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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.get_rosetta_sequence_to_atom_json_map | def get_rosetta_sequence_to_atom_json_map(self):
'''Returns the mapping from Rosetta residue IDs to PDB ATOM residue IDs in JSON format.'''
import json
if not self.rosetta_to_atom_sequence_maps and self.rosetta_sequences:
raise Exception('The PDB to Rosetta mapping has not been deter... | python | def get_rosetta_sequence_to_atom_json_map(self):
'''Returns the mapping from Rosetta residue IDs to PDB ATOM residue IDs in JSON format.'''
import json
if not self.rosetta_to_atom_sequence_maps and self.rosetta_sequences:
raise Exception('The PDB to Rosetta mapping has not been deter... | [
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.assert_wildtype_matches | def assert_wildtype_matches(self, mutation):
'''Check that the wildtype of the Mutation object matches the PDB sequence.'''
readwt = self.getAminoAcid(self.getAtomLine(mutation.Chain, mutation.ResidueID))
assert(mutation.WildTypeAA == residue_type_3to1_map[readwt]) | python | def assert_wildtype_matches(self, mutation):
'''Check that the wildtype of the Mutation object matches the PDB sequence.'''
readwt = self.getAminoAcid(self.getAtomLine(mutation.Chain, mutation.ResidueID))
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.get_B_factors | def get_B_factors(self, force = False):
'''This reads in all ATOM lines and compute the mean and standard deviation of each
residue's B-factors. It returns a table of the mean and standard deviation per
residue as well as the mean and standard deviation over all residues with each
... | python | def get_B_factors(self, force = False):
'''This reads in all ATOM lines and compute the mean and standard deviation of each
residue's B-factors. It returns a table of the mean and standard deviation per
residue as well as the mean and standard deviation over all residues with each
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.validate_mutations | def validate_mutations(self, mutations):
'''This function has been refactored to use the SimpleMutation class.
The parameter is a list of Mutation objects. The function has no return value but raises a PDBValidationException
if the wildtype in the Mutation m does not match the residue type... | python | def validate_mutations(self, mutations):
'''This function has been refactored to use the SimpleMutation class.
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.fix_chain_id | def fix_chain_id(self):
"""fill in missing chain identifier"""
for i in xrange(len(self.lines)):
line = self.lines[i]
if line.startswith("ATOM") and line[21] == ' ':
self.lines[i] = line[:21] + 'A' + line[22:] | python | def fix_chain_id(self):
"""fill in missing chain identifier"""
for i in xrange(len(self.lines)):
line = self.lines[i]
if line.startswith("ATOM") and line[21] == ' ':
self.lines[i] = line[:21] + 'A' + line[22:] | [
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.getAtomLine | def getAtomLine(self, chain, resid):
'''This function assumes that all lines are ATOM or HETATM lines.
resid should have the proper PDB format i.e. an integer left-padded
to length 4 followed by the insertion code which may be a blank space.'''
for line in self.lines:
f... | python | def getAtomLine(self, chain, resid):
'''This function assumes that all lines are ATOM or HETATM lines.
resid should have the proper PDB format i.e. an integer left-padded
to length 4 followed by the insertion code which may be a blank space.'''
for line in self.lines:
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.getAtomLinesForResidueInRosettaStructure | def getAtomLinesForResidueInRosettaStructure(self, resid):
'''We assume a Rosetta-generated structure where residues are uniquely identified by number.'''
lines = [line for line in self.lines if line[0:4] == "ATOM" and resid == int(line[22:27])]
if not lines:
#print('Failed searching... | python | def getAtomLinesForResidueInRosettaStructure(self, resid):
'''We assume a Rosetta-generated structure where residues are uniquely identified by number.'''
lines = [line for line in self.lines if line[0:4] == "ATOM" and resid == int(line[22:27])]
if not lines:
#print('Failed searching... | [
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.stripForDDG | def stripForDDG(self, chains = True, keepHETATM = False, numberOfModels = None, raise_exception = True):
'''Strips a PDB to ATOM lines. If keepHETATM is True then also retain HETATM lines.
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In the latter case... | python | def stripForDDG(self, chains = True, keepHETATM = False, numberOfModels = None, raise_exception = True):
'''Strips a PDB to ATOM lines. If keepHETATM is True then also retain HETATM lines.
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.CheckForPresenceOf | def CheckForPresenceOf(self, reslist):
'''This checks whether residues in reslist exist in the ATOM lines.
It returns a list of the residues in reslist which did exist.'''
if type(reslist) == type(""):
reslist = [reslist]
foundRes = {}
for line in self.lines:
... | python | def CheckForPresenceOf(self, reslist):
'''This checks whether residues in reslist exist in the ATOM lines.
It returns a list of the residues in reslist which did exist.'''
if type(reslist) == type(""):
reslist = [reslist]
foundRes = {}
for line in self.lines:
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.fix_residue_numbering | def fix_residue_numbering(self):
"""this function renumbers the res ids in order to avoid strange behaviour of Rosetta"""
resid_list = self.aa_resids()
resid_set = set(resid_list)
resid_lst1 = list(resid_set)
resid_lst1.sort()
map_res_id = {}
x = 1
old_... | python | def fix_residue_numbering(self):
"""this function renumbers the res ids in order to avoid strange behaviour of Rosetta"""
resid_list = self.aa_resids()
resid_set = set(resid_list)
resid_lst1 = list(resid_set)
resid_lst1.sort()
map_res_id = {}
x = 1
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.neighbors2 | def neighbors2(self, distance, chain_residue, atom = None, resid_list = None):
#atom = " CA "
'''this one is more precise since it uses the chain identifier also'''
if atom == None: # consider all atoms
lines = [line for line in self.atomlines(resid_list) if line[17:20] in allo... | python | def neighbors2(self, distance, chain_residue, atom = None, resid_list = None):
#atom = " CA "
'''this one is more precise since it uses the chain identifier also'''
if atom == None: # consider all atoms
lines = [line for line in self.atomlines(resid_list) if line[17:20] in allo... | [
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Kortemme-Lab/klab | klab/bio/pdb.py | PDB.extract_xyz_matrix_from_chain | def extract_xyz_matrix_from_chain(self, chain_id, atoms_of_interest = []):
'''Create a pandas coordinates dataframe from the lines in the specified chain.'''
chains = [l[21] for l in self.structure_lines if len(l) > 21]
chain_lines = [l for l in self.structure_lines if len(l) > 21 and l[21] == c... | python | def extract_xyz_matrix_from_chain(self, chain_id, atoms_of_interest = []):
'''Create a pandas coordinates dataframe from the lines in the specified chain.'''
chains = [l[21] for l in self.structure_lines if len(l) > 21]
chain_lines = [l for l in self.structure_lines if len(l) > 21 and l[21] == c... | [
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cozy/python_cozy_management | cozy_management/couchdb.py | create_token_file | def create_token_file(username=id_generator(), password=id_generator()):
'''
Store the admins password for further retrieve
'''
cozy_ds_uid = helpers.get_uid('cozy-data-system')
if not os.path.isfile(LOGIN_FILENAME):
with open(LOGIN_FILENAME, 'w+') as token_file:
token_file.... | python | def create_token_file(username=id_generator(), password=id_generator()):
'''
Store the admins password for further retrieve
'''
cozy_ds_uid = helpers.get_uid('cozy-data-system')
if not os.path.isfile(LOGIN_FILENAME):
with open(LOGIN_FILENAME, 'w+') as token_file:
token_file.... | [
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cozy/python_cozy_management | cozy_management/couchdb.py | get_admin | def get_admin():
'''
Return the actual admin from token file
'''
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return old_login, old_password
else:
return None,... | python | def get_admin():
'''
Return the actual admin from token file
'''
if os.path.isfile(LOGIN_FILENAME):
with open(LOGIN_FILENAME, 'r') as token_file:
old_login, old_password = token_file.read().splitlines()[:2]
return old_login, old_password
else:
return None,... | [
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cozy/python_cozy_management | cozy_management/couchdb.py | curl_couchdb | def curl_couchdb(url, method='GET', base_url=BASE_URL, data=None):
'''
Launch a curl on CouchDB instance
'''
(username, password) = get_admin()
if username is None:
auth = None
else:
auth = (username, password)
if method == 'PUT':
req = requests.put('{}{}'.format... | python | def curl_couchdb(url, method='GET', base_url=BASE_URL, data=None):
'''
Launch a curl on CouchDB instance
'''
(username, password) = get_admin()
if username is None:
auth = None
else:
auth = (username, password)
if method == 'PUT':
req = requests.put('{}{}'.format... | [
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cozy/python_cozy_management | cozy_management/couchdb.py | get_couchdb_admins | def get_couchdb_admins():
'''
Return the actual CouchDB admins
'''
user_list = []
req = curl_couchdb('/_config/admins/')
for user in req.json().keys():
user_list.append(user)
return user_list | python | def get_couchdb_admins():
'''
Return the actual CouchDB admins
'''
user_list = []
req = curl_couchdb('/_config/admins/')
for user in req.json().keys():
user_list.append(user)
return user_list | [
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cozy/python_cozy_management | cozy_management/couchdb.py | create_couchdb_admin | def create_couchdb_admin(username, password):
'''
Create a CouchDB user
'''
curl_couchdb('/_config/admins/{}'.format(username),
method='PUT',
data='"{}"'.format(password)) | python | def create_couchdb_admin(username, password):
'''
Create a CouchDB user
'''
curl_couchdb('/_config/admins/{}'.format(username),
method='PUT',
data='"{}"'.format(password)) | [
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cozy/python_cozy_management | cozy_management/couchdb.py | is_cozy_registered | def is_cozy_registered():
'''
Check if a Cozy is registered
'''
req = curl_couchdb('/cozy/_design/user/_view/all')
users = req.json()['rows']
if len(users) > 0:
return True
else:
return False | python | def is_cozy_registered():
'''
Check if a Cozy is registered
'''
req = curl_couchdb('/cozy/_design/user/_view/all')
users = req.json()['rows']
if len(users) > 0:
return True
else:
return False | [
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cozy/python_cozy_management | cozy_management/couchdb.py | unregister_cozy | def unregister_cozy():
'''
Unregister a cozy
'''
req = curl_couchdb('/cozy/_design/user/_view/all')
users = req.json()['rows']
if len(users) > 0:
user = users[0]['value']
user_id = user['_id']
user_rev = user['_rev']
print 'Delete cozy user: {}'.format(user_... | python | def unregister_cozy():
'''
Unregister a cozy
'''
req = curl_couchdb('/cozy/_design/user/_view/all')
users = req.json()['rows']
if len(users) > 0:
user = users[0]['value']
user_id = user['_id']
user_rev = user['_rev']
print 'Delete cozy user: {}'.format(user_... | [
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cozy/python_cozy_management | cozy_management/couchdb.py | delete_all_couchdb_admins | def delete_all_couchdb_admins():
'''
Delete all CouchDB users
'''
# Get current cozy token
username = get_admin()[0]
# Get CouchDB admin list
admins = get_couchdb_admins()
# Delete all admin user excluding current
for admin in admins:
if admin == username:
pr... | python | def delete_all_couchdb_admins():
'''
Delete all CouchDB users
'''
# Get current cozy token
username = get_admin()[0]
# Get CouchDB admin list
admins = get_couchdb_admins()
# Delete all admin user excluding current
for admin in admins:
if admin == username:
pr... | [
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cozy/python_cozy_management | cozy_management/couchdb.py | delete_token | def delete_token():
'''
Delete current token, file & CouchDB admin user
'''
username = get_admin()[0]
admins = get_couchdb_admins()
# Delete current admin if exist
if username in admins:
print 'I delete {} CouchDB user'.format(username)
delete_couchdb_admin(username)
... | python | def delete_token():
'''
Delete current token, file & CouchDB admin user
'''
username = get_admin()[0]
admins = get_couchdb_admins()
# Delete current admin if exist
if username in admins:
print 'I delete {} CouchDB user'.format(username)
delete_couchdb_admin(username)
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cozy/python_cozy_management | cozy_management/couchdb.py | create_token | def create_token():
'''
Create token file & create user
'''
username = id_generator()
password = id_generator()
create_couchdb_admin(username, password)
create_token_file(username, password)
return 'Token {} created'.format(username) | python | def create_token():
'''
Create token file & create user
'''
username = id_generator()
password = id_generator()
create_couchdb_admin(username, password)
create_token_file(username, password)
return 'Token {} created'.format(username) | [
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cozy/python_cozy_management | cozy_management/couchdb.py | ping | def ping():
'''
Ping CozyDB with existing credentials
'''
try:
curl_couchdb('/cozy/')
ping = True
except requests.exceptions.ConnectionError, error:
print error
ping = False
return ping | python | def ping():
'''
Ping CozyDB with existing credentials
'''
try:
curl_couchdb('/cozy/')
ping = True
except requests.exceptions.ConnectionError, error:
print error
ping = False
return ping | [
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cozy/python_cozy_management | cozy_management/couchdb.py | get_cozy_param | def get_cozy_param(param):
'''
Get parameter in Cozy configuration
'''
try:
req = curl_couchdb('/cozy/_design/cozyinstance/_view/all')
rows = req.json()['rows']
if len(rows) == 0:
return None
else:
return rows[0].get('value', {}).get(param, Non... | python | def get_cozy_param(param):
'''
Get parameter in Cozy configuration
'''
try:
req = curl_couchdb('/cozy/_design/cozyinstance/_view/all')
rows = req.json()['rows']
if len(rows) == 0:
return None
else:
return rows[0].get('value', {}).get(param, Non... | [
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adaptive-learning/proso-apps | proso/conversion.py | str2type | def str2type(value):
"""
Take a string and convert it to a value of proper type.
.. testsetup::
from proso.coversion import str2type
.. doctest::
>>> print(str2type("[1, 2, 3]")
[1, 2, 3]
"""
if not isinstance(value, str):
return value
... | python | def str2type(value):
"""
Take a string and convert it to a value of proper type.
.. testsetup::
from proso.coversion import str2type
.. doctest::
>>> print(str2type("[1, 2, 3]")
[1, 2, 3]
"""
if not isinstance(value, str):
return value
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Alveo/pyalveo | pyalveo/pyalveo.py | OAuth2.get_authorisation_url | def get_authorisation_url(self, reset=False):
""" Initialises the OAuth2 Process by asking the auth server for a login URL.
Once called, the user can login by being redirected to the url returned by
this function.
If there is an error during authorisation, None is returned.""... | python | def get_authorisation_url(self, reset=False):
""" Initialises the OAuth2 Process by asking the auth server for a login URL.
Once called, the user can login by being redirected to the url returned by
this function.
If there is an error during authorisation, None is returned.""... | [
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Alveo/pyalveo | pyalveo/pyalveo.py | OAuth2.on_callback | def on_callback(self,auth_resp):
""" Must be called once the authorisation server has responded after
redirecting to the url provided by 'get_authorisation_url' and completing
the login there.
Returns True if a token was successfully retrieved, False otherwise."""
try... | python | def on_callback(self,auth_resp):
""" Must be called once the authorisation server has responded after
redirecting to the url provided by 'get_authorisation_url' and completing
the login there.
Returns True if a token was successfully retrieved, False otherwise."""
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Alveo/pyalveo | pyalveo/pyalveo.py | OAuth2.validate | def validate(self):
""" Confirms the current token is still valid.
Returns True if it is valid, False otherwise. """
try:
resp = self.request().get(self.validate_url, verify=self.verifySSL).json()
except TokenExpiredError:
return False
except AttributeEr... | python | def validate(self):
""" Confirms the current token is still valid.
Returns True if it is valid, False otherwise. """
try:
resp = self.request().get(self.validate_url, verify=self.verifySSL).json()
except TokenExpiredError:
return False
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Alveo/pyalveo | pyalveo/pyalveo.py | OAuth2.refresh_token | def refresh_token(self):
""" Refreshes access token using refresh token. Returns true if successful, false otherwise. """
try:
if self.token:
self.token = self.request().refresh_token(self.refresh_url, self.token['refresh_token'])
return True
except ... | python | def refresh_token(self):
""" Refreshes access token using refresh token. Returns true if successful, false otherwise. """
try:
if self.token:
self.token = self.request().refresh_token(self.refresh_url, self.token['refresh_token'])
return True
except ... | [
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Alveo/pyalveo | pyalveo/pyalveo.py | OAuth2.revoke_access | def revoke_access(self):
""" Requests that the currently used token becomes invalid. Call this should a user logout. """
if self.token is None:
return True
#Don't try to revoke if token is invalid anyway, will cause an error response anyway.
if self.validate():
d... | python | def revoke_access(self):
""" Requests that the currently used token becomes invalid. Call this should a user logout. """
if self.token is None:
return True
#Don't try to revoke if token is invalid anyway, will cause an error response anyway.
if self.validate():
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Alveo/pyalveo | pyalveo/pyalveo.py | OAuth2.request | def request(self):
""" Returns an OAuth2 Session to be used to make requests.
Returns None if a token hasn't yet been received."""
headers = {'Accept': 'application/json'}
# Use API Key if possible
if self.api_key:
headers['X-API-KEY'] = self.api_key
ret... | python | def request(self):
""" Returns an OAuth2 Session to be used to make requests.
Returns None if a token hasn't yet been received."""
headers = {'Accept': 'application/json'}
# Use API Key if possible
if self.api_key:
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.to_json | def to_json(self):
"""
Returns a json string containing all relevant data to recreate this pyalveo.Client.
"""
data = dict(self.__dict__)
data.pop('context',None)
data['oauth'] = self.oauth.to_dict()
data['cache'] = self.cache.to_dict()
return json.dum... | python | def to_json(self):
"""
Returns a json string containing all relevant data to recreate this pyalveo.Client.
"""
data = dict(self.__dict__)
data.pop('context',None)
data['oauth'] = self.oauth.to_dict()
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including the specified data
:type url: String
:param url: the URL to which to make the request
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.get_collections | def get_collections(self):
"""Retrieve a list of the collection URLs for all collections
hosted on the server.
:rtype: List
:returns: a List of tuples of (name, url) for each collection
"""
result = self.api_request('/catalog')
# get the collection name from the... | python | def get_collections(self):
"""Retrieve a list of the collection URLs for all collections
hosted on the server.
:rtype: List
:returns: a List of tuples of (name, url) for each collection
"""
result = self.api_request('/catalog')
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.get_item | def get_item(self, item_url, force_download=False):
""" Retrieve the item metadata from the server, as an Item object
:type item_url: String or Item
:param item_url: URL of the item, or an Item object
:rtype: Item
:returns: the corresponding metadata, as an Item object
... | python | def get_item(self, item_url, force_download=False):
""" Retrieve the item metadata from the server, as an Item object
:type item_url: String or Item
:param item_url: URL of the item, or an Item object
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""" Retrieve the data for the given document from the server
:type doc_url: String or Document
:param doc_url: the URL of the document, or a Document object
:type force_download: Boolean
:param force_download: True to downlo... | python | def get_document(self, doc_url, force_download=False):
""" Retrieve the data for the given document from the server
:type doc_url: String or Document
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.get_primary_text | def get_primary_text(self, item_url, force_download=False):
""" Retrieve the primary text for an item from the server
:type item_url: String or Item
:param item_url: URL of the item, or an Item object
:type force_download: Boolean
:param force_download: True to download from the... | python | def get_primary_text(self, item_url, force_download=False):
""" Retrieve the primary text for an item from the server
:type item_url: String or Item
:param item_url: URL of the item, or an Item object
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.get_item_annotations | def get_item_annotations(self, item_url, annotation_type=None, label=None):
""" Retrieve the annotations for an item from the server
:type item_url: String or Item
:param item_url: URL of the item, or an Item object
:type annotation_type: String
:param annotation_type: return on... | python | def get_item_annotations(self, item_url, annotation_type=None, label=None):
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.get_annotation_types | def get_annotation_types(self, item_url):
""" Retrieve the annotation types for the given item from the server
:type item_url: String or Item
:param item_url: URL of the item, or an Item object
:rtype: List
:returns: a List specifying the annotation types
:raises: APIE... | python | def get_annotation_types(self, item_url):
""" Retrieve the annotation types for the given item from the server
:type item_url: String or Item
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.add_annotations | def add_annotations(self, item_url, annotations):
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:type item_url: String or Item
:param item_url: the URL of the item corresponding to the annotation,
or an Item object
:type annotation: list
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.create_collection | def create_collection(self, name, metadata):
""" Create a new collection with the given name
and attach the metadata.
:param name: the collection name, suitable for use in a URL (no spaces)
:type name: String
:param metadata: a dictionary of metadata values to associate with the... | python | def create_collection(self, name, metadata):
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.modify_collection_metadata | def modify_collection_metadata(self, collection_uri, metadata, replace=None, name=''):
"""Modify the metadata for the given collection.
:param collection_uri: The URI that references the collection
:type collection_uri: String
:param metadata: a dictionary of metadata values to add/mod... | python | def modify_collection_metadata(self, collection_uri, metadata, replace=None, name=''):
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.get_items | def get_items(self, collection_uri):
"""Return all items in this collection.
:param collection_uri: The URI that references the collection
:type collection_uri: String
:rtype: List
:returns: a list of the URIs of the items in this collection
"""
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"""Return all items in this collection.
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.add_text_item | def add_text_item(self, collection_uri, name, metadata, text, title=None):
"""Add a new item to a collection containing a single
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The full text of the text document is specified as the text
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.modify_item | def modify_item(self, item_uri, metadata):
"""Modify the metadata on an item
"""
md = json.dumps({'metadata': metadata})
response = self.api_request(item_uri, method='PUT', data=md)
return self.__check_success(response) | python | def modify_item(self, item_uri, metadata):
"""Modify the metadata on an item
"""
md = json.dumps({'metadata': metadata})
response = self.api_request(item_uri, method='PUT', data=md)
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"""Delete an item from a collection
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:type item_uri: String
:rtype: String
:returns: a message confirming that the metadata is modified
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contrib_id=None):
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.__check_success | def __check_success(resp):
""" Check a JSON server response to see if it was successful
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:param resp: the response string
:rtype: String
:returns: the success message, if it exists
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""" Retrieve a file from the server containing the metadata
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:type items: List or ItemGroup
:param items: List of the the URLs of the items to download,
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.search_metadata | def search_metadata(self, query):
""" Submit a search query to the server and retrieve the results
:type query: String
:param query: the search query
:rtype: ItemGroup
:returns: the search results
:raises: APIError if the API request is not successful
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... | python | def search_metadata(self, query):
""" Submit a search query to the server and retrieve the results
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:type item_urls: List or ItemGroup
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.rename_item_list | def rename_item_list(self, item_list_url, new_name):
""" Rename an Item List on the server
:type item_list_url: String or ItemList
:param item_list_url: the URL of the list to which to add the items,
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:type new_name: String
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.delete_item_list | def delete_item_list(self, item_list_url):
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:type item_list_url: String or ItemList
:param item_list_url: the URL of the list to which to add the items,
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:type metadata: Dict
:param metadata: dictionary of metadata properties and values
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.sparql_query | def sparql_query(self, collection_name, query):
""" Submit a sparql query to the server to search metadata
and annotations.
:type collection_name: String
:param collection_name: the name of the collection to search
:type query: String
:param query: the sparql query
... | python | def sparql_query(self, collection_name, query):
""" Submit a sparql query to the server to search metadata
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:type query: String
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.get_contribution | def get_contribution(self, url):
"""Get the details of a particular contribution given it's
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result = self.api_request(url)
# add the contrib id into the metadata
result['id'] = os.path.split(result['url'])[1]
return result | python | def get_contribution(self, url):
"""Get the details of a particular contribution given it's
url"""
result = self.api_request(url)
# add the contrib id into the metadata
result['id'] = os.path.split(result['url'])[1]
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Alveo/pyalveo | pyalveo/pyalveo.py | Client.delete_contribution | def delete_contribution(self, url):
"""Delete the contribution with this identifier
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:returns: True if the contribution was deleted, False otherwise (eg. if it didn't exist)
"""
# first validate that this is a real contrib
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:returns: True if the contribution was deleted, False otherwise (eg. if it didn't exist)
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TUNE-Archive/freight_forwarder | build.py | lint | def lint():
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"""
run linter on our code base.
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print(stmt)
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assamite/creamas | creamas/core/environment.py | Environment.get_agents | def get_agents(self, addr=True, agent_cls=None, include_manager=False):
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:param agent_cls:
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assamite/creamas | creamas/core/environment.py | Environment.trigger_act | async def trigger_act(self, *args, addr=None, agent=None, **kwargs):
'''Trigger agent to act.
If *agent* is None, then looks the agent by the address.
:raises ValueError: if both *agent* and *addr* are None.
'''
if agent is None and addr is None:
raise TypeError("Ei... | python | async def trigger_act(self, *args, addr=None, agent=None, **kwargs):
'''Trigger agent to act.
If *agent* is None, then looks the agent by the address.
:raises ValueError: if both *agent* and *addr* are None.
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assamite/creamas | creamas/core/environment.py | Environment.trigger_all | async def trigger_all(self, *args, **kwargs):
'''Trigger all agents in the environment to act asynchronously.
:returns: A list of agents' :meth:`act` return values.
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... | python | async def trigger_all(self, *args, **kwargs):
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assamite/creamas | creamas/core/environment.py | Environment.create_random_connections | def create_random_connections(self, n=5):
'''Create random connections for all agents in the environment.
:param int n: the number of connections for each agent
Existing agent connections that would be created by chance are not
doubled in the agent's :attr:`connections`, but count towa... | python | def create_random_connections(self, n=5):
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assamite/creamas | creamas/core/environment.py | Environment.create_connections | def create_connections(self, connection_map):
'''Create agent connections from a given connection map.
:param dict connection_map:
A map of connections to be created. Dictionary where keys are
agent addresses and values are lists of (addr, attitude)-tuples
suitable f... | python | def create_connections(self, connection_map):
'''Create agent connections from a given connection map.
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assamite/creamas | creamas/core/environment.py | Environment.get_connections | def get_connections(self, data=True):
"""Return connections from all the agents in the environment.
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assamite/creamas | creamas/core/environment.py | Environment.get_random_agent | def get_random_agent(self, agent):
'''Return random agent that is not the same as agent given as
parameter.
:param agent: Agent that is not wanted to return
:type agent: :py:class:`~creamas.core.agent.CreativeAgent`
:returns: random, non-connected, agent from the environment
... | python | def get_random_agent(self, agent):
'''Return random agent that is not the same as agent given as
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:type agent: :py:class:`~creamas.core.agent.CreativeAgent`
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assamite/creamas | creamas/core/environment.py | Environment.add_artifact | def add_artifact(self, artifact):
'''Add artifact with given framing to the environment.
:param object artifact: Artifact to be added.
'''
artifact.env_time = self.age
self.artifacts.append(artifact)
self._log(logging.DEBUG, "ARTIFACTS appended: '{}', length={}"
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'''Add artifact with given framing to the environment.
:param object artifact: Artifact to be added.
'''
artifact.env_time = self.age
self.artifacts.append(artifact)
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assamite/creamas | creamas/core/environment.py | Environment.get_artifacts | async def get_artifacts(self, agent=None):
'''Return artifacts published to the environment.
:param agent:
If not ``None``, then returns only artifacts created by the agent.
:returns: All artifacts published (by the agent).
:rtype: list
If environment has a :attr:`... | python | async def get_artifacts(self, agent=None):
'''Return artifacts published to the environment.
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assamite/creamas | creamas/core/environment.py | Environment.destroy | def destroy(self, folder=None, as_coro=False):
'''Destroy the environment.
Does the following:
1. calls :py:meth:`~creamas.core.Environment.save_info`
2. for each agent: calls :py:meth:`close`
3. Shuts down its RPC-service.
'''
async def _destroy(folder):
... | python | def destroy(self, folder=None, as_coro=False):
'''Destroy the environment.
Does the following:
1. calls :py:meth:`~creamas.core.Environment.save_info`
2. for each agent: calls :py:meth:`close`
3. Shuts down its RPC-service.
'''
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Kortemme-Lab/klab | klab/process.py | tee | def tee(*popenargs, **kwargs):
"""
Run a command as if it were piped though tee.
Output generated by the command is displayed in real time to the terminal.
It is also captured in strings and returned once the process terminated.
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"""
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.save | def save(self, user, commit=True):
""" Persist user and emit event """
self.is_instance(user)
schema = UpdateSchema()
valid = schema.process(user)
if not valid:
return valid
db.session.add(user)
if commit:
db.session.commit()
eve... | python | def save(self, user, commit=True):
""" Persist user and emit event """
self.is_instance(user)
schema = UpdateSchema()
valid = schema.process(user)
if not valid:
return valid
db.session.add(user)
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db.session.commit()
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.login | def login(self, email=None, password=None, remember=False):
""" Authenticate user and emit event. """
from flask_login import login_user
user = self.first(email=email)
if user is None:
events.login_failed_nonexistent_event.send()
return False
# check for ... | python | def login(self, email=None, password=None, remember=False):
""" Authenticate user and emit event. """
from flask_login import login_user
user = self.first(email=email)
if user is None:
events.login_failed_nonexistent_event.send()
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.force_login | def force_login(self, user):
""" Force login a user without credentials """
from flask_login import login_user
# check for account being locked
if user.is_locked():
raise x.AccountLocked(locked_until=user.locked_until)
# check for email being confirmed
is_ne... | python | def force_login(self, user):
""" Force login a user without credentials """
from flask_login import login_user
# check for account being locked
if user.is_locked():
raise x.AccountLocked(locked_until=user.locked_until)
# check for email being confirmed
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.logout | def logout(self):
""" Logout user and emit event."""
from flask_login import logout_user, current_user
if not current_user.is_authenticated:
return True
# logout otherwise
user = current_user
events.logout_event.send(user)
logout_user()
# not... | python | def logout(self):
""" Logout user and emit event."""
from flask_login import logout_user, current_user
if not current_user.is_authenticated:
return True
# logout otherwise
user = current_user
events.logout_event.send(user)
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.attempt_social_login | def attempt_social_login(self, provider, id):
""" Attempt social login and return boolean result """
if not provider or not id:
return False
params = dict()
params[provider.lower() + '_id'] = id
user = self.first(**params)
if not user:
return Fals... | python | def attempt_social_login(self, provider, id):
""" Attempt social login and return boolean result """
if not provider or not id:
return False
params = dict()
params[provider.lower() + '_id'] = id
user = self.first(**params)
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.get_token | def get_token(self, user_id):
"""
Get user token
Checks if a custom token implementation is registered and uses that.
Otherwise falls back to default token implementation. Returns a string
token on success.
:param user_id: int, user id
:return: str
"""
... | python | def get_token(self, user_id):
"""
Get user token
Checks if a custom token implementation is registered and uses that.
Otherwise falls back to default token implementation. Returns a string
token on success.
:param user_id: int, user id
:return: str
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.get_user_by_token | def get_user_by_token(self, token):
"""
Get user by token
Using for logging in. Check to see if a custom token user loader was
registered and uses that. Otherwise falls back to default loader
implementation. You should be fine with default implementation as long
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.default_token_implementation | def default_token_implementation(self, user_id):
"""
Default JWT token implementation
This is used by default for generating user tokens if custom
implementation was not configured. The token will contain user_id and
expiration date. If you need more information added to the toke... | python | def default_token_implementation(self, user_id):
"""
Default JWT token implementation
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.default_token_user_loader | def default_token_user_loader(self, token):
"""
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Accepts a token and decodes it checking signature and expiration. Then
loads user by id from the token to see if account is not locked. If
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"""
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.register | def register(self, user_data, base_confirm_url='', send_welcome=True):
"""
Register user
Accepts user data, validates it and performs registration. Will send
a welcome message with a confirmation link on success.
:param user_data: dic, populate user with data
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.send_welcome_message | def send_welcome_message(self, user, base_url):
""" Send welcome mail with email confirmation link """
if not self.require_confirmation and not self.welcome_message:
return
# get subject
subject = ''
subjects = self.email_subjects
if self.require_confirmation... | python | def send_welcome_message(self, user, base_url):
""" Send welcome mail with email confirmation link """
if not self.require_confirmation and not self.welcome_message:
return
# get subject
subject = ''
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.resend_welcome_message | def resend_welcome_message(self, user, base_url):
""" Regenerate email link and resend welcome """
user.require_email_confirmation()
self.save(user)
self.send_welcome_message(user, base_url) | python | def resend_welcome_message(self, user, base_url):
""" Regenerate email link and resend welcome """
user.require_email_confirmation()
self.save(user)
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.confirm_email_with_link | def confirm_email_with_link(self, link):
"""
Confirm email with link
A universal method to confirm email. used for both initial
confirmation and when email is changed.
"""
user = self.first(email_link=link)
if not user:
return False
elif user a... | python | def confirm_email_with_link(self, link):
"""
Confirm email with link
A universal method to confirm email. used for both initial
confirmation and when email is changed.
"""
user = self.first(email_link=link)
if not user:
return False
elif user a... | [
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A universal method to confirm email. used for both initial
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.change_email | def change_email(
self, user, new_email, base_confirm_url='', send_message=True):
"""
Change email
Saves new email and sends confirmation before doing the switch.
Can optionally skip sending out message for testing purposes.
The email will be sent to the new email addres... | python | def change_email(
self, user, new_email, base_confirm_url='', send_message=True):
"""
Change email
Saves new email and sends confirmation before doing the switch.
Can optionally skip sending out message for testing purposes.
The email will be sent to the new email addres... | [
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Saves new email and sends confirmation before doing the switch.
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.resend_email_changed_message | def resend_email_changed_message(self, user, base_url):
""" Regenerate email confirmation link and resend message """
user.require_email_confirmation()
self.save(user)
self.send_email_changed_message(user, base_url) | python | def resend_email_changed_message(self, user, base_url):
""" Regenerate email confirmation link and resend message """
user.require_email_confirmation()
self.save(user)
self.send_email_changed_message(user, base_url) | [
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.request_password_reset | def request_password_reset(self, user, base_url):
""" Regenerate password link and send message """
user.generate_password_link()
db.session.add(user)
db.session.commit()
events.password_change_requested_event.send(user)
self.send_password_change_message(user, base_url) | python | def request_password_reset(self, user, base_url):
""" Regenerate password link and send message """
user.generate_password_link()
db.session.add(user)
db.session.commit()
events.password_change_requested_event.send(user)
self.send_password_change_message(user, base_url) | [
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.change_password | def change_password(self, user, new_password):
""" Change user password and logout """
from boiler.user.models import UpdateSchema
from flask_login import logout_user
schema = UpdateSchema()
user.password = new_password
user.password_link=None
user.password_link_... | python | def change_password(self, user, new_password):
""" Change user password and logout """
from boiler.user.models import UpdateSchema
from flask_login import logout_user
schema = UpdateSchema()
user.password = new_password
user.password_link=None
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.send_password_change_message | def send_password_change_message(self, user, base_url):
""" Send password change message"""
subject = 'Change your password here'
if 'password_change' in self.email_subjects.keys():
subject = self.email_subjects['password_change']
sender = current_app.config['MAIL_DEFAULT_SE... | python | def send_password_change_message(self, user, base_url):
""" Send password change message"""
subject = 'Change your password here'
if 'password_change' in self.email_subjects.keys():
subject = self.email_subjects['password_change']
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.add_role_to_user | def add_role_to_user(self, user, role):
""" Adds a role to user """
user.add_role(role)
self.save(user)
events.user_got_role_event.send(user, role=role) | python | def add_role_to_user(self, user, role):
""" Adds a role to user """
user.add_role(role)
self.save(user)
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projectshift/shift-boiler | boiler/user/user_service.py | UserService.remove_role_from_user | def remove_role_from_user(self, user, role):
""" Removes role from user """
user.remove_role(role)
self.save(user)
events.user_lost_role_event.send(user, role=role) | python | def remove_role_from_user(self, user, role):
""" Removes role from user """
user.remove_role(role)
self.save(user)
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berkeley-cocosci/Wallace | wallace/processes.py | random_walk | def random_walk(network):
"""Take a random walk from a source.
Start at a node randomly selected from those that receive input from a
source. At each step, transmit to a randomly-selected downstream node.
"""
latest = network.latest_transmission_recipient()
if (not network.transmissions() or l... | python | def random_walk(network):
"""Take a random walk from a source.
Start at a node randomly selected from those that receive input from a
source. At each step, transmit to a randomly-selected downstream node.
"""
latest = network.latest_transmission_recipient()
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berkeley-cocosci/Wallace | wallace/processes.py | moran_cultural | def moran_cultural(network):
"""Generalized cultural Moran process.
At eachtime step, an individual is chosen to receive information from
another individual. Nobody dies, but perhaps their ideas do.
"""
if not network.transmissions(): # first step, replacer is a source
replacer = random.ch... | python | def moran_cultural(network):
"""Generalized cultural Moran process.
At eachtime step, an individual is chosen to receive information from
another individual. Nobody dies, but perhaps their ideas do.
"""
if not network.transmissions(): # first step, replacer is a source
replacer = random.ch... | [
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berkeley-cocosci/Wallace | wallace/processes.py | moran_sexual | def moran_sexual(network):
"""The generalized sexual Moran process.
Ateach time step, and individual is chosen for replication and another
individual is chosen to die. The replication replaces the one who dies.
For this process to work you need to add a new agent before calling step.
"""
if not... | python | def moran_sexual(network):
"""The generalized sexual Moran process.
Ateach time step, and individual is chosen for replication and another
individual is chosen to die. The replication replaces the one who dies.
For this process to work you need to add a new agent before calling step.
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sprockets/sprockets.mixins.mediatype | sprockets/mixins/mediatype/transcoders.py | JSONTranscoder.dump_object | def dump_object(self, obj):
"""
Called to encode unrecognized object.
:param object obj: the object to encode
:return: the encoded object
:raises TypeError: when `obj` cannot be encoded
This method is passed as the ``default`` keyword parameter
to :func:`json.du... | python | def dump_object(self, obj):
"""
Called to encode unrecognized object.
:param object obj: the object to encode
:return: the encoded object
:raises TypeError: when `obj` cannot be encoded
This method is passed as the ``default`` keyword parameter
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sprockets/sprockets.mixins.mediatype | sprockets/mixins/mediatype/transcoders.py | MsgPackTranscoder.normalize_datum | def normalize_datum(self, datum):
"""
Convert `datum` into something that umsgpack likes.
:param datum: something that we want to process with umsgpack
:return: a packable version of `datum`
:raises TypeError: if `datum` cannot be packed
This message is called by :meth:... | python | def normalize_datum(self, datum):
"""
Convert `datum` into something that umsgpack likes.
:param datum: something that we want to process with umsgpack
:return: a packable version of `datum`
:raises TypeError: if `datum` cannot be packed
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