlo
gmail_account = '[email protected]'
if pw_filepath:
smtpserver.login(gmail_account, read_file(pw_filepath))
else:
smtpserver.login(gmail_account, read_file('pw'))
for recipient in recipients:
if htmltext:
msg = MIMEText(htmltext, 'html')
msg['From'] = gmail_account
msg['To'] = recipient
msg['Subject'] = subject
smtpserver.sendmail(gmail_account, recipient, msg.as_string())
else:
header = 'To:' + recipient + '\n' + 'From: ' + gmail_account + '\n' + 'Subject:' + subject + '\n'
msg = header + '\n ' + plaintext + '\n\n'
smtpserver.sendmail(gmail_account, recipient, msg)
smtpserver.close() | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/comms/mail.py#L72-L95 | train |
adaptive-learning/proso-apps | proso_common/views.py | show_one | def show_one(request, post_process_fun, object_class, id, template='common_json.html'):
"""
Return object of the given type with the specified identifier.
GET parameters:
user:
identifier of the current user
stats:
turn on the enrichment of the objects by some statistics
html
turn on the HTML version of the API
"""
obj = get_object_or_404(object_class, pk=id)
json = post_process_fun(request, obj)
return render_json(request, json, template=template, help_text=show_one.__doc__) | python | def show_one(request, post_process_fun, object_class, id, template='common_json.html'):
"""
Return object of the given type with the specified identifier.
GET parameters:
user:
identifier of the current user
stats:
turn on the enrichment of the objects by some statistics
html
turn on the HTML version of the API
"""
obj = get_object_or_404(object_class, pk=id)
json = post_process_fun(request, obj)
return render_json(request, json, template=template, help_text=show_one.__doc__) | [
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turn on the HTML version of the API | [
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| 8278c72e498d6ef8d392cc47b48473f4ec037142 | https://github.com/adaptive-learning/proso-apps/blob/8278c72e498d6ef8d392cc47b48473f4ec037142/proso_common/views.py#L29-L43 | train |
adaptive-learning/proso-apps | proso_common/views.py | show_more | def show_more(request, post_process_fun, get_fun, object_class, should_cache=True, template='common_json.html', to_json_kwargs=None):
"""
Return list of objects of the given type.
GET parameters:
limit:
number of returned objects (default 10, maximum 100)
page:
current page number
filter_column:
column name used to filter the results
filter_value:
value for the specified column used to filter the results
user:
identifier of the current user
all:
return all objects available instead of paging; be aware this parameter
can be used only for objects for wich the caching is turned on
db_orderby:
database column which the result should be ordered by
json_orderby:
field of the JSON object which the result should be ordered by, it is
less effective than the ordering via db_orderby; be aware this parameter
can be used only for objects for which the caching is turned on
desc
turn on the descending order
stats:
turn on the enrichment of the objects by some statistics
html
turn on the HTML version of the API
environment
turn on the enrichment of the related environment values
"""
if not should_cache and 'json_orderby' in request.GET:
return render_json(request, {
'error': "Can't order the result according to the JSON field, because the caching for this type of object is turned off. See the documentation."
},
template='questions_json.html', help_text=show_more.__doc__, status=501)
if not should_cache and 'all' in request.GET:
return render_json(request, {
'error': "Can't get all objects, because the caching for this type of object is turned off. See the documentation."
},
template='questions_json.html', help_text=show_more.__doc__, status=501)
if to_json_kwargs is None:
to_json_kwargs = {}
time_start = time_lib()
limit = min(int(request.GET.get('limit', 10)), 100)
page = int(request.GET.get('page', 0))
try:
objs = get_fun(request, object_class)
if 'db_orderby' in request.GET:
objs = objs.order_by(('-' if 'desc' in request.GET else '') + request.GET['db_orderby'].strip('/'))
if 'all' not in request.GET and 'json_orderby' not in request.GET:
objs = objs[page * limit:(page + 1) * limit]
cache_key = 'proso_common_sql_json_%s' % hashlib.sha1((str(objs.query) + str(to_json_kwargs)).encode()).hexdigest()
cached = cache.get(cache_key)
if should_cache and cached:
list_objs = json_lib.loads(cached)
else:
list_objs = [x.to_json(**to_json_kwargs) for x in list(objs)]
if should_cache:
cache.set(cache_key, json_lib.dumps(list_objs), 60 * 60 * 24 * 30)
LOGGER.debug('loading objects in show_more view took %s seconds', (time_lib() - time_start))
json = post_process_fun(request, list_objs)
if 'json_orderby' in request.GET:
time_before_json_sort = time_lib()
json.sort(key=lambda x: (-1 if 'desc' in request.GET else 1) * x[request.GET['json_orderby']])
if 'all' not in request.GET:
json = json[page * limit:(page + 1) * limit]
LOGGER.debug('sorting objects according to JSON field took %s seconds', (time_lib() - time_before_json_sort))
return render_json(request, json, template=template, help_text=show_more.__doc__)
except EmptyResultSet:
return render_json(request, [], template=template, help_text=show_more.__doc__) | python | def show_more(request, post_process_fun, get_fun, object_class, should_cache=True, template='common_json.html', to_json_kwargs=None):
"""
Return list of objects of the given type.
GET parameters:
limit:
number of returned objects (default 10, maximum 100)
page:
current page number
filter_column:
column name used to filter the results
filter_value:
value for the specified column used to filter the results
user:
identifier of the current user
all:
return all objects available instead of paging; be aware this parameter
can be used only for objects for wich the caching is turned on
db_orderby:
database column which the result should be ordered by
json_orderby:
field of the JSON object which the result should be ordered by, it is
less effective than the ordering via db_orderby; be aware this parameter
can be used only for objects for which the caching is turned on
desc
turn on the descending order
stats:
turn on the enrichment of the objects by some statistics
html
turn on the HTML version of the API
environment
turn on the enrichment of the related environment values
"""
if not should_cache and 'json_orderby' in request.GET:
return render_json(request, {
'error': "Can't order the result according to the JSON field, because the caching for this type of object is turned off. See the documentation."
},
template='questions_json.html', help_text=show_more.__doc__, status=501)
if not should_cache and 'all' in request.GET:
return render_json(request, {
'error': "Can't get all objects, because the caching for this type of object is turned off. See the documentation."
},
template='questions_json.html', help_text=show_more.__doc__, status=501)
if to_json_kwargs is None:
to_json_kwargs = {}
time_start = time_lib()
limit = min(int(request.GET.get('limit', 10)), 100)
page = int(request.GET.get('page', 0))
try:
objs = get_fun(request, object_class)
if 'db_orderby' in request.GET:
objs = objs.order_by(('-' if 'desc' in request.GET else '') + request.GET['db_orderby'].strip('/'))
if 'all' not in request.GET and 'json_orderby' not in request.GET:
objs = objs[page * limit:(page + 1) * limit]
cache_key = 'proso_common_sql_json_%s' % hashlib.sha1((str(objs.query) + str(to_json_kwargs)).encode()).hexdigest()
cached = cache.get(cache_key)
if should_cache and cached:
list_objs = json_lib.loads(cached)
else:
list_objs = [x.to_json(**to_json_kwargs) for x in list(objs)]
if should_cache:
cache.set(cache_key, json_lib.dumps(list_objs), 60 * 60 * 24 * 30)
LOGGER.debug('loading objects in show_more view took %s seconds', (time_lib() - time_start))
json = post_process_fun(request, list_objs)
if 'json_orderby' in request.GET:
time_before_json_sort = time_lib()
json.sort(key=lambda x: (-1 if 'desc' in request.GET else 1) * x[request.GET['json_orderby']])
if 'all' not in request.GET:
json = json[page * limit:(page + 1) * limit]
LOGGER.debug('sorting objects according to JSON field took %s seconds', (time_lib() - time_before_json_sort))
return render_json(request, json, template=template, help_text=show_more.__doc__)
except EmptyResultSet:
return render_json(request, [], template=template, help_text=show_more.__doc__) | [
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number of returned objects (default 10, maximum 100)
page:
current page number
filter_column:
column name used to filter the results
filter_value:
value for the specified column used to filter the results
user:
identifier of the current user
all:
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db_orderby:
database column which the result should be ordered by
json_orderby:
field of the JSON object which the result should be ordered by, it is
less effective than the ordering via db_orderby; be aware this parameter
can be used only for objects for which the caching is turned on
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turn on the descending order
stats:
turn on the enrichment of the objects by some statistics
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turn on the HTML version of the API
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| 8278c72e498d6ef8d392cc47b48473f4ec037142 | https://github.com/adaptive-learning/proso-apps/blob/8278c72e498d6ef8d392cc47b48473f4ec037142/proso_common/views.py#L46-L118 | train |
adaptive-learning/proso-apps | proso_common/views.py | log | def log(request):
"""
Log an event from the client to the server.
POST parameters (JSON keys):
message:
description (str) of the logged event
level:
debug|info|warn|error
data:
additional data (JSON) describing the logged event
"""
if request.method == "POST":
log_dict = json_body(request.body.decode("utf-8"))
if 'message' not in log_dict:
return HttpResponseBadRequest('There is no message to log!')
levels = {
'debug': JAVASCRIPT_LOGGER.debug,
'info': JAVASCRIPT_LOGGER.info,
'warn': JAVASCRIPT_LOGGER.warn,
'error': JAVASCRIPT_LOGGER.error,
}
log_fun = JAVASCRIPT_LOGGER.info
if 'level' in log_dict:
log_fun = levels[log_dict['level']]
log_fun(log_dict['message'], extra={
'request': request,
'user': request.user.id if request.user.is_authenticated() else None,
'client_data': json_lib.dumps(log_dict.get('data', {})),
})
return HttpResponse('ok', status=201)
else:
return render_json(request, {}, template='common_log_service.html', help_text=log.__doc__) | python | def log(request):
"""
Log an event from the client to the server.
POST parameters (JSON keys):
message:
description (str) of the logged event
level:
debug|info|warn|error
data:
additional data (JSON) describing the logged event
"""
if request.method == "POST":
log_dict = json_body(request.body.decode("utf-8"))
if 'message' not in log_dict:
return HttpResponseBadRequest('There is no message to log!')
levels = {
'debug': JAVASCRIPT_LOGGER.debug,
'info': JAVASCRIPT_LOGGER.info,
'warn': JAVASCRIPT_LOGGER.warn,
'error': JAVASCRIPT_LOGGER.error,
}
log_fun = JAVASCRIPT_LOGGER.info
if 'level' in log_dict:
log_fun = levels[log_dict['level']]
log_fun(log_dict['message'], extra={
'request': request,
'user': request.user.id if request.user.is_authenticated() else None,
'client_data': json_lib.dumps(log_dict.get('data', {})),
})
return HttpResponse('ok', status=201)
else:
return render_json(request, {}, template='common_log_service.html', help_text=log.__doc__) | [
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| 8278c72e498d6ef8d392cc47b48473f4ec037142 | https://github.com/adaptive-learning/proso-apps/blob/8278c72e498d6ef8d392cc47b48473f4ec037142/proso_common/views.py#L122-L154 | train |
adaptive-learning/proso-apps | proso_common/views.py | custom_config | def custom_config(request):
"""
Save user-specific configuration property.
POST parameters (JSON keys):
app_name: application name for which the configuration property is
valid (e.g., proso_models)
key: name of the property (e.g., predictive_model.class)
value: value of the property (number, string, boolean, ...,
e.g, proso.models.prediction.PriorCurrentPredictiveModel)
condition_key (optional): name of the condition which is used to filter
the property (e.g., practice_filter)
condition_value (optional): value for the condition filtering the
property (e.g., [["context/world"],["category/state"]])
"""
if request.method == 'POST':
config_dict = json_body(request.body.decode('utf-8'))
CustomConfig.objects.try_create(
config_dict['app_name'],
config_dict['key'],
config_dict['value'],
request.user.id,
config_dict.get('condition_key') if config_dict.get('condition_key') else None,
urllib.parse.unquote(config_dict.get('condition_value')) if config_dict.get('condition_value') else None
)
return config(request)
else:
return render_json(request, {}, template='common_custom_config.html', help_text=custom_config.__doc__) | python | def custom_config(request):
"""
Save user-specific configuration property.
POST parameters (JSON keys):
app_name: application name for which the configuration property is
valid (e.g., proso_models)
key: name of the property (e.g., predictive_model.class)
value: value of the property (number, string, boolean, ...,
e.g, proso.models.prediction.PriorCurrentPredictiveModel)
condition_key (optional): name of the condition which is used to filter
the property (e.g., practice_filter)
condition_value (optional): value for the condition filtering the
property (e.g., [["context/world"],["category/state"]])
"""
if request.method == 'POST':
config_dict = json_body(request.body.decode('utf-8'))
CustomConfig.objects.try_create(
config_dict['app_name'],
config_dict['key'],
config_dict['value'],
request.user.id,
config_dict.get('condition_key') if config_dict.get('condition_key') else None,
urllib.parse.unquote(config_dict.get('condition_value')) if config_dict.get('condition_value') else None
)
return config(request)
else:
return render_json(request, {}, template='common_custom_config.html', help_text=custom_config.__doc__) | [
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value: value of the property (number, string, boolean, ...,
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| 8278c72e498d6ef8d392cc47b48473f4ec037142 | https://github.com/adaptive-learning/proso-apps/blob/8278c72e498d6ef8d392cc47b48473f4ec037142/proso_common/views.py#L158-L185 | train |
adaptive-learning/proso-apps | proso_common/views.py | languages | def languages(request):
"""
Returns languages that are available in the system.
Returns Dict: language_code -> domain
"""
return render_json(request,
settings.LANGUAGE_DOMAINS if hasattr(settings, 'LANGUAGE_DOMAINS') else
{"error": "Languages are not set. (Set LANGUAGE_DOMAINS in settings.py)"},
template='common_json.html', help_text=languages.__doc__) | python | def languages(request):
"""
Returns languages that are available in the system.
Returns Dict: language_code -> domain
"""
return render_json(request,
settings.LANGUAGE_DOMAINS if hasattr(settings, 'LANGUAGE_DOMAINS') else
{"error": "Languages are not set. (Set LANGUAGE_DOMAINS in settings.py)"},
template='common_json.html', help_text=languages.__doc__) | [
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| 8278c72e498d6ef8d392cc47b48473f4ec037142 | https://github.com/adaptive-learning/proso-apps/blob/8278c72e498d6ef8d392cc47b48473f4ec037142/proso_common/views.py#L192-L201 | train |
reillysiemens/layabout | examples/early-connection/example.py | channel_to_id | def channel_to_id(slack, channel):
""" Surely there's a better way to do this... """
channels = slack.api_call('channels.list').get('channels') or []
groups = slack.api_call('groups.list').get('groups') or []
if not channels and not groups:
raise RuntimeError("Couldn't get channels and groups.")
ids = [c['id'] for c in channels + groups if c['name'] == channel]
if not ids:
raise ValueError(f"Couldn't find #{channel}")
return ids[0] | python | def channel_to_id(slack, channel):
""" Surely there's a better way to do this... """
channels = slack.api_call('channels.list').get('channels') or []
groups = slack.api_call('groups.list').get('groups') or []
if not channels and not groups:
raise RuntimeError("Couldn't get channels and groups.")
ids = [c['id'] for c in channels + groups if c['name'] == channel]
if not ids:
raise ValueError(f"Couldn't find #{channel}")
return ids[0] | [
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| a146c47f2558e66bb51cf708d39909b93eaea7f4 | https://github.com/reillysiemens/layabout/blob/a146c47f2558e66bb51cf708d39909b93eaea7f4/examples/early-connection/example.py#L15-L28 | train |
reillysiemens/layabout | examples/early-connection/example.py | send_message | def send_message(slack):
""" Prompt for and send a message to a channel. """
channel = input('Which channel would you like to message? ')
message = input('What should the message be? ')
channel_id = channel_to_id(slack, channel)
print(f"Sending message to #{channel} (id: {channel_id})!")
slack.rtm_send_message(channel_id, message) | python | def send_message(slack):
""" Prompt for and send a message to a channel. """
channel = input('Which channel would you like to message? ')
message = input('What should the message be? ')
channel_id = channel_to_id(slack, channel)
print(f"Sending message to #{channel} (id: {channel_id})!")
slack.rtm_send_message(channel_id, message) | [
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| a146c47f2558e66bb51cf708d39909b93eaea7f4 | https://github.com/reillysiemens/layabout/blob/a146c47f2558e66bb51cf708d39909b93eaea7f4/examples/early-connection/example.py#L31-L38 | train |
truveris/py-mdstat | mdstat/device.py | parse_device | def parse_device(lines):
"""Parse all the lines of a device block.
A device block is composed of a header line with the name of the device and
at least one extra line describing the device and its status. The extra
lines have a varying format depending on the status and personality of the
device (e.g. RAID1 vs RAID5, healthy vs recovery/resync).
"""
name, status_line, device = parse_device_header(lines.pop(0))
# There are edge cases when the device list is empty and the status line is
# merged with the header line, in those cases, the status line is returned
# from parse_device_header(), the rest of the time, it's the next line.
if not status_line:
status_line = lines.pop(0)
status = parse_device_status(status_line, device["personality"])
bitmap = None
resync = None
for line in lines:
if line.startswith(" bitmap:"):
bitmap = parse_device_bitmap(line)
elif line.startswith(" ["):
resync = parse_device_resync_progress(line)
elif line.startswith(" \tresync="):
resync = parse_device_resync_standby(line)
else:
raise NotImplementedError("unknown device line: {0}".format(line))
device.update({
"status": status,
"bitmap": bitmap,
"resync": resync,
})
return (name, device) | python | def parse_device(lines):
"""Parse all the lines of a device block.
A device block is composed of a header line with the name of the device and
at least one extra line describing the device and its status. The extra
lines have a varying format depending on the status and personality of the
device (e.g. RAID1 vs RAID5, healthy vs recovery/resync).
"""
name, status_line, device = parse_device_header(lines.pop(0))
# There are edge cases when the device list is empty and the status line is
# merged with the header line, in those cases, the status line is returned
# from parse_device_header(), the rest of the time, it's the next line.
if not status_line:
status_line = lines.pop(0)
status = parse_device_status(status_line, device["personality"])
bitmap = None
resync = None
for line in lines:
if line.startswith(" bitmap:"):
bitmap = parse_device_bitmap(line)
elif line.startswith(" ["):
resync = parse_device_resync_progress(line)
elif line.startswith(" \tresync="):
resync = parse_device_resync_standby(line)
else:
raise NotImplementedError("unknown device line: {0}".format(line))
device.update({
"status": status,
"bitmap": bitmap,
"resync": resync,
})
return (name, device) | [
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| 881af99d1168694d2f38e606af377ef6cabe2297 | https://github.com/truveris/py-mdstat/blob/881af99d1168694d2f38e606af377ef6cabe2297/mdstat/device.py#L14-L51 | train |
trendels/rhino | rhino/http.py | match_etag | def match_etag(etag, header, weak=False):
"""Try to match an ETag against a header value.
If `weak` is True, uses the weak comparison function.
"""
if etag is None:
return False
m = etag_re.match(etag)
if not m:
raise ValueError("Not a well-formed ETag: '%s'" % etag)
(is_weak, etag) = m.groups()
parsed_header = parse_etag_header(header)
if parsed_header == '*':
return True
if is_weak and not weak:
return False
if weak:
return etag in [t[1] for t in parsed_header]
else:
return etag in [t[1] for t in parsed_header if not t[0]] | python | def match_etag(etag, header, weak=False):
"""Try to match an ETag against a header value.
If `weak` is True, uses the weak comparison function.
"""
if etag is None:
return False
m = etag_re.match(etag)
if not m:
raise ValueError("Not a well-formed ETag: '%s'" % etag)
(is_weak, etag) = m.groups()
parsed_header = parse_etag_header(header)
if parsed_header == '*':
return True
if is_weak and not weak:
return False
if weak:
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else:
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| Try to match an ETag against a header value.
If `weak` is True, uses the weak comparison function. | [
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| f1f0ef21b6080a2bd130b38b5bef163074c94aed | https://github.com/trendels/rhino/blob/f1f0ef21b6080a2bd130b38b5bef163074c94aed/rhino/http.py#L60-L79 | train |
trendels/rhino | rhino/http.py | datetime_to_httpdate | def datetime_to_httpdate(dt):
"""Convert datetime.datetime or Unix timestamp to HTTP date."""
if isinstance(dt, (int, float)):
return format_date_time(dt)
elif isinstance(dt, datetime):
return format_date_time(datetime_to_timestamp(dt))
else:
raise TypeError("expected datetime.datetime or timestamp (int/float),"
" got '%s'" % dt) | python | def datetime_to_httpdate(dt):
"""Convert datetime.datetime or Unix timestamp to HTTP date."""
if isinstance(dt, (int, float)):
return format_date_time(dt)
elif isinstance(dt, datetime):
return format_date_time(datetime_to_timestamp(dt))
else:
raise TypeError("expected datetime.datetime or timestamp (int/float),"
" got '%s'" % dt) | [
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| f1f0ef21b6080a2bd130b38b5bef163074c94aed | https://github.com/trendels/rhino/blob/f1f0ef21b6080a2bd130b38b5bef163074c94aed/rhino/http.py#L99-L107 | train |
trendels/rhino | rhino/http.py | timedelta_to_httpdate | def timedelta_to_httpdate(td):
"""Convert datetime.timedelta or number of seconds to HTTP date.
Returns an HTTP date in the future.
"""
if isinstance(td, (int, float)):
return format_date_time(time.time() + td)
elif isinstance(td, timedelta):
return format_date_time(time.time() + total_seconds(td))
else:
raise TypeError("expected datetime.timedelta or number of seconds"
"(int/float), got '%s'" % td) | python | def timedelta_to_httpdate(td):
"""Convert datetime.timedelta or number of seconds to HTTP date.
Returns an HTTP date in the future.
"""
if isinstance(td, (int, float)):
return format_date_time(time.time() + td)
elif isinstance(td, timedelta):
return format_date_time(time.time() + total_seconds(td))
else:
raise TypeError("expected datetime.timedelta or number of seconds"
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| f1f0ef21b6080a2bd130b38b5bef163074c94aed | https://github.com/trendels/rhino/blob/f1f0ef21b6080a2bd130b38b5bef163074c94aed/rhino/http.py#L110-L121 | train |
trendels/rhino | rhino/http.py | cache_control | def cache_control(max_age=None, private=False, public=False, s_maxage=None,
must_revalidate=False, proxy_revalidate=False, no_cache=False,
no_store=False):
"""Generate the value for a Cache-Control header.
Example:
>>> from rhino.http import cache_control as cc
>>> from datetime import timedelta
>>> cc(public=1, max_age=3600)
'public, max-age=3600'
>>> cc(public=1, max_age=timedelta(hours=1))
'public, max-age=3600'
>>> cc(private=True, no_cache=True, no_store=True)
'private, no-cache, no-store'
"""
if all([private, public]):
raise ValueError("'private' and 'public' are mutually exclusive")
if isinstance(max_age, timedelta):
max_age = int(total_seconds(max_age))
if isinstance(s_maxage, timedelta):
s_maxage = int(total_seconds(s_maxage))
directives = []
if public: directives.append('public')
if private: directives.append('private')
if max_age is not None: directives.append('max-age=%d' % max_age)
if s_maxage is not None: directives.append('s-maxage=%d' % s_maxage)
if no_cache: directives.append('no-cache')
if no_store: directives.append('no-store')
if must_revalidate: directives.append('must-revalidate')
if proxy_revalidate: directives.append('proxy-revalidate')
return ', '.join(directives) | python | def cache_control(max_age=None, private=False, public=False, s_maxage=None,
must_revalidate=False, proxy_revalidate=False, no_cache=False,
no_store=False):
"""Generate the value for a Cache-Control header.
Example:
>>> from rhino.http import cache_control as cc
>>> from datetime import timedelta
>>> cc(public=1, max_age=3600)
'public, max-age=3600'
>>> cc(public=1, max_age=timedelta(hours=1))
'public, max-age=3600'
>>> cc(private=True, no_cache=True, no_store=True)
'private, no-cache, no-store'
"""
if all([private, public]):
raise ValueError("'private' and 'public' are mutually exclusive")
if isinstance(max_age, timedelta):
max_age = int(total_seconds(max_age))
if isinstance(s_maxage, timedelta):
s_maxage = int(total_seconds(s_maxage))
directives = []
if public: directives.append('public')
if private: directives.append('private')
if max_age is not None: directives.append('max-age=%d' % max_age)
if s_maxage is not None: directives.append('s-maxage=%d' % s_maxage)
if no_cache: directives.append('no-cache')
if no_store: directives.append('no-store')
if must_revalidate: directives.append('must-revalidate')
if proxy_revalidate: directives.append('proxy-revalidate')
return ', '.join(directives) | [
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Example:
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>>> from datetime import timedelta
>>> cc(public=1, max_age=3600)
'public, max-age=3600'
>>> cc(public=1, max_age=timedelta(hours=1))
'public, max-age=3600'
>>> cc(private=True, no_cache=True, no_store=True)
'private, no-cache, no-store' | [
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| f1f0ef21b6080a2bd130b38b5bef163074c94aed | https://github.com/trendels/rhino/blob/f1f0ef21b6080a2bd130b38b5bef163074c94aed/rhino/http.py#L124-L156 | train |
chrillux/brottsplatskartan | brottsplatskartan/__init__.py | BrottsplatsKartan.get_incidents | def get_incidents(self) -> Union[list, bool]:
""" Get today's incidents. """
brotts_entries_left = True
incidents_today = []
url = self.url
while brotts_entries_left:
requests_response = requests.get(
url, params=self.parameters)
rate_limited = requests_response.headers.get('x-ratelimit-reset')
if rate_limited:
print("You have been rate limited until " +
time.strftime(
'%Y-%m-%d %H:%M:%S%z',
time.localtime(rate_limited)
))
return False
requests_response = requests_response.json()
incidents = requests_response.get("data")
if not incidents:
break
datetime_today = datetime.date.today()
datetime_today_as_time = time.strptime(
str(datetime_today), "%Y-%m-%d"
)
today_date_ymd = self._get_datetime_as_ymd(datetime_today_as_time)
for incident in incidents:
incident_pubdate = incident["pubdate_iso8601"]
incident_date = time.strptime(
incident_pubdate, "%Y-%m-%dT%H:%M:%S%z"
)
incident_date_ymd = self._get_datetime_as_ymd(incident_date)
if today_date_ymd == incident_date_ymd:
incidents_today.append(incident)
else:
brotts_entries_left = False
break
if requests_response.get("links"):
url = requests_response["links"]["next_page_url"]
else:
break
return incidents_today | python | def get_incidents(self) -> Union[list, bool]:
""" Get today's incidents. """
brotts_entries_left = True
incidents_today = []
url = self.url
while brotts_entries_left:
requests_response = requests.get(
url, params=self.parameters)
rate_limited = requests_response.headers.get('x-ratelimit-reset')
if rate_limited:
print("You have been rate limited until " +
time.strftime(
'%Y-%m-%d %H:%M:%S%z',
time.localtime(rate_limited)
))
return False
requests_response = requests_response.json()
incidents = requests_response.get("data")
if not incidents:
break
datetime_today = datetime.date.today()
datetime_today_as_time = time.strptime(
str(datetime_today), "%Y-%m-%d"
)
today_date_ymd = self._get_datetime_as_ymd(datetime_today_as_time)
for incident in incidents:
incident_pubdate = incident["pubdate_iso8601"]
incident_date = time.strptime(
incident_pubdate, "%Y-%m-%dT%H:%M:%S%z"
)
incident_date_ymd = self._get_datetime_as_ymd(incident_date)
if today_date_ymd == incident_date_ymd:
incidents_today.append(incident)
else:
brotts_entries_left = False
break
if requests_response.get("links"):
url = requests_response["links"]["next_page_url"]
else:
break
return incidents_today | [
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| f38df4debd1799ddb384e467999d601cffbe9d94 | https://github.com/chrillux/brottsplatskartan/blob/f38df4debd1799ddb384e467999d601cffbe9d94/brottsplatskartan/__init__.py#L42-L92 | train |
TheGhouls/oct | oct/utilities/newproject.py | from_template | def from_template(args):
"""Create a new oct project from existing template
:param Namespace args: command line arguments
"""
project_name = args.name
template = args.template
with tarfile.open(template) as tar:
prefix = os.path.commonprefix(tar.getnames())
check_template(tar.getnames(), prefix)
tar.extractall(project_name, members=get_members(tar, prefix)) | python | def from_template(args):
"""Create a new oct project from existing template
:param Namespace args: command line arguments
"""
project_name = args.name
template = args.template
with tarfile.open(template) as tar:
prefix = os.path.commonprefix(tar.getnames())
check_template(tar.getnames(), prefix)
tar.extractall(project_name, members=get_members(tar, prefix)) | [
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| 7e9bddeb3b8495a26442b1c86744e9fb187fe88f | https://github.com/TheGhouls/oct/blob/7e9bddeb3b8495a26442b1c86744e9fb187fe88f/oct/utilities/newproject.py#L39-L50 | train |
TheGhouls/oct | oct/utilities/newproject.py | from_oct | def from_oct(args):
"""Create a new oct project
:param Namespace args: the command line arguments
"""
project_name = args.name
env = Environment(loader=PackageLoader('oct.utilities', 'templates'))
config_content = env.get_template('configuration/config.json').render(script_name='v_user.py')
script_content = env.get_template('scripts/v_user.j2').render()
try:
os.makedirs(project_name)
os.makedirs(os.path.join(project_name, 'test_scripts'))
os.makedirs(os.path.join(project_name, 'templates'))
os.makedirs(os.path.join(project_name, 'templates', 'img'))
shutil.copytree(os.path.join(BASE_DIR, 'templates', 'css'),
os.path.join(project_name, 'templates', 'css'))
shutil.copytree(os.path.join(BASE_DIR, 'templates', 'javascript'),
os.path.join(project_name, 'templates', 'scripts'))
shutil.copytree(os.path.join(BASE_DIR, 'templates', 'fonts'),
os.path.join(project_name, 'templates', 'fonts'))
shutil.copy(os.path.join(BASE_DIR, 'templates', 'html', 'report.html'),
os.path.join(project_name, 'templates'))
except OSError:
print('ERROR: can not create directory for %r' % project_name, file=sys.stderr)
raise
with open(os.path.join(project_name, 'config.json'), 'w') as f:
f.write(config_content)
with open(os.path.join(project_name, 'test_scripts', 'v_user.py'), 'w') as f:
f.write(script_content) | python | def from_oct(args):
"""Create a new oct project
:param Namespace args: the command line arguments
"""
project_name = args.name
env = Environment(loader=PackageLoader('oct.utilities', 'templates'))
config_content = env.get_template('configuration/config.json').render(script_name='v_user.py')
script_content = env.get_template('scripts/v_user.j2').render()
try:
os.makedirs(project_name)
os.makedirs(os.path.join(project_name, 'test_scripts'))
os.makedirs(os.path.join(project_name, 'templates'))
os.makedirs(os.path.join(project_name, 'templates', 'img'))
shutil.copytree(os.path.join(BASE_DIR, 'templates', 'css'),
os.path.join(project_name, 'templates', 'css'))
shutil.copytree(os.path.join(BASE_DIR, 'templates', 'javascript'),
os.path.join(project_name, 'templates', 'scripts'))
shutil.copytree(os.path.join(BASE_DIR, 'templates', 'fonts'),
os.path.join(project_name, 'templates', 'fonts'))
shutil.copy(os.path.join(BASE_DIR, 'templates', 'html', 'report.html'),
os.path.join(project_name, 'templates'))
except OSError:
print('ERROR: can not create directory for %r' % project_name, file=sys.stderr)
raise
with open(os.path.join(project_name, 'config.json'), 'w') as f:
f.write(config_content)
with open(os.path.join(project_name, 'test_scripts', 'v_user.py'), 'w') as f:
f.write(script_content) | [
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:param Namespace args: the command line arguments | [
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| 7e9bddeb3b8495a26442b1c86744e9fb187fe88f | https://github.com/TheGhouls/oct/blob/7e9bddeb3b8495a26442b1c86744e9fb187fe88f/oct/utilities/newproject.py#L53-L85 | train |
clement-alexandre/TotemBionet | totembionet/src/resource_table/resource_table_with_model.py | ResourceTableWithModel.as_data_frame | def as_data_frame(self) -> pandas.DataFrame:
""" Create a panda DataFrame representation of the resource table. """
header_gene = {}
header_multiplex = {}
headr_transitions = {}
for gene in self.influence_graph.genes:
header_gene[gene] = repr(gene)
header_multiplex[gene] = f"active multiplex on {gene!r}"
headr_transitions[gene] = f"K_{gene!r}"
columns = defaultdict(list)
for state in self.table.keys():
for gene in self.influence_graph.genes:
columns[header_gene[gene]].append(state[gene])
columns[header_multiplex[gene]].append(self._repr_multiplexes(gene, state))
columns[headr_transitions[gene]].append(self._repr_transition(gene, state))
header = list(header_gene.values()) + list(header_multiplex.values()) + list(headr_transitions.values())
return pandas.DataFrame(columns, columns=header) | python | def as_data_frame(self) -> pandas.DataFrame:
""" Create a panda DataFrame representation of the resource table. """
header_gene = {}
header_multiplex = {}
headr_transitions = {}
for gene in self.influence_graph.genes:
header_gene[gene] = repr(gene)
header_multiplex[gene] = f"active multiplex on {gene!r}"
headr_transitions[gene] = f"K_{gene!r}"
columns = defaultdict(list)
for state in self.table.keys():
for gene in self.influence_graph.genes:
columns[header_gene[gene]].append(state[gene])
columns[header_multiplex[gene]].append(self._repr_multiplexes(gene, state))
columns[headr_transitions[gene]].append(self._repr_transition(gene, state))
header = list(header_gene.values()) + list(header_multiplex.values()) + list(headr_transitions.values())
return pandas.DataFrame(columns, columns=header) | [
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| f37a2f9358c1ce49f21c4a868b904da5dcd4614f | https://github.com/clement-alexandre/TotemBionet/blob/f37a2f9358c1ce49f21c4a868b904da5dcd4614f/totembionet/src/resource_table/resource_table_with_model.py#L25-L43 | train |
assamite/creamas | creamas/examples/spiro/spiro_agent_mp.py | SpiroAgent.create | def create(self, r, r_, R=200):
'''Create new spirograph image with given arguments. Returned image is
scaled to agent's preferred image size.
'''
x, y = give_dots(R, r, r_, spins=20)
xy = np.array([x, y]).T
xy = np.array(np.around(xy), dtype=np.int64)
xy = xy[(xy[:, 0] >= -250) & (xy[:, 1] >= -250) &
(xy[:, 0] < 250) & (xy[:, 1] < 250)]
xy = xy + 250
img = np.ones([500, 500], dtype=np.uint8)
img[:] = 255
img[xy[:, 0], xy[:, 1]] = 0
img = misc.imresize(img, [self.img_size, self.img_size])
fimg = img / 255.0
return fimg | python | def create(self, r, r_, R=200):
'''Create new spirograph image with given arguments. Returned image is
scaled to agent's preferred image size.
'''
x, y = give_dots(R, r, r_, spins=20)
xy = np.array([x, y]).T
xy = np.array(np.around(xy), dtype=np.int64)
xy = xy[(xy[:, 0] >= -250) & (xy[:, 1] >= -250) &
(xy[:, 0] < 250) & (xy[:, 1] < 250)]
xy = xy + 250
img = np.ones([500, 500], dtype=np.uint8)
img[:] = 255
img[xy[:, 0], xy[:, 1]] = 0
img = misc.imresize(img, [self.img_size, self.img_size])
fimg = img / 255.0
return fimg | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/examples/spiro/spiro_agent_mp.py#L140-L155 | train |
assamite/creamas | creamas/examples/spiro/spiro_agent_mp.py | SpiroAgent.hedonic_value | def hedonic_value(self, novelty):
'''Given the agent's desired novelty, how good the novelty value is.
Not used if *desired_novelty*=-1
'''
lmax = gaus_pdf(self.desired_novelty, self.desired_novelty, 4)
pdf = gaus_pdf(novelty, self.desired_novelty, 4)
return pdf / lmax | python | def hedonic_value(self, novelty):
'''Given the agent's desired novelty, how good the novelty value is.
Not used if *desired_novelty*=-1
'''
lmax = gaus_pdf(self.desired_novelty, self.desired_novelty, 4)
pdf = gaus_pdf(novelty, self.desired_novelty, 4)
return pdf / lmax | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/examples/spiro/spiro_agent_mp.py#L170-L177 | train |
assamite/creamas | creamas/examples/spiro/spiro_agent_mp.py | SpiroAgent.evaluate | def evaluate(self, artifact):
'''Evaluate the artifact with respect to the agents short term memory.
Returns value in [0, 1].
'''
if self.desired_novelty > 0:
return self.hedonic_value(self.novelty(artifact.obj))
return self.novelty(artifact.obj) / self.img_size, None | python | def evaluate(self, artifact):
'''Evaluate the artifact with respect to the agents short term memory.
Returns value in [0, 1].
'''
if self.desired_novelty > 0:
return self.hedonic_value(self.novelty(artifact.obj))
return self.novelty(artifact.obj) / self.img_size, None | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/examples/spiro/spiro_agent_mp.py#L186-L193 | train |
assamite/creamas | creamas/examples/spiro/spiro_agent_mp.py | SpiroAgent.learn | def learn(self, spiro, iterations=1):
'''Train short term memory with given spirograph.
:param spiro:
:py:class:`SpiroArtifact` object
'''
for i in range(iterations):
self.stmem.train_cycle(spiro.obj.flatten()) | python | def learn(self, spiro, iterations=1):
'''Train short term memory with given spirograph.
:param spiro:
:py:class:`SpiroArtifact` object
'''
for i in range(iterations):
self.stmem.train_cycle(spiro.obj.flatten()) | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/examples/spiro/spiro_agent_mp.py#L292-L299 | train |
assamite/creamas | creamas/examples/spiro/spiro_agent_mp.py | SpiroAgent.plot_places | def plot_places(self):
'''Plot places where the agent has been and generated a spirograph.
'''
from matplotlib import pyplot as plt
fig, ax = plt.subplots()
x = []
y = []
if len(self.arg_history) > 1:
xs = []
ys = []
for p in self.arg_history:
xs.append(p[0])
ys.append(p[1])
ax.plot(xs, ys, color=(0.0, 0.0, 1.0, 0.1))
for a in self.A:
if a.self_criticism == 'pass':
args = a.framings[a.creator]['args']
x.append(args[0])
y.append(args[1])
sc = ax.scatter(x, y, marker="x", color='red')
ax.set_xlim([-200, 200])
ax.set_ylim([-200, 200])
agent_vars = "{}_{}_{}{}_last={}_stmem=list{}_veto={}_sc={}_jump={}_sw={}_mr={}_maxN".format(
self.name, self.age, self.env_learning_method, self.env_learning_amount, self.env_learn_on_add,
self.stmem.length, self._novelty_threshold, self._own_threshold,
self.jump, self.search_width, self.move_radius)
if self.logger is not None:
imname = os.path.join(self.logger.folder, '{}.png'.format(agent_vars))
plt.savefig(imname)
plt.close()
fname = os.path.join(self.logger.folder, '{}.txt'.format(agent_vars))
with open(fname, "w") as f:
f.write(" ".join([str(e) for e in xs]))
f.write("\n")
f.write(" ".join([str(e) for e in ys]))
f.write("\n")
f.write(" ".join([str(e) for e in x]))
f.write("\n")
f.write(" ".join([str(e) for e in y]))
f.write("\n")
else:
plt.show() | python | def plot_places(self):
'''Plot places where the agent has been and generated a spirograph.
'''
from matplotlib import pyplot as plt
fig, ax = plt.subplots()
x = []
y = []
if len(self.arg_history) > 1:
xs = []
ys = []
for p in self.arg_history:
xs.append(p[0])
ys.append(p[1])
ax.plot(xs, ys, color=(0.0, 0.0, 1.0, 0.1))
for a in self.A:
if a.self_criticism == 'pass':
args = a.framings[a.creator]['args']
x.append(args[0])
y.append(args[1])
sc = ax.scatter(x, y, marker="x", color='red')
ax.set_xlim([-200, 200])
ax.set_ylim([-200, 200])
agent_vars = "{}_{}_{}{}_last={}_stmem=list{}_veto={}_sc={}_jump={}_sw={}_mr={}_maxN".format(
self.name, self.age, self.env_learning_method, self.env_learning_amount, self.env_learn_on_add,
self.stmem.length, self._novelty_threshold, self._own_threshold,
self.jump, self.search_width, self.move_radius)
if self.logger is not None:
imname = os.path.join(self.logger.folder, '{}.png'.format(agent_vars))
plt.savefig(imname)
plt.close()
fname = os.path.join(self.logger.folder, '{}.txt'.format(agent_vars))
with open(fname, "w") as f:
f.write(" ".join([str(e) for e in xs]))
f.write("\n")
f.write(" ".join([str(e) for e in ys]))
f.write("\n")
f.write(" ".join([str(e) for e in x]))
f.write("\n")
f.write(" ".join([str(e) for e in y]))
f.write("\n")
else:
plt.show() | [
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| Plot places where the agent has been and generated a spirograph. | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/examples/spiro/spiro_agent_mp.py#L398-L445 | train |
assamite/creamas | creamas/examples/spiro/spiro_agent_mp.py | SpiroMultiEnvironment.destroy | def destroy(self, folder=None):
'''Destroy the environment and the subprocesses.
'''
ameans = [(0, 0, 0) for _ in range(3)]
ret = [self.save_info(folder, ameans)]
aiomas.run(until=self.stop_slaves(folder))
# Close and join the process pool nicely.
self._pool.close()
self._pool.terminate()
self._pool.join()
self._env.shutdown()
return ret | python | def destroy(self, folder=None):
'''Destroy the environment and the subprocesses.
'''
ameans = [(0, 0, 0) for _ in range(3)]
ret = [self.save_info(folder, ameans)]
aiomas.run(until=self.stop_slaves(folder))
# Close and join the process pool nicely.
self._pool.close()
self._pool.terminate()
self._pool.join()
self._env.shutdown()
return ret | [
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| 54dc3e31c97a3f938e58272f8ab80b6bcafeff58 | https://github.com/assamite/creamas/blob/54dc3e31c97a3f938e58272f8ab80b6bcafeff58/creamas/examples/spiro/spiro_agent_mp.py#L704-L715 | train |
Kortemme-Lab/klab | klab/bio/basics.py | Sequence.add | def add(self, r):
'''Takes an id and a Residue r and adds them to the Sequence.'''
id = r.get_residue_id()
if self.order:
last_id = self.order[-1]
# KAB - allow for multiresidue noncanonicals
if id in self.order:
raise colortext.Exception('Warning: using code to "allow for multiresidue noncanonicals" - check this case manually.')
id = '%s.%d'%(str(id),self.special_insertion_count)
self.special_insertion_count += 1
assert(r.Chain == self.sequence[last_id].Chain)
assert(r.residue_type == self.sequence[last_id].residue_type)
self.order.append(id)
self.sequence[id] = r | python | def add(self, r):
'''Takes an id and a Residue r and adds them to the Sequence.'''
id = r.get_residue_id()
if self.order:
last_id = self.order[-1]
# KAB - allow for multiresidue noncanonicals
if id in self.order:
raise colortext.Exception('Warning: using code to "allow for multiresidue noncanonicals" - check this case manually.')
id = '%s.%d'%(str(id),self.special_insertion_count)
self.special_insertion_count += 1
assert(r.Chain == self.sequence[last_id].Chain)
assert(r.residue_type == self.sequence[last_id].residue_type)
self.order.append(id)
self.sequence[id] = r | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/basics.py#L381-L396 | train |
Kortemme-Lab/klab | klab/bio/basics.py | Sequence.set_type | def set_type(self, sequence_type):
'''Set the type of a Sequence if it has not been set.'''
if not(self.sequence_type):
for id, r in self.sequence.iteritems():
assert(r.residue_type == None)
r.residue_type = sequence_type
self.sequence_type = sequence_type | python | def set_type(self, sequence_type):
'''Set the type of a Sequence if it has not been set.'''
if not(self.sequence_type):
for id, r in self.sequence.iteritems():
assert(r.residue_type == None)
r.residue_type = sequence_type
self.sequence_type = sequence_type | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/basics.py#L398-L404 | train |
Kortemme-Lab/klab | klab/bio/basics.py | Sequence.from_sequence | def from_sequence(chain, list_of_residues, sequence_type = None):
'''Takes in a chain identifier and protein sequence and returns a Sequence object of Residues, indexed from 1.'''
s = Sequence(sequence_type)
count = 1
for ResidueAA in list_of_residues:
s.add(Residue(chain, count, ResidueAA, sequence_type))
count += 1
return s | python | def from_sequence(chain, list_of_residues, sequence_type = None):
'''Takes in a chain identifier and protein sequence and returns a Sequence object of Residues, indexed from 1.'''
s = Sequence(sequence_type)
count = 1
for ResidueAA in list_of_residues:
s.add(Residue(chain, count, ResidueAA, sequence_type))
count += 1
return s | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/basics.py#L413-L420 | train |
Kortemme-Lab/klab | klab/bio/basics.py | SequenceMap.substitution_scores_match | def substitution_scores_match(self, other):
'''Check to make sure that the substitution scores agree. If one map has a null score and the other has a non-null score, we trust the other's score and vice versa.'''
overlap = set(self.substitution_scores.keys()).intersection(set(other.substitution_scores.keys()))
for k in overlap:
if not(self.substitution_scores[k] == None or other.substitution_scores[k] == None):
if self.substitution_scores[k] != other.substitution_scores[k]:
return False
return True | python | def substitution_scores_match(self, other):
'''Check to make sure that the substitution scores agree. If one map has a null score and the other has a non-null score, we trust the other's score and vice versa.'''
overlap = set(self.substitution_scores.keys()).intersection(set(other.substitution_scores.keys()))
for k in overlap:
if not(self.substitution_scores[k] == None or other.substitution_scores[k] == None):
if self.substitution_scores[k] != other.substitution_scores[k]:
return False
return True | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/basics.py#L465-L472 | train |
Kortemme-Lab/klab | klab/bio/basics.py | ElementCounter.merge | def merge(self, other):
'''Merge two element counters. For all elements, we take the max count from both counters.'''
our_element_frequencies = self.items
their_element_frequencies = other.items
for element_name, freq in sorted(our_element_frequencies.iteritems()):
our_element_frequencies[element_name] = max(our_element_frequencies.get(element_name, 0), their_element_frequencies.get(element_name, 0))
for element_name, freq in sorted(their_element_frequencies.iteritems()):
if element_name not in our_element_frequencies:
our_element_frequencies[element_name] = their_element_frequencies[element_name] | python | def merge(self, other):
'''Merge two element counters. For all elements, we take the max count from both counters.'''
our_element_frequencies = self.items
their_element_frequencies = other.items
for element_name, freq in sorted(our_element_frequencies.iteritems()):
our_element_frequencies[element_name] = max(our_element_frequencies.get(element_name, 0), their_element_frequencies.get(element_name, 0))
for element_name, freq in sorted(their_element_frequencies.iteritems()):
if element_name not in our_element_frequencies:
our_element_frequencies[element_name] = their_element_frequencies[element_name] | [
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| 6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b | https://github.com/Kortemme-Lab/klab/blob/6d410ad08f1bd9f7cbbb28d7d946e94fbaaa2b6b/klab/bio/basics.py#L721-L729 | train |
gamechanger/avro_codec | avro_codec/__init__.py | AvroCodec.dump | def dump(self, obj, fp):
"""
Serializes obj as an avro-format byte stream to the provided
fp file-like object stream.
"""
if not validate(obj, self._raw_schema):
raise AvroTypeException(self._avro_schema, obj)
fastavro_write_data(fp, obj, self._raw_schema) | python | def dump(self, obj, fp):
"""
Serializes obj as an avro-format byte stream to the provided
fp file-like object stream.
"""
if not validate(obj, self._raw_schema):
raise AvroTypeException(self._avro_schema, obj)
fastavro_write_data(fp, obj, self._raw_schema) | [
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| 57468bee8972a26b31b16a3437b3eeaa5ace2af6 | https://github.com/gamechanger/avro_codec/blob/57468bee8972a26b31b16a3437b3eeaa5ace2af6/avro_codec/__init__.py#L14-L21 | train |
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