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SheffieldML/GPyOpt | GPyOpt/acquisitions/EI.py | AcquisitionEI._compute_acq | def _compute_acq(self, x):
"""
Computes the Expected Improvement per unit of cost
"""
m, s = self.model.predict(x)
fmin = self.model.get_fmin()
phi, Phi, u = get_quantiles(self.jitter, fmin, m, s)
f_acqu = s * (u * Phi + phi)
return f_acqu | python | def _compute_acq(self, x):
"""
Computes the Expected Improvement per unit of cost
"""
m, s = self.model.predict(x)
fmin = self.model.get_fmin()
phi, Phi, u = get_quantiles(self.jitter, fmin, m, s)
f_acqu = s * (u * Phi + phi)
return f_acqu | [
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SheffieldML/GPyOpt | GPyOpt/interface/config_parser.py | update_config | def update_config(config_new, config_default):
'''
Updates the loaded method configuration with default values.
'''
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u... | python | def update_config(config_new, config_default):
'''
Updates the loaded method configuration with default values.
'''
if any([isinstance(v, dict) for v in list(config_new.values())]):
for k,v in list(config_new.items()):
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SheffieldML/GPyOpt | GPyOpt/interface/config_parser.py | parser | def parser(input_file_path='config.json'):
'''
Parser for the .json file containing the configuration of the method.
'''
# --- Read .json file
try:
with open(input_file_path, 'r') as config_file:
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config_file.close()
except:
... | python | def parser(input_file_path='config.json'):
'''
Parser for the .json file containing the configuration of the method.
'''
# --- Read .json file
try:
with open(input_file_path, 'r') as config_file:
config_new = json.load(config_file)
config_file.close()
except:
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SheffieldML/GPyOpt | GPyOpt/util/mcmc_sampler.py | AffineInvariantEnsembleSampler.get_samples | def get_samples(self, n_samples, log_p_function, burn_in_steps=50):
"""
Generates samples.
Parameters:
n_samples - number of samples to generate
log_p_function - a function that returns log density for a specific sample
burn_in_steps - number of burn-in steps... | python | def get_samples(self, n_samples, log_p_function, burn_in_steps=50):
"""
Generates samples.
Parameters:
n_samples - number of samples to generate
log_p_function - a function that returns log density for a specific sample
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SheffieldML/GPyOpt | GPyOpt/core/bo.py | BO.suggest_next_locations | def suggest_next_locations(self, context = None, pending_X = None, ignored_X = None):
"""
Run a single optimization step and return the next locations to evaluate the objective.
Number of suggested locations equals to batch_size.
:param context: fixes specified variables to a particular... | python | def suggest_next_locations(self, context = None, pending_X = None, ignored_X = None):
"""
Run a single optimization step and return the next locations to evaluate the objective.
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SheffieldML/GPyOpt | GPyOpt/core/bo.py | BO._print_convergence | def _print_convergence(self):
"""
Prints the reason why the optimization stopped.
"""
if self.verbosity:
if (self.num_acquisitions == self.max_iter) and (not self.initial_iter):
print(' ** Maximum number of iterations reached **')
return 1
... | python | def _print_convergence(self):
"""
Prints the reason why the optimization stopped.
"""
if self.verbosity:
if (self.num_acquisitions == self.max_iter) and (not self.initial_iter):
print(' ** Maximum number of iterations reached **')
return 1
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SheffieldML/GPyOpt | GPyOpt/core/bo.py | BO.evaluate_objective | def evaluate_objective(self):
"""
Evaluates the objective
"""
self.Y_new, cost_new = self.objective.evaluate(self.suggested_sample)
self.cost.update_cost_model(self.suggested_sample, cost_new)
self.Y = np.vstack((self.Y,self.Y_new)) | python | def evaluate_objective(self):
"""
Evaluates the objective
"""
self.Y_new, cost_new = self.objective.evaluate(self.suggested_sample)
self.cost.update_cost_model(self.suggested_sample, cost_new)
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SheffieldML/GPyOpt | GPyOpt/core/bo.py | BO._compute_results | def _compute_results(self):
"""
Computes the optimum and its value.
"""
self.Y_best = best_value(self.Y)
self.x_opt = self.X[np.argmin(self.Y),:]
self.fx_opt = np.min(self.Y) | python | def _compute_results(self):
"""
Computes the optimum and its value.
"""
self.Y_best = best_value(self.Y)
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SheffieldML/GPyOpt | GPyOpt/core/bo.py | BO._distance_last_evaluations | def _distance_last_evaluations(self):
"""
Computes the distance between the last two evaluations.
"""
if self.X.shape[0] < 2:
# less than 2 evaluations
return np.inf
return np.sqrt(np.sum((self.X[-1, :] - self.X[-2, :]) ** 2)) | python | def _distance_last_evaluations(self):
"""
Computes the distance between the last two evaluations.
"""
if self.X.shape[0] < 2:
# less than 2 evaluations
return np.inf
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SheffieldML/GPyOpt | GPyOpt/core/bo.py | BO.save_evaluations | def save_evaluations(self, evaluations_file = None):
"""
Saves evaluations at each iteration of the optimization
:param evaluations_file: name of the file in which the results are saved.
"""
iterations = np.array(range(1, self.Y.shape[0] + 1))[:, None]
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"""
Saves evaluations at each iteration of the optimization
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"""
iterations = np.array(range(1, self.Y.shape[0] + 1))[:, None]
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SheffieldML/GPyOpt | GPyOpt/core/bo.py | BO.save_models | def save_models(self, models_file):
"""
Saves model parameters at each iteration of the optimization
:param models_file: name of the file or a file buffer, in which the results are saved.
"""
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Saves model parameters at each iteration of the optimization
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"""
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SheffieldML/GPyOpt | GPyOpt/methods/bayesian_optimization.py | BayesianOptimization._init_design_chooser | def _init_design_chooser(self):
"""
Initializes the choice of X and Y based on the selected initial design and number of points selected.
"""
# If objective function was not provided, we require some initial sample data
if self.f is None and (self.X is None or self.Y is None):
... | python | def _init_design_chooser(self):
"""
Initializes the choice of X and Y based on the selected initial design and number of points selected.
"""
# If objective function was not provided, we require some initial sample data
if self.f is None and (self.X is None or self.Y is None):
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coleifer/huey | huey/api.py | crontab | def crontab(minute='*', hour='*', day='*', month='*', day_of_week='*'):
"""
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Acceptable input... | python | def crontab(minute='*', hour='*', day='*', month='*', day_of_week='*'):
"""
Convert a "crontab"-style set of parameters into a test function that will
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coleifer/huey | huey/storage.py | BaseStorage.put_if_empty | def put_if_empty(self, key, value):
"""
Atomically write data only if the key is not already set.
:param bytes key: Key to check/set.
:param bytes value: Arbitrary data.
:return: Boolean whether key/value was set.
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re... | python | def put_if_empty(self, key, value):
"""
Atomically write data only if the key is not already set.
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coleifer/huey | huey/utils.py | make_naive | def make_naive(dt):
"""
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"""
tt = dt.utctimetuple()
ts = calendar.timegm(tt)
local_tt = time.localtime(ts)
return datetime.datetime(*local_tt[:6]) | python | def make_naive(dt):
"""
Makes an aware datetime.datetime naive in local time zone.
"""
tt = dt.utctimetuple()
ts = calendar.timegm(tt)
local_tt = time.localtime(ts)
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coleifer/huey | huey/consumer.py | BaseProcess.sleep_for_interval | def sleep_for_interval(self, start_ts, nseconds):
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coleifer/huey | huey/consumer.py | Consumer.start | def start(self):
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Start all consumer processes and register signal handlers.
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coleifer/huey | huey/consumer.py | Consumer.stop | def stop(self, graceful=False):
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coleifer/huey | huey/consumer.py | Consumer.check_worker_health | def check_worker_health(self):
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"""
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restart_occurred = False
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coleifer/huey | huey/contrib/djhuey/__init__.py | close_db | def close_db(fn):
"""Decorator to be used with tasks that may operate on the database."""
@wraps(fn)
def inner(*args, **kwargs):
try:
return fn(*args, **kwargs)
finally:
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close_old_connections()
return inner | python | def close_db(fn):
"""Decorator to be used with tasks that may operate on the database."""
@wraps(fn)
def inner(*args, **kwargs):
try:
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johnwheeler/flask-ask | samples/purchase/model.py | Product.list | def list(self):
""" return list of purchasable and not entitled products"""
mylist = []
for prod in self.product_list:
if self.purchasable(prod) and not self.entitled(prod):
mylist.append(prod)
return mylist | python | def list(self):
""" return list of purchasable and not entitled products"""
mylist = []
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mylist.append(prod)
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johnwheeler/flask-ask | samples/tidepooler/tidepooler.py | _find_tide_info | def _find_tide_info(predictions):
"""
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"""
last_prediction = None
first_high_tide = None
second_high_tide = None
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Algorithm to find the 2 high tides for the day, the first of which is smaller and occurs
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last_prediction = None
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johnwheeler/flask-ask | flask_ask/models.py | audio.enqueue | def enqueue(self, stream_url, offset=0, opaque_token=None):
"""Adds stream to the queue. Does not impact the currently playing stream."""
directive = self._play_directive('ENQUEUE')
audio_item = self._audio_item(stream_url=stream_url,
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... | python | def enqueue(self, stream_url, offset=0, opaque_token=None):
"""Adds stream to the queue. Does not impact the currently playing stream."""
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johnwheeler/flask-ask | flask_ask/models.py | audio.play_next | def play_next(self, stream_url=None, offset=0, opaque_token=None):
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directive = self._play_directive('REPLACE_ENQUEUED')
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johnwheeler/flask-ask | flask_ask/models.py | audio.resume | def resume(self):
"""Sends Play Directive to resume playback at the paused offset"""
directive = self._play_directive('REPLACE_ALL')
directive['audioItem'] = self._audio_item()
self._response['directives'].append(directive)
return self | python | def resume(self):
"""Sends Play Directive to resume playback at the paused offset"""
directive = self._play_directive('REPLACE_ALL')
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self._response['directives'].append(directive)
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johnwheeler/flask-ask | flask_ask/models.py | audio._audio_item | def _audio_item(self, stream_url=None, offset=0, push_buffer=True, opaque_token=None):
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audio_item = {'stream': {}}
stream = audio_item['stream']
# existing stream
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# stream... | python | def _audio_item(self, stream_url=None, offset=0, push_buffer=True, opaque_token=None):
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johnwheeler/flask-ask | flask_ask/models.py | audio.clear_queue | def clear_queue(self, stop=False):
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stop {bool} set True to stop current current stream and clear queued streams.
set False to clear queued streams and allow current stream to finish
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johnwheeler/flask-ask | flask_ask/core.py | find_ask | def find_ask():
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Note: This only supports returning a reference to the first instance
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"""
if hasattr(current_app, 'ask'):
return getattr(current_app, 'ask')
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Find our instance of Ask, navigating Local's and possible blueprints.
Note: This only supports returning a reference to the first instance
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johnwheeler/flask-ask | flask_ask/core.py | Ask.init_app | def init_app(self, app, path='templates.yaml'):
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`ASK_APPLICATION_ID`:
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johnwheeler/flask-ask | flask_ask/core.py | Ask.launch | def launch(self, f):
"""Decorator maps a view function as the endpoint for an Alexa LaunchRequest and starts the skill.
@ask.launch
def launched():
return question('Welcome to Foo')
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johnwheeler/flask-ask | flask_ask/core.py | Ask.session_ended | def session_ended(self, f):
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def session_ended():
return "{}", 200
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johnwheeler/flask-ask | flask_ask/core.py | Ask.intent | def intent(self, intent_name, mapping={}, convert={}, default={}):
"""Decorator routes an Alexa IntentRequest and provides the slot parameters to the wrapped function.
Functions decorated as an intent are registered as the view function for the Intent's URL,
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johnwheeler/flask-ask | flask_ask/core.py | Ask.default_intent | def default_intent(self, f):
"""Decorator routes any Alexa IntentRequest that is not matched by any existing @ask.intent routing."""
self._default_intent_view_func = f
@wraps(f)
def wrapper(*args, **kw):
self._flask_view_func(*args, **kw)
return f | python | def default_intent(self, f):
"""Decorator routes any Alexa IntentRequest that is not matched by any existing @ask.intent routing."""
self._default_intent_view_func = f
@wraps(f)
def wrapper(*args, **kw):
self._flask_view_func(*args, **kw)
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johnwheeler/flask-ask | flask_ask/core.py | Ask.display_element_selected | def display_element_selected(self, f):
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def eval_element():
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"""Decorator routes Alexa Display.ElementSelected request to the wrapped view function.
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def eval_element():
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johnwheeler/flask-ask | flask_ask/core.py | Ask.on_purchase_completed | def on_purchase_completed(self, mapping={'payload': 'payload','name':'name','status':'status','token':'token'}, convert={}, default={}):
"""Decorator routes an Connections.Response to the wrapped function.
Request is sent when Alexa completes the purchase flow.
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johnwheeler/flask-ask | flask_ask/core.py | Ask.run_aws_lambda | def run_aws_lambda(self, event):
"""Invoke the Flask Ask application from an AWS Lambda function handler.
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skill. This method will invoke your Flask application providing a
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johnwheeler/flask-ask | flask_ask/core.py | Ask._parse_timestamp | def _parse_timestamp(timestamp):
"""
Parse a given timestamp value, raising ValueError if None or Flasey
"""
if timestamp:
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return aniso8601.parse_datetime(timestamp)
except AttributeError:
# raised by aniso8601 if raw_timestamp... | python | def _parse_timestamp(timestamp):
"""
Parse a given timestamp value, raising ValueError if None or Flasey
"""
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johnwheeler/flask-ask | flask_ask/core.py | Ask._map_player_request_to_func | def _map_player_request_to_func(self, player_request_type):
"""Provides appropriate parameters to the on_playback functions."""
# calbacks for on_playback requests are optional
view_func = self._intent_view_funcs.get(player_request_type, lambda: None)
argspec = inspect.getargspec(view_f... | python | def _map_player_request_to_func(self, player_request_type):
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view_func = self._intent_view_funcs.get(player_request_type, lambda: None)
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johnwheeler/flask-ask | flask_ask/core.py | Ask._map_purchase_request_to_func | def _map_purchase_request_to_func(self, purchase_request_type):
"""Provides appropriate parameters to the on_purchase functions."""
if purchase_request_type in self._intent_view_funcs:
view_func = self._intent_view_funcs[purchase_request_type]
else:
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johnwheeler/flask-ask | flask_ask/cache.py | push_stream | def push_stream(cache, user_id, stream):
"""
Push a stream onto the stream stack in cache.
:param cache: werkzeug BasicCache-like object
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:param stream: stream object to push onto stack
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johnwheeler/flask-ask | flask_ask/cache.py | pop_stream | def pop_stream(cache, user_id):
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:param cache: werkzeug BasicCache-like object
:param user_id: id of user, used as key in cache
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"""
stack = cache.g... | python | def pop_stream(cache, user_id):
"""
Pop an item off the stack in the cache. If stack
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johnwheeler/flask-ask | flask_ask/cache.py | top_stream | def top_stream(cache, user_id):
"""
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:param user_id: id of user, used as key in cache
:return: top item in user's cached stack, otherwise None
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ecederstrand/exchangelib | exchangelib/transport.py | wrap | def wrap(content, version, account=None):
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Generate the necessary boilerplate XML for a raw SOAP request. The XML is specific to the server version.
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"""
envelope = create_element('s:Envelope', nsmap=ns_translation)
header... | python | def wrap(content, version, account=None):
"""
Generate the necessary boilerplate XML for a raw SOAP request. The XML is specific to the server version.
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ecederstrand/exchangelib | exchangelib/autodiscover.py | discover | def discover(email, credentials):
"""
Performs the autodiscover dance and returns the primary SMTP address of the account and a Protocol on success. The
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ecederstrand/exchangelib | exchangelib/properties.py | TimeZone.to_server_timezone | def to_server_timezone(self, timezones, for_year):
"""Returns the Microsoft timezone ID corresponding to this timezone. There may not be a match at all, and there
may be multiple matches. If so, we return a random timezone ID.
:param timezones: A list of server timezones, as returned by
... | python | def to_server_timezone(self, timezones, for_year):
"""Returns the Microsoft timezone ID corresponding to this timezone. There may not be a match at all, and there
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ecederstrand/exchangelib | exchangelib/protocol.py | BaseProtocol.decrease_poolsize | def decrease_poolsize(self):
"""Decreases the session pool size in response to error messages from the server requesting to rate-limit
requests. We decrease by one session per call.
"""
# Take a single session from the pool and discard it. We need to protect this with a lock while we are... | python | def decrease_poolsize(self):
"""Decreases the session pool size in response to error messages from the server requesting to rate-limit
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"""
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ecederstrand/exchangelib | exchangelib/util.py | is_iterable | def is_iterable(value, generators_allowed=False):
"""
Checks if value is a list-like object. Don't match generators and generator-like objects here by default, because
callers don't necessarily guarantee that they only iterate the value once. Take care to not match string types and
bytes.
:param va... | python | def is_iterable(value, generators_allowed=False):
"""
Checks if value is a list-like object. Don't match generators and generator-like objects here by default, because
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ecederstrand/exchangelib | exchangelib/util.py | chunkify | def chunkify(iterable, chunksize):
"""
Splits an iterable into chunks of size ``chunksize``. The last chunk may be smaller than ``chunksize``.
"""
from .queryset import QuerySet
if hasattr(iterable, '__getitem__') and not isinstance(iterable, QuerySet):
# tuple, list. QuerySet has __getitem_... | python | def chunkify(iterable, chunksize):
"""
Splits an iterable into chunks of size ``chunksize``. The last chunk may be smaller than ``chunksize``.
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ecederstrand/exchangelib | exchangelib/util.py | peek | def peek(iterable):
"""
Checks if an iterable is empty and returns status and the rewinded iterable
"""
from .queryset import QuerySet
if isinstance(iterable, QuerySet):
# QuerySet has __len__ but that evaluates the entire query greedily. We don't want that here. Instead, peek()
# sh... | python | def peek(iterable):
"""
Checks if an iterable is empty and returns status and the rewinded iterable
"""
from .queryset import QuerySet
if isinstance(iterable, QuerySet):
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ecederstrand/exchangelib | exchangelib/util.py | xml_to_str | def xml_to_str(tree, encoding=None, xml_declaration=False):
"""Serialize an XML tree. Returns unicode if 'encoding' is None. Otherwise, we return encoded 'bytes'."""
if xml_declaration and not encoding:
raise ValueError("'xml_declaration' is not supported when 'encoding' is None")
if encoding:
... | python | def xml_to_str(tree, encoding=None, xml_declaration=False):
"""Serialize an XML tree. Returns unicode if 'encoding' is None. Otherwise, we return encoded 'bytes'."""
if xml_declaration and not encoding:
raise ValueError("'xml_declaration' is not supported when 'encoding' is None")
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ecederstrand/exchangelib | exchangelib/util.py | is_xml | def is_xml(text):
"""
Helper function. Lightweight test if response is an XML doc
"""
# BOM_UTF8 is an UTF-8 byte order mark which may precede the XML from an Exchange server
bom_len = len(BOM_UTF8)
if text[:bom_len] == BOM_UTF8:
return text[bom_len:bom_len + 5] == b'<?xml'
return te... | python | def is_xml(text):
"""
Helper function. Lightweight test if response is an XML doc
"""
# BOM_UTF8 is an UTF-8 byte order mark which may precede the XML from an Exchange server
bom_len = len(BOM_UTF8)
if text[:bom_len] == BOM_UTF8:
return text[bom_len:bom_len + 5] == b'<?xml'
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ecederstrand/exchangelib | exchangelib/services.py | GetItem.call | def call(self, items, additional_fields, shape):
"""
Returns all items in an account that correspond to a list of ID's, in stable order.
:param items: a list of (id, changekey) tuples or Item objects
:param additional_fields: the extra fields that should be returned with the item, as Fi... | python | def call(self, items, additional_fields, shape):
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Returns all items in an account that correspond to a list of ID's, in stable order.
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ecederstrand/exchangelib | exchangelib/services.py | FindFolder.call | def call(self, additional_fields, restriction, shape, depth, max_items, offset):
"""
Find subfolders of a folder.
:param additional_fields: the extra fields that should be returned with the folder, as FieldPath objects
:param shape: The set of attributes to return
:param depth: ... | python | def call(self, additional_fields, restriction, shape, depth, max_items, offset):
"""
Find subfolders of a folder.
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ecederstrand/exchangelib | exchangelib/services.py | GetFolder.call | def call(self, folders, additional_fields, shape):
"""
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:param folders: a list of Folder objects
:param additional_fields: the extra fields that should be returned with the folder, as FieldPath objects
:param sha... | python | def call(self, folders, additional_fields, shape):
"""
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ecederstrand/exchangelib | exchangelib/services.py | UploadItems.get_payload | def get_payload(self, items):
"""Upload given items to given account
data is an iterable of tuples where the first element is a Folder
instance representing the ParentFolder that the item will be placed in
and the second element is a Data string returned from an ExportItems
call... | python | def get_payload(self, items):
"""Upload given items to given account
data is an iterable of tuples where the first element is a Folder
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ecederstrand/exchangelib | exchangelib/folders.py | FolderCollection.find_items | def find_items(self, q, shape=ID_ONLY, depth=SHALLOW, additional_fields=None, order_fields=None,
calendar_view=None, page_size=None, max_items=None, offset=0):
"""
Private method to call the FindItem service
:param q: a Q instance containing any restrictions
:param sh... | python | def find_items(self, q, shape=ID_ONLY, depth=SHALLOW, additional_fields=None, order_fields=None,
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ecederstrand/exchangelib | exchangelib/folders.py | RootOfHierarchy.get_distinguished | def get_distinguished(cls, account):
"""Gets the distinguished folder for this folder class"""
if not cls.DISTINGUISHED_FOLDER_ID:
raise ValueError('Class %s must have a DISTINGUISHED_FOLDER_ID value' % cls)
folders = list(FolderCollection(
account=account,
fo... | python | def get_distinguished(cls, account):
"""Gets the distinguished folder for this folder class"""
if not cls.DISTINGUISHED_FOLDER_ID:
raise ValueError('Class %s must have a DISTINGUISHED_FOLDER_ID value' % cls)
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ecederstrand/exchangelib | exchangelib/folders.py | RootOfHierarchy.folder_cls_from_folder_name | def folder_cls_from_folder_name(cls, folder_name, locale):
"""Returns the folder class that matches a localized folder name.
locale is a string, e.g. 'da_DK'
"""
for folder_cls in cls.WELLKNOWN_FOLDERS + NON_DELETEABLE_FOLDERS:
if folder_name.lower() in folder_cls.localized_... | python | def folder_cls_from_folder_name(cls, folder_name, locale):
"""Returns the folder class that matches a localized folder name.
locale is a string, e.g. 'da_DK'
"""
for folder_cls in cls.WELLKNOWN_FOLDERS + NON_DELETEABLE_FOLDERS:
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ecederstrand/exchangelib | exchangelib/items.py | RegisterMixIn.register | def register(cls, attr_name, attr_cls):
"""
Register a custom extended property in this item class so they can be accessed just like any other attribute
"""
if not cls.INSERT_AFTER_FIELD:
raise ValueError('Class %s is missing INSERT_AFTER_FIELD value' % cls)
try:
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"""
Register a custom extended property in this item class so they can be accessed just like any other attribute
"""
if not cls.INSERT_AFTER_FIELD:
raise ValueError('Class %s is missing INSERT_AFTER_FIELD value' % cls)
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"""Add an attachment, or a list of attachments, to this item. If the item has already been saved, the
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be created on the server the item is saved.
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"""Add an attachment, or a list of attachments, to this item. If the item has already been saved, the
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ecederstrand/exchangelib | exchangelib/items.py | Item.detach | def detach(self, attachments):
"""Remove an attachment, or a list of attachments, from this item. If the item has already been saved, the
attachments will be deleted on the server immediately. If the item has not yet been saved, the attachments will
simply not be created on the server the item i... | python | def detach(self, attachments):
"""Remove an attachment, or a list of attachments, from this item. If the item has already been saved, the
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ecederstrand/exchangelib | exchangelib/credentials.py | ServiceAccount.back_off_until | def back_off_until(self):
"""Returns the back off value as a datetime. Resets the current back off value if it has expired."""
if self._back_off_until is None:
return None
with self._back_off_lock:
if self._back_off_until is None:
return None
i... | python | def back_off_until(self):
"""Returns the back off value as a datetime. Resets the current back off value if it has expired."""
if self._back_off_until is None:
return None
with self._back_off_lock:
if self._back_off_until is None:
return None
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ecederstrand/exchangelib | exchangelib/winzone.py | generate_map | def generate_map(timeout=10):
""" Helper method to update the map if the CLDR database is updated """
r = requests.get(CLDR_WINZONE_URL, timeout=timeout)
if r.status_code != 200:
raise ValueError('Unexpected response: %s' % r)
tz_map = {}
for e in to_xml(r.content).find('windowsZones').find(... | python | def generate_map(timeout=10):
""" Helper method to update the map if the CLDR database is updated """
r = requests.get(CLDR_WINZONE_URL, timeout=timeout)
if r.status_code != 200:
raise ValueError('Unexpected response: %s' % r)
tz_map = {}
for e in to_xml(r.content).find('windowsZones').find(... | [
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tanghaibao/goatools | scripts/compare_gos.py | run | def run():
"""Compare two or more sets of GO IDs. Best done using sections."""
obj = CompareGOsCli()
obj.write(obj.kws.get('xlsx'), obj.kws.get('ofile'), obj.kws.get('verbose', False)) | python | def run():
"""Compare two or more sets of GO IDs. Best done using sections."""
obj = CompareGOsCli()
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tanghaibao/goatools | goatools/grouper/sorter_gos.py | SorterGoIds.sortby | def sortby(self, ntd):
"""Return function for sorting."""
if 'reldepth' in self.grprobj.gosubdag.prt_attr['flds']:
return [ntd.NS, -1*ntd.dcnt, ntd.reldepth]
else:
return [ntd.NS, -1*ntd.dcnt, ntd.depth] | python | def sortby(self, ntd):
"""Return function for sorting."""
if 'reldepth' in self.grprobj.gosubdag.prt_attr['flds']:
return [ntd.NS, -1*ntd.dcnt, ntd.reldepth]
else:
return [ntd.NS, -1*ntd.dcnt, ntd.depth] | [
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tanghaibao/goatools | goatools/grouper/sorter_gos.py | SorterGoIds.get_nts_sorted | def get_nts_sorted(self, hdrgo_prt, hdrgos, hdrgo_sort):
"""Return a flat list of grouped and sorted GO terms."""
nts_flat = []
self.get_sorted_hdrgo2usrgos(hdrgos, nts_flat, hdrgo_prt, hdrgo_sort)
return nts_flat | python | def get_nts_sorted(self, hdrgo_prt, hdrgos, hdrgo_sort):
"""Return a flat list of grouped and sorted GO terms."""
nts_flat = []
self.get_sorted_hdrgo2usrgos(hdrgos, nts_flat, hdrgo_prt, hdrgo_sort)
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tanghaibao/goatools | goatools/grouper/sorter_gos.py | SorterGoIds.get_sorted_hdrgo2usrgos | def get_sorted_hdrgo2usrgos(self, hdrgos, flat_list=None, hdrgo_prt=True, hdrgo_sort=True):
"""Return GO IDs sorting using go2nt's namedtuple."""
# Return user-specfied sort or default sort of header and user GO IDs
sorted_hdrgos_usrgos = []
h2u_get = self.grprobj.hdrgo2usrgos.get
... | python | def get_sorted_hdrgo2usrgos(self, hdrgos, flat_list=None, hdrgo_prt=True, hdrgo_sort=True):
"""Return GO IDs sorting using go2nt's namedtuple."""
# Return user-specfied sort or default sort of header and user GO IDs
sorted_hdrgos_usrgos = []
h2u_get = self.grprobj.hdrgo2usrgos.get
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tanghaibao/goatools | goatools/grouper/sorter_gos.py | SorterGoIds._get_go2nt | def _get_go2nt(self, goids):
"""Get go2nt for given goids."""
go2nt_all = self.grprobj.go2nt
return {go:go2nt_all[go] for go in goids} | python | def _get_go2nt(self, goids):
"""Get go2nt for given goids."""
go2nt_all = self.grprobj.go2nt
return {go:go2nt_all[go] for go in goids} | [
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tanghaibao/goatools | goatools/grouper/sorter_gos.py | SorterGoIds._init_hdrgo_sortby | def _init_hdrgo_sortby(self, hdrgo_sortby, sortby):
"""Initialize header sort function."""
if hdrgo_sortby is not None:
return hdrgo_sortby
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return sortby
return self.sortby | python | def _init_hdrgo_sortby(self, hdrgo_sortby, sortby):
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if hdrgo_sortby is not None:
return hdrgo_sortby
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return sortby
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tanghaibao/goatools | goatools/godag_plot.py | plot_goid2goobj | def plot_goid2goobj(fout_png, goid2goobj, *args, **kws):
"""Given a dict containing GO id and its goobj, create a plot of paths from GO ids."""
engine = kws['engine'] if 'engine' in kws else 'pydot'
godagsmall = OboToGoDagSmall(goid2goobj=goid2goobj).godag
godagplot = GODagSmallPlot(godagsmall, *args, *... | python | def plot_goid2goobj(fout_png, goid2goobj, *args, **kws):
"""Given a dict containing GO id and its goobj, create a plot of paths from GO ids."""
engine = kws['engine'] if 'engine' in kws else 'pydot'
godagsmall = OboToGoDagSmall(goid2goobj=goid2goobj).godag
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tanghaibao/goatools | goatools/godag_plot.py | GODagSmallPlot._init_study_items_max | def _init_study_items_max(self):
"""User can limit the number of genes printed in a GO term."""
if self.study_items is None:
return None
if self.study_items is True:
return None
if isinstance(self.study_items, int):
return self.study_items
retu... | python | def _init_study_items_max(self):
"""User can limit the number of genes printed in a GO term."""
if self.study_items is None:
return None
if self.study_items is True:
return None
if isinstance(self.study_items, int):
return self.study_items
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tanghaibao/goatools | goatools/godag_plot.py | GODagSmallPlot._init_go2res | def _init_go2res(**kws):
"""Initialize GOEA results."""
if 'goea_results' in kws:
return {res.GO:res for res in kws['goea_results']}
if 'go2nt' in kws:
return kws['go2nt'] | python | def _init_go2res(**kws):
"""Initialize GOEA results."""
if 'goea_results' in kws:
return {res.GO:res for res in kws['goea_results']}
if 'go2nt' in kws:
return kws['go2nt'] | [
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tanghaibao/goatools | goatools/godag_plot.py | GODagSmallPlot._get_pydot | def _get_pydot(self):
"""Return pydot package. Load pydot, if necessary."""
if self.pydot:
return self.pydot
self.pydot = __import__("pydot")
return self.pydot | python | def _get_pydot(self):
"""Return pydot package. Load pydot, if necessary."""
if self.pydot:
return self.pydot
self.pydot = __import__("pydot")
return self.pydot | [
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tanghaibao/goatools | goatools/wr_tbl.py | wr_xlsx | def wr_xlsx(fout_xlsx, data_xlsx, **kws):
"""Write a spreadsheet into a xlsx file."""
from goatools.wr_tbl_class import WrXlsx
# optional keyword args: fld2col_widths hdrs prt_if sort_by fld2fmt prt_flds
items_str = kws.get("items", "items") if "items" not in kws else kws["items"]
if data_xlsx:
... | python | def wr_xlsx(fout_xlsx, data_xlsx, **kws):
"""Write a spreadsheet into a xlsx file."""
from goatools.wr_tbl_class import WrXlsx
# optional keyword args: fld2col_widths hdrs prt_if sort_by fld2fmt prt_flds
items_str = kws.get("items", "items") if "items" not in kws else kws["items"]
if data_xlsx:
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tanghaibao/goatools | goatools/wr_tbl.py | wr_xlsx_sections | def wr_xlsx_sections(fout_xlsx, xlsx_data, **kws):
"""Write xlsx file containing section names followed by lines of namedtuple data."""
from goatools.wr_tbl_class import WrXlsx
items_str = "items" if "items" not in kws else kws["items"]
prt_hdr_min = 10
num_items = 0
if xlsx_data:
# Basi... | python | def wr_xlsx_sections(fout_xlsx, xlsx_data, **kws):
"""Write xlsx file containing section names followed by lines of namedtuple data."""
from goatools.wr_tbl_class import WrXlsx
items_str = "items" if "items" not in kws else kws["items"]
prt_hdr_min = 10
num_items = 0
if xlsx_data:
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tanghaibao/goatools | goatools/wr_tbl.py | wr_tsv | def wr_tsv(fout_tsv, tsv_data, **kws):
"""Write a file of tab-separated table data"""
items_str = "items" if "items" not in kws else kws["items"]
if tsv_data:
ifstrm = sys.stdout if fout_tsv is None else open(fout_tsv, 'w')
num_items = prt_tsv(ifstrm, tsv_data, **kws)
if fout_tsv is ... | python | def wr_tsv(fout_tsv, tsv_data, **kws):
"""Write a file of tab-separated table data"""
items_str = "items" if "items" not in kws else kws["items"]
if tsv_data:
ifstrm = sys.stdout if fout_tsv is None else open(fout_tsv, 'w')
num_items = prt_tsv(ifstrm, tsv_data, **kws)
if fout_tsv is ... | [
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tanghaibao/goatools | goatools/wr_tbl.py | prt_tsv_sections | def prt_tsv_sections(prt, tsv_data, **kws):
"""Write tsv file containing section names followed by lines of namedtuple data."""
prt_hdr_min = 10 # Print hdr on the 1st section and for any following 'large' sections
num_items = 0
if tsv_data:
# Basic data checks
assert len(tsv_data[0]) =... | python | def prt_tsv_sections(prt, tsv_data, **kws):
"""Write tsv file containing section names followed by lines of namedtuple data."""
prt_hdr_min = 10 # Print hdr on the 1st section and for any following 'large' sections
num_items = 0
if tsv_data:
# Basic data checks
assert len(tsv_data[0]) =... | [
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tanghaibao/goatools | goatools/wr_tbl.py | prt_tsv | def prt_tsv(prt, data_nts, **kws):
"""Print tab-separated table headers and data"""
# User-controlled printing options
prt_tsv_hdr(prt, data_nts, **kws)
return prt_tsv_dat(prt, data_nts, **kws) | python | def prt_tsv(prt, data_nts, **kws):
"""Print tab-separated table headers and data"""
# User-controlled printing options
prt_tsv_hdr(prt, data_nts, **kws)
return prt_tsv_dat(prt, data_nts, **kws) | [
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tanghaibao/goatools | goatools/wr_tbl.py | prt_tsv_hdr | def prt_tsv_hdr(prt, data_nts, **kws):
"""Print tab-separated table headers"""
sep = "\t" if 'sep' not in kws else kws['sep']
flds_all = data_nts[0]._fields
hdrs = get_hdrs(flds_all, **kws)
prt.write("# {}\n".format(sep.join(hdrs))) | python | def prt_tsv_hdr(prt, data_nts, **kws):
"""Print tab-separated table headers"""
sep = "\t" if 'sep' not in kws else kws['sep']
flds_all = data_nts[0]._fields
hdrs = get_hdrs(flds_all, **kws)
prt.write("# {}\n".format(sep.join(hdrs))) | [
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tanghaibao/goatools | goatools/wr_tbl.py | prt_tsv_dat | def prt_tsv_dat(prt, data_nts, **kws):
"""Print tab-separated table data"""
sep = "\t" if 'sep' not in kws else kws['sep']
fld2fmt = None if 'fld2fmt' not in kws else kws['fld2fmt']
if 'sort_by' in kws:
data_nts = sorted(data_nts, key=kws['sort_by'])
prt_if = kws['prt_if'] if 'prt_if' in kws... | python | def prt_tsv_dat(prt, data_nts, **kws):
"""Print tab-separated table data"""
sep = "\t" if 'sep' not in kws else kws['sep']
fld2fmt = None if 'fld2fmt' not in kws else kws['fld2fmt']
if 'sort_by' in kws:
data_nts = sorted(data_nts, key=kws['sort_by'])
prt_if = kws['prt_if'] if 'prt_if' in kws... | [
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tanghaibao/goatools | goatools/wr_tbl.py | _chk_flds_fmt | def _chk_flds_fmt(nt_fields, prtfmt):
"""Check that all fields in the prtfmt have corresponding data in the namedtuple."""
fmtflds = get_fmtflds(prtfmt)
missing_data = set(fmtflds).difference(set(nt_fields))
# All data needed for print is present, return.
if not missing_data:
return
#rai... | python | def _chk_flds_fmt(nt_fields, prtfmt):
"""Check that all fields in the prtfmt have corresponding data in the namedtuple."""
fmtflds = get_fmtflds(prtfmt)
missing_data = set(fmtflds).difference(set(nt_fields))
# All data needed for print is present, return.
if not missing_data:
return
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tanghaibao/goatools | goatools/wr_tbl.py | _prt_txt_hdr | def _prt_txt_hdr(prt, prtfmt):
"""Print header for text report."""
tblhdrs = get_fmtfldsdict(prtfmt)
# If needed, reformat for format_string for header, which has strings, not floats.
hdrfmt = re.sub(r':(\d+)\.\S+}', r':\1}', prtfmt)
hdrfmt = re.sub(r':(0+)(\d+)}', r':\2}', hdrfmt)
prt.write("#{... | python | def _prt_txt_hdr(prt, prtfmt):
"""Print header for text report."""
tblhdrs = get_fmtfldsdict(prtfmt)
# If needed, reformat for format_string for header, which has strings, not floats.
hdrfmt = re.sub(r':(\d+)\.\S+}', r':\1}', prtfmt)
hdrfmt = re.sub(r':(0+)(\d+)}', r':\2}', hdrfmt)
prt.write("#{... | [
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tanghaibao/goatools | goatools/wr_tbl.py | mk_fmtfld | def mk_fmtfld(nt_item, joinchr=" ", eol="\n"):
"""Given a namedtuple, return a format_field string."""
fldstrs = []
# Default formats based on fieldname
fld2fmt = {
'hdrgo' : lambda f: "{{{FLD}:1,}}".format(FLD=f),
'dcnt' : lambda f: "{{{FLD}:6,}}".format(FLD=f),
'level' : lambda... | python | def mk_fmtfld(nt_item, joinchr=" ", eol="\n"):
"""Given a namedtuple, return a format_field string."""
fldstrs = []
# Default formats based on fieldname
fld2fmt = {
'hdrgo' : lambda f: "{{{FLD}:1,}}".format(FLD=f),
'dcnt' : lambda f: "{{{FLD}:6,}}".format(FLD=f),
'level' : lambda... | [
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tanghaibao/goatools | goatools/cli/compare_gos.py | CompareGOsCli._get_prtfmt | def _get_prtfmt(self, objgowr, verbose):
"""Get print format containing markers."""
prtfmt = objgowr.get_prtfmt('fmt')
prtfmt = prtfmt.replace('# ', '')
# print('PPPPPPPPPPP', prtfmt)
if not verbose:
prtfmt = prtfmt.replace('{hdr1usr01:2}', '')
prtfmt = pr... | python | def _get_prtfmt(self, objgowr, verbose):
"""Get print format containing markers."""
prtfmt = objgowr.get_prtfmt('fmt')
prtfmt = prtfmt.replace('# ', '')
# print('PPPPPPPPPPP', prtfmt)
if not verbose:
prtfmt = prtfmt.replace('{hdr1usr01:2}', '')
prtfmt = pr... | [
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tanghaibao/goatools | goatools/cli/compare_gos.py | CompareGOsCli._wr_ver_n_key | def _wr_ver_n_key(self, fout_txt, verbose):
"""Write GO DAG version and key indicating presence of GO ID in a list."""
with open(fout_txt, 'w') as prt:
self._prt_ver_n_key(prt, verbose)
print(' WROTE: {TXT}'.format(TXT=fout_txt)) | python | def _wr_ver_n_key(self, fout_txt, verbose):
"""Write GO DAG version and key indicating presence of GO ID in a list."""
with open(fout_txt, 'w') as prt:
self._prt_ver_n_key(prt, verbose)
print(' WROTE: {TXT}'.format(TXT=fout_txt)) | [
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tanghaibao/goatools | goatools/cli/compare_gos.py | CompareGOsCli._prt_ver_n_key | def _prt_ver_n_key(self, prt, verbose):
"""Print GO DAG version and key indicating presence of GO ID in a list."""
pre = '# '
prt.write('# ----------------------------------------------------------------\n')
prt.write('# - Description of GO ID fields\n')
prt.write('# ------------... | python | def _prt_ver_n_key(self, prt, verbose):
"""Print GO DAG version and key indicating presence of GO ID in a list."""
pre = '# '
prt.write('# ----------------------------------------------------------------\n')
prt.write('# - Description of GO ID fields\n')
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tanghaibao/goatools | goatools/cli/compare_gos.py | _Init.get_grouped | def get_grouped(self, go_ntsets, go_all, gosubdag, **kws):
"""Get Grouped object."""
kws_grpd = {k:v for k, v in kws.items() if k in Grouped.kws_dict}
kws_grpd['go2nt'] = self._init_go2ntpresent(go_ntsets, go_all, gosubdag)
return Grouped(gosubdag, self.godag.version, **kws_grpd) | python | def get_grouped(self, go_ntsets, go_all, gosubdag, **kws):
"""Get Grouped object."""
kws_grpd = {k:v for k, v in kws.items() if k in Grouped.kws_dict}
kws_grpd['go2nt'] = self._init_go2ntpresent(go_ntsets, go_all, gosubdag)
return Grouped(gosubdag, self.godag.version, **kws_grpd) | [
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tanghaibao/goatools | goatools/cli/compare_gos.py | _Init._init_go2ntpresent | def _init_go2ntpresent(go_ntsets, go_all, gosubdag):
"""Mark all GO IDs with an X if present in the user GO list."""
go2ntpresent = {}
ntobj = namedtuple('NtPresent', " ".join(nt.hdr for nt in go_ntsets))
# Get present marks for GO sources
for goid_all in go_all:
pres... | python | def _init_go2ntpresent(go_ntsets, go_all, gosubdag):
"""Mark all GO IDs with an X if present in the user GO list."""
go2ntpresent = {}
ntobj = namedtuple('NtPresent', " ".join(nt.hdr for nt in go_ntsets))
# Get present marks for GO sources
for goid_all in go_all:
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tanghaibao/goatools | goatools/cli/compare_gos.py | _Init.get_go_ntsets | def get_go_ntsets(self, go_fins):
"""For each file containing GOs, extract GO IDs, store filename and header."""
nts = []
ntobj = namedtuple('NtGOFiles', 'hdr go_set, go_fin')
go_sets = self._init_go_sets(go_fins)
hdrs = [os.path.splitext(os.path.basename(f))[0] for f in go_fins]... | python | def get_go_ntsets(self, go_fins):
"""For each file containing GOs, extract GO IDs, store filename and header."""
nts = []
ntobj = namedtuple('NtGOFiles', 'hdr go_set, go_fin')
go_sets = self._init_go_sets(go_fins)
hdrs = [os.path.splitext(os.path.basename(f))[0] for f in go_fins]... | [
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tanghaibao/goatools | goatools/cli/compare_gos.py | _Init._init_go_sets | def _init_go_sets(self, go_fins):
"""Get lists of GO IDs."""
go_sets = []
assert go_fins, "EXPECTED FILES CONTAINING GO IDs"
assert len(go_fins) >= 2, "EXPECTED 2+ GO LISTS. FOUND: {L}".format(
L=' '.join(go_fins))
obj = GetGOs(self.godag)
for fin in go_fins:
... | python | def _init_go_sets(self, go_fins):
"""Get lists of GO IDs."""
go_sets = []
assert go_fins, "EXPECTED FILES CONTAINING GO IDs"
assert len(go_fins) >= 2, "EXPECTED 2+ GO LISTS. FOUND: {L}".format(
L=' '.join(go_fins))
obj = GetGOs(self.godag)
for fin in go_fins:
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tanghaibao/goatools | goatools/gosubdag/godag_rcnt.py | CountRelatives.get_parents_letters | def get_parents_letters(self, goobj):
"""Get the letters representing all parent terms which are depth-01 GO terms."""
parents_all = set.union(self.go2parents[goobj.id])
parents_all.add(goobj.id)
# print "{}({}) D{:02}".format(goobj.id, goobj.name, goobj.depth), parents_all
paren... | python | def get_parents_letters(self, goobj):
"""Get the letters representing all parent terms which are depth-01 GO terms."""
parents_all = set.union(self.go2parents[goobj.id])
parents_all.add(goobj.id)
# print "{}({}) D{:02}".format(goobj.id, goobj.name, goobj.depth), parents_all
paren... | [
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tanghaibao/goatools | goatools/gosubdag/godag_rcnt.py | CountRelatives.get_d1str | def get_d1str(self, goobj, reverse=False):
"""Get D1-string representing all parent terms which are depth-01 GO terms."""
return "".join(sorted(self.get_parents_letters(goobj), reverse=reverse)) | python | def get_d1str(self, goobj, reverse=False):
"""Get D1-string representing all parent terms which are depth-01 GO terms."""
return "".join(sorted(self.get_parents_letters(goobj), reverse=reverse)) | [
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tanghaibao/goatools | goatools/gosubdag/go_most_specific.py | get_most_specific_dcnt | def get_most_specific_dcnt(goids, go2nt):
"""Get the GO ID with the lowest descendants count."""
# go2nt_usr = {go:go2nt[go] for go in goids}
# return min(go2nt_usr.items(), key=lambda t: t[1].dcnt)[0]
return min(_get_go2nt(goids, go2nt), key=lambda t: t[1].dcnt)[0] | python | def get_most_specific_dcnt(goids, go2nt):
"""Get the GO ID with the lowest descendants count."""
# go2nt_usr = {go:go2nt[go] for go in goids}
# return min(go2nt_usr.items(), key=lambda t: t[1].dcnt)[0]
return min(_get_go2nt(goids, go2nt), key=lambda t: t[1].dcnt)[0] | [
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tanghaibao/goatools | goatools/gosubdag/go_most_specific.py | _get_go2nt | def _get_go2nt(goids, go2nt_all):
"""Get user go2nt using main GO IDs, not alt IDs."""
go_nt_list = []
goids_seen = set()
for goid_usr in goids:
ntgo = go2nt_all[goid_usr]
goid_main = ntgo.id
if goid_main not in goids_seen:
goids_seen.add(goid_main)
go_nt_... | python | def _get_go2nt(goids, go2nt_all):
"""Get user go2nt using main GO IDs, not alt IDs."""
go_nt_list = []
goids_seen = set()
for goid_usr in goids:
ntgo = go2nt_all[goid_usr]
goid_main = ntgo.id
if goid_main not in goids_seen:
goids_seen.add(goid_main)
go_nt_... | [
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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | AArtGeneProductSetsOne.prt_gos_grouped | def prt_gos_grouped(self, prt, **kws_grp):
"""Print grouped GO list."""
prtfmt = self.datobj.kws['fmtgo']
wrobj = WrXlsxSortedGos(self.name, self.sortobj)
# Keyword arguments: control content: hdrgo_prt section_prt top_n use_sections
desc2nts = self.sortobj.get_desc2nts(**kws_grp... | python | def prt_gos_grouped(self, prt, **kws_grp):
"""Print grouped GO list."""
prtfmt = self.datobj.kws['fmtgo']
wrobj = WrXlsxSortedGos(self.name, self.sortobj)
# Keyword arguments: control content: hdrgo_prt section_prt top_n use_sections
desc2nts = self.sortobj.get_desc2nts(**kws_grp... | [
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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | AArtGeneProductSetsOne.prt_gos_flat | def prt_gos_flat(self, prt):
"""Print flat GO list."""
prtfmt = self.datobj.kws['fmtgo']
_go2nt = self.sortobj.grprobj.go2nt
go2nt = {go:_go2nt[go] for go in self.go2nt}
prt.write("\n{N} GO IDs:\n".format(N=len(go2nt)))
_sortby = self._get_sortgo()
for ntgo in sor... | python | def prt_gos_flat(self, prt):
"""Print flat GO list."""
prtfmt = self.datobj.kws['fmtgo']
_go2nt = self.sortobj.grprobj.go2nt
go2nt = {go:_go2nt[go] for go in self.go2nt}
prt.write("\n{N} GO IDs:\n".format(N=len(go2nt)))
_sortby = self._get_sortgo()
for ntgo in sor... | [
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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | AArtGeneProductSetsOne._get_sortgo | def _get_sortgo(self):
"""Get function for sorting GO terms in a list of namedtuples."""
if 'sortgo' in self.datobj.kws:
return self.datobj.kws['sortgo']
return self.datobj.grprdflt.gosubdag.prt_attr['sort'] + "\n" | python | def _get_sortgo(self):
"""Get function for sorting GO terms in a list of namedtuples."""
if 'sortgo' in self.datobj.kws:
return self.datobj.kws['sortgo']
return self.datobj.grprdflt.gosubdag.prt_attr['sort'] + "\n" | [
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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | AArtGeneProductSetsOne.get_gene2binvec | def get_gene2binvec(self):
"""Return a boolean vector for each gene representing GO section membership."""
_sec2chr = self.sec2chr
return {g:[s in s2gos for s in _sec2chr] for g, s2gos in self.gene2section2gos.items()} | python | def get_gene2binvec(self):
"""Return a boolean vector for each gene representing GO section membership."""
_sec2chr = self.sec2chr
return {g:[s in s2gos for s in _sec2chr] for g, s2gos in self.gene2section2gos.items()} | [
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tanghaibao/goatools | goatools/grouper/aart_geneproducts_one.py | _Init.get_go2nt | def get_go2nt(self, goea_results):
"""Return go2nt with added formatted string versions of the P-values."""
go2obj = self.objaartall.grprdflt.gosubdag.go2obj
# Add string version of P-values
goea_nts = MgrNtGOEAs(goea_results).get_nts_strpval()
return {go2obj[nt.GO].id:nt for nt ... | python | def get_go2nt(self, goea_results):
"""Return go2nt with added formatted string versions of the P-values."""
go2obj = self.objaartall.grprdflt.gosubdag.go2obj
# Add string version of P-values
goea_nts = MgrNtGOEAs(goea_results).get_nts_strpval()
return {go2obj[nt.GO].id:nt for nt ... | [
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