text_prompt stringlengths 157 13.1k | code_prompt stringlengths 7 19.8k ⌀ |
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def convert_from(fname, ext=COMPLETE, fmt=HTML):
""" Reads in a file and performs MultiMarkdown conversion, with transclusion ocurring based on the file director... |
dname = os.path.abspath(os.path.dirname(fname))
with open(fname, 'r') as fp:
src = fp.read()
return convert(src, ext, fmt, dname) |
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def manifest(txt, dname):
"""Extracts file manifest for a body of text with the given directory.""" |
_, files = _expand_source(txt, dname, HTML)
return files |
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def keys(source, ext=COMPLETE):
"""Extracts metadata keys from the provided MultiMarkdown text. Keyword arguments: source -- string containing MultiMarkdown text... |
_MMD_LIB.extract_metadata_keys.restype = ctypes.c_char_p
_MMD_LIB.extract_metadata_keys.argtypes = [ctypes.c_char_p, ctypes.c_ulong]
src = source.encode('utf-8')
all_keys = _MMD_LIB.extract_metadata_keys(src, ext)
all_keys = all_keys.decode('utf-8') if all_keys else ''
key_list = [ii for ii in ... |
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def value(source, key, ext=COMPLETE):
"""Extracts value for the specified metadata key from the given extension set. Keyword arguments: source -- string containi... |
_MMD_LIB.extract_metadata_value.restype = ctypes.c_char_p
_MMD_LIB.extract_metadata_value.argtypes = [ctypes.c_char_p, ctypes.c_ulong, ctypes.c_char_p]
src = source.encode('utf-8')
dkey = key.encode('utf-8')
value = _MMD_LIB.extract_metadata_value(src, ext, dkey)
return value.decode('utf-8') ... |
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def tweet(self, text, in_reply_to=None, filename=None, file=None):
""" Post a new tweet. :param text: the text to post :param in_reply_to: The ID of the tweet to... |
if filename is None:
return Tweet(self._client.update_status(status=text, in_reply_to_status_id=in_reply_to)._json)
else:
return Tweet(self._client.update_with_media(filename=filename, file=file,
status=text, in_reply_to_s... |
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def retweet(self, id):
""" Retweet a tweet. :param id: ID of the tweet in question :return: True if success, False otherwise """ |
try:
self._client.retweet(id=id)
return True
except TweepError as e:
if e.api_code == TWITTER_PAGE_DOES_NOT_EXISTS_ERROR:
return False
raise |
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def get_tweet(self, id):
""" Get an existing tweet. :param id: ID of the tweet in question :return: Tweet object. None if not found """ |
try:
return Tweet(self._client.get_status(id=id)._json)
except TweepError as e:
if e.api_code == TWITTER_TWEET_NOT_FOUND_ERROR:
return None
raise |
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def get_user(self, id):
""" Get a user's info. :param id: ID of the user in question :return: User object. None if not found """ |
try:
return User(self._client.get_user(user_id=id)._json)
except TweepError as e:
if e.api_code == TWITTER_USER_NOT_FOUND_ERROR:
return None
raise |
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def remove_tweet(self, id):
""" Delete a tweet. :param id: ID of the tweet in question :return: True if success, False otherwise """ |
try:
self._client.destroy_status(id=id)
return True
except TweepError as e:
if e.api_code in [TWITTER_PAGE_DOES_NOT_EXISTS_ERROR, TWITTER_DELETE_OTHER_USER_TWEET]:
return False
raise |
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def create_list(self, name, mode='public', description=None):
""" Create a list :param name: Name of the new list :param mode: :code:`'public'` (default) or :cod... |
return List(tweepy_list_to_json(self._client.create_list(name=name, mode=mode, description=description))) |
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def destroy_list(self, list_id):
""" Destroy a list :param list_id: list ID number :return: The destroyed list object :rtype: :class:`~responsebot.models.List` "... |
return List(tweepy_list_to_json(self._client.destroy_list(list_id=list_id))) |
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def update_list(self, list_id, name=None, mode=None, description=None):
""" Update a list :param list_id: list ID number :param name: New name for the list :para... |
return List(tweepy_list_to_json(
self._client.update_list(list_id=list_id, name=name, mode=mode, description=description))
) |
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def list_timeline(self, list_id, since_id=None, max_id=None, count=20):
""" List the tweets of specified list. :param list_id: list ID number :param since_id: re... |
statuses = self._client.list_timeline(list_id=list_id, since_id=since_id, max_id=max_id, count=count)
return [Tweet(tweet._json) for tweet in statuses] |
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def get_list(self, list_id):
""" Get info of specified list :param list_id: list ID number :return: :class:`~responsebot.models.List` object """ |
return List(tweepy_list_to_json(self._client.get_list(list_id=list_id))) |
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def add_list_member(self, list_id, user_id):
""" Add a user to list :param list_id: list ID number :param user_id: user ID number :return: :class:`~responsebot.m... |
return List(tweepy_list_to_json(self._client.add_list_member(list_id=list_id, user_id=user_id))) |
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def remove_list_member(self, list_id, user_id):
""" Remove a user from a list :param list_id: list ID number :param user_id: user ID number :return: :class:`~res... |
return List(tweepy_list_to_json(self._client.remove_list_member(list_id=list_id, user_id=user_id))) |
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def list_members(self, list_id):
""" List users in a list :param list_id: list ID number :return: list of :class:`~responsebot.models.User` objects """ |
return [User(user._json) for user in self._client.list_members(list_id=list_id)] |
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def is_list_member(self, list_id, user_id):
""" Check if a user is member of a list :param list_id: list ID number :param user_id: user ID number :return: :code:... |
try:
return bool(self._client.show_list_member(list_id=list_id, user_id=user_id))
except TweepError as e:
if e.api_code == TWITTER_USER_IS_NOT_LIST_MEMBER_SUBSCRIBER:
return False
raise |
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def subscribe_list(self, list_id):
""" Subscribe to a list :param list_id: list ID number :return: :class:`~responsebot.models.List` object """ |
return List(tweepy_list_to_json(self._client.subscribe_list(list_id=list_id))) |
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def unsubscribe_list(self, list_id):
""" Unsubscribe to a list :param list_id: list ID number :return: :class:`~responsebot.models.List` object """ |
return List(tweepy_list_to_json(self._client.unsubscribe_list(list_id=list_id))) |
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def list_subscribers(self, list_id):
""" List subscribers of a list :param list_id: list ID number :return: :class:`~responsebot.models.User` object """ |
return [User(user._json) for user in self._client.list_subscribers(list_id=list_id)] |
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def is_subscribed_list(self, list_id, user_id):
""" Check if user is a subscribed of specified list :param list_id: list ID number :param user_id: user ID number... |
try:
return bool(self._client.show_list_subscriber(list_id=list_id, user_id=user_id))
except TweepError as e:
if e.api_code == TWITTER_USER_IS_NOT_LIST_MEMBER_SUBSCRIBER:
return False
raise |
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def auth(config):
""" Perform authentication with Twitter and return a client instance to communicate with Twitter :param config: ResponseBot config :type config... |
auth = tweepy.OAuthHandler(config.get('consumer_key'), config.get('consumer_secret'))
auth.set_access_token(config.get('token_key'), config.get('token_secret'))
api = tweepy.API(auth)
try:
api.verify_credentials()
except RateLimitError as e:
raise APIQuotaError(e.args[0][0]['messag... |
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def bind(self, instance_id: str, binding_id: str, details: BindDetails) -> Binding: """Binding the instance see openbrokerapi documentation """ |
# Find the instance
instance = self._backend.find(instance_id)
# Find or create the binding
binding = self._backend.find(binding_id, instance)
# Create the binding if needed
return self._backend.bind(binding, details.parameters) |
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| def post(self, path, data={}):
'''Perform POST Request '''
response = requests.post(API_URL + path, data=json.dumps(data), headers=self._set_headers())
return self._check_response(response, self.post, path, data) |
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| def delete(self, path, data={}):
'''Perform DELETE Request'''
if len(data) != 0:
parameter_string = ''
for k,v in data.items():
parameter_string += '{}={}'.format(k,v)
parameter_string += '&'
path += '?' + parameter_string
resp... |
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def parsed(self):
"""Get the ConfigParser object which represents the content. This property is cached and only parses the content once. """ |
if not self._parsed:
self._parsed = ConfigParser()
self._parsed.readfp(io.StringIO(self.content))
return self._parsed |
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def create_cache(directory, compress_level=6, value_type_is_binary=False, **kwargs):
""" Create a html cache. Html string will be automatically compressed. :para... |
cache = diskcache.Cache(
directory,
disk=CompressedDisk,
disk_compress_level=compress_level,
disk_value_type_is_binary=value_type_is_binary,
**kwargs
)
return cache |
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def timeticks(tdiff):
""" NOTE do NOT use "interval" or ticks are misaligned! use "bysecond" only! """ |
if isinstance(tdiff, xarray.DataArray): # len==1
tdiff = timedelta(seconds=tdiff.values / np.timedelta64(1, 's'))
assert isinstance(tdiff, timedelta), 'expecting datetime.timedelta'
if tdiff > timedelta(hours=2):
return None, None
elif tdiff > timedelta(minutes=20):
return M... |
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def consume(self, msg):
"""Called with each incoming fedmsg. From here we trigger an rpm-ostree compose by touching a specific file under the `touch_dir`. Then o... |
self.log.info(msg)
body = msg['body']
topic = body['topic']
repo = None
if 'rawhide' in topic:
arch = body['msg']['arch']
self.log.info('New rawhide %s compose ready', arch)
repo = 'rawhide'
elif 'branched' in topic:
arch ... |
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| def parse_addr(text):
"Parse a 1- to 3-part address spec."
if text:
parts = text.split(':')
length = len(parts)
if length== 3:
return parts[0], parts[1], int(parts[2])
elif length == 2:
return None, parts[0], int(parts[1])
elif length == 1:
... |
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| def start(self):
"Start the service"
# register signals
gevent.signal(signal.SIGINT, self._shutdown)
# spawn the flush trigger
def _flush_impl():
while 1:
gevent.sleep(self._stats.interval)
# rotate stats
stats = self.... |
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| def _process(self, data):
"Process a single packet and update the internal tables."
parts = data.split(':')
if self._debug:
self.error('packet: %r' % data)
if not parts:
return
# interpret the packet and update stats
stats = self._stats
ke... |
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def section(self, resources):
""" Which section is this in, if any """ |
section = [p for p in self.parents(resources) if p.rtype == 'section']
if section:
return section[0]
return None |
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def in_navitem(self, resources, nav_href):
""" Given href of nav item, determine if resource is in it """ |
# The navhref might end with '/index' so remove it if so
if nav_href.endswith('/index'):
nav_href = nav_href[:-6]
return self.docname.startswith(nav_href) |
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def is_published(self):
""" Return true if this resource has published date in the past """ |
now = datetime.now()
published = self.props.published
if published:
return published < now
return False |
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def _create_driver(self, **kwargs):
""" Create webdriver, assign it to ``self.driver``, and run webdriver initiation process, which is usually used for manual lo... |
if self.driver is None:
self.driver = self.create_driver(**kwargs)
self.init_driver_func(self.driver) |
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def deserialize_time(data):
"""Return a time instance based on the values of the data param""" |
parsed = parser.parse(data)
return parsed.time().replace(tzinfo=parsed.tzinfo) |
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| def require(*args, **kwargs):
'''
Install a set of packages using pip
This is designed to be an interface for IPython notebooks that
replicates the requirements.txt pip format. This lets notebooks
specify which versions of packages they need inside the notebook
itself.
This function is... |
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def handle(self, *args, **options):
""" Compares current database with a migrations. Creates a temporary database, applies all the migrations to it, and then dum... |
self.db = options.get("database", DEFAULT_DB_ALIAS)
self.current_name = connections[self.db].settings_dict["NAME"]
self.compare_name = options.get("db_name")
self.lines = options.get("lines")
self.ignore = int(options.get('ignore'))
if not self.compare_name:
... |
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def render_widgets(kb_app: kb, sphinx_app: Sphinx, doctree: doctree, fromdocname: str, ):
""" Go through docs and replace widget directive with rendering """ |
builder: StandaloneHTMLBuilder = sphinx_app.builder
for node in doctree.traverse(widget):
# Render the output
w = sphinx_app.env.widgets.get(node.name)
context = builder.globalcontext.copy()
# Add in certain globals
context['resources'] = sphinx_app.env.resources
... |
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def auth_string(self):
""" Get the auth string. If the token is expired and auto refresh enabled, a new token will be fetched :return: the auth string :rtype: st... |
if not self._token:
self.execute()
if not self._token.expired:
return 'Bearer {}'.format(self._token.access_token)
if self.auto_refresh:
self.execute()
return 'Bearer {}'.format(self._token.access_token)
raise TokenExpired() |
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def admin_penalty(self, column=None, value=None, **kwargs):
""" An enforcement action that results in levying the permit holder with a penalty or fine. It is use... |
return self._resolve_call('PCS_ADMIN_PENALTY_ORDER', column,
value, **kwargs) |
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def compliance_schedule(self, column=None, value=None, **kwargs):
""" A sequence of activities with associated milestones which pertains to a given permit. """ |
return self._resolve_call('PCS_CMPL_SCHD', column, value, **kwargs) |
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def compliance_violation(self, column=None, value=None, **kwargs):
""" A compliance schedule violation reflects the non-achievement of a given compliance schedul... |
return self._resolve_call('PCS_CMPL_SCHD_VIOL', column, value, **kwargs) |
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def enforcement_action(self, column=None, value=None, **kwargs):
""" A disciplinary action taken against a permit facility. The action may be applicable to one o... |
return self._resolve_call('PCS_ENFOR_ACTION', column, value, **kwargs) |
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def hearing(self, column=None, value=None, **kwargs):
""" An evidentiary hearing. """ |
return self._resolve_call('PCS_EVIDENTIARY_HEARING_EVENT', column,
value, **kwargs) |
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def industrial_user(self, column=None, value=None, **kwargs):
""" Information from the PCI_AUDIT table pertaining to industrial users, i.e. the number of signifi... |
return self._resolve_call('PCS_INDUSTRIAL_USER_INFO', column,
value, **kwargs) |
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def permit_event(self, column=None, value=None, **kwargs):
""" A permit event tracks the lifecycle of a permit from issuance to expiration. Examples include 'App... |
return self._resolve_call('PCS_PERMIT_EVENT', column, value, **kwargs) |
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def pipe_schedule(self, column=None, value=None, **kwargs):
""" Particular discharge points at a permit facility that are governed by effluent limitations and mo... |
return self._resolve_call('PCS_PIPE_SCHED', column, value, **kwargs) |
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def single_violation(self, column=None, value=None, **kwargs):
""" A single event violation is a one-time event that occurred on a fixed date, and is associated ... |
return self._resolve_call('PCS_SINGLE_EVENT_VIOL', column,
value, **kwargs) |
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def typify(value: Union[dict, list, set, str]):
""" Enhance block operation with native types. Typify takes a blockchain operation or dict/list/value, and then i... |
if type(value) == dict:
return walk_values(typify, value)
if type(value) in [list, set]:
return list(map(typify, value))
if type(value) == str:
if re.match('^\d+\.\d+ (STEEM|SBD|VESTS)$', value):
return keep_in_dict(dict(Amount(value)), ['amount', 'asset'])
if... |
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def json_expand(json_op):
""" For custom_json ops. """ |
if type(json_op) == dict and 'json' in json_op:
return update_in(json_op, ['json'], safe_json_loads)
return json_op |
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def delete(self, subnet_id):
""" This is bad delete function because one vpc can have more than one subnet. It is Ok if user only use CAL for manage cloud resour... |
# 1 : show subnet
subnet = self.client.describe_subnets(
SubnetIds=[subnet_id]).get('Subnets')[0]
vpc_id = subnet.get('VpcId')
# 2 : delete subnet
self.client.delete_subnet(SubnetId=subnet_id)
# 3 : delete vpc
return self.client.delete_vpc(VpcId=vpc_i... |
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Description:
def _clean_terminals(self):
""" Because of the optimization, there are some non existing terminals on the generated list. Remove them by checking for terms in fo... |
new_terminals = []
for term in self.grammar.grammar_terminals:
x_term = term.rfind('@')
y_term = term.rfind('A')
if y_term > x_term:
x_term = y_term
ids = term[x_term + 1:].split(',')
if len(ids) < 2:
"""It'inpu... |
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def _check_self_replicate(self, myntr):
""" For each Rule B -> c where c is a known terminal, this function searches for B occurences in rules with the form A ->... |
# print 'BFS Dictionary Update - Self Replicate'
find = 0
for nonterm in self.grammar.grammar_nonterminals_map:
for i in self.grammar.grammar_nonterminals_map[nonterm]:
if self.grammar.grammar_rules[i][0] not in self.resolved and not isinstance(
... |
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def describe(self):
""" describes a Symbol, returns a string """ |
lines = []
lines.append("Symbol = {}".format(self.name))
if len(self.tags):
tgs = ", ".join(x.tag for x in self.tags)
lines.append(" tagged = {}".format(tgs))
if len(self.aliases):
als = ", ".join(x.alias for x in self.aliases)
li... |
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def datatable_df(self):
""" returns the dataframe representation of the symbol's final data """ |
data = self._all_datatable_data()
adf = pd.DataFrame(data)
adf.columns = self.dt_all_cols
return self._finish_df(adf, 'ALL') |
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def _init_datatable(self):
"""
Instantiates the .datatable attribute, pointing to a table in the
database that stores all the cached data
""" |
try:
self.datatable = Table(self.name, Base.metadata, autoload=True)
except NoSuchTableError:
print "Creating datatable, cause it doesn't exist"
self.datatable = self._datatable_factory()
self.datatable.create()
self.datatable_exists = True |
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def _datatable_factory(self):
"""
creates a SQLAlchemy Table object with the appropriate number of
columns given the number of feeds
""" |
feed_cols = ['feed{0:03d}'.format(i + 1) for i in range(self.n_feeds)]
feed_cols = ['override_feed000'] + feed_cols + ['failsafe_feed999']
ind_sqlatyp = indexingtypes[self.index.indimp].sqlatyp
dat_sqlatyp = datadefs[self.dtype.datadef].sqlatyp
atbl = Table(self.name, B... |
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def add_tags(self, tags):
""" add a tag or tags to a Feed """ |
if isinstance(tags, (str, unicode)):
tags = [tags]
objs = object_session(self)
tmps = [FeedTag(tag=t, feed=self) for t in tags]
objs.add_all(tmps)
objs.commit() |
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def initiate_browser(self):
# Create a unique tempdir for downloaded files tempdir = os.getenv(TEMPDIR_ENVVAR, DEFAULT_TEMPDIR) tempsubdir = uuid4().hex # TODO: ... |
# Wait for a content element, and 3 extra seconds just in case
WebDriverWait(self.browser, PAGELOAD_TIMEOUT)\
.until(EC.presence_of_element_located((By.CLASS_NAME,
detailed_cls)))
self.browser.implicitly_wait(3)
self.browse... |
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def step_I_create_logrecords_with_table(context):
""" Step definition that creates one more log records by using a table. .. code-block: gherkin When I create lo... |
assert context.table, "REQUIRE: context.table"
context.table.require_columns(["category", "level", "message"])
for row in context.table.rows:
category = row["category"]
if category == "__ROOT__":
category = None
level = LogLevel.parse_type(row["level"])
message =... |
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def step_I_create_logrecord_with_table(context):
""" Create an log record by using a table to provide the parts. .. seealso: :func:`step_I_create_logrecords_with... |
assert context.table, "REQUIRE: context.table"
assert len(context.table.rows) == 1, "REQUIRE: table.row.size == 1"
step_I_create_logrecords_with_table(context) |
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def step_use_log_record_configuration(context):
""" Define log record configuration parameters. .. code-block: gherkin Given I use the log record configuration: ... |
assert context.table, "REQUIRE: context.table"
context.table.require_columns(["property", "value"])
for row in context.table.rows:
property_name = row["property"]
value = row["value"]
if property_name == "format":
context.log_record_format = value
elif property_n... |
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def smart_decode(binary, errors="strict"):
""" Automatically find the right codec to decode binary data to string. :param binary: binary data :param errors: one ... |
d = chardet.detect(binary)
encoding = d["encoding"]
confidence = d["confidence"]
text = binary.decode(encoding, errors=errors)
return text, encoding, confidence |
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def decode(self, binary, url, encoding=None, errors="strict"):
""" Decode binary to string. :param binary: binary content of a http request. :param url: endpoint... |
if encoding is None:
domain = util.get_domain(url)
if domain in self.domain_encoding_table:
encoding = self.domain_encoding_table[domain]
html = binary.decode(encoding, errors=errors)
else:
html, encoding, confidence = smart_de... |
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def modify_number_pattern(number_pattern, **kwargs):
"""Modifies a number pattern by specified keyword arguments.""" |
params = ['pattern', 'prefix', 'suffix', 'grouping',
'int_prec', 'frac_prec', 'exp_prec', 'exp_plus']
for param in params:
if param in kwargs:
continue
kwargs[param] = getattr(number_pattern, param)
return NumberPattern(**kwargs) |
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def format_currency_field(__, prec, number, locale):
"""Formats a currency field.""" |
locale = Locale.parse(locale)
currency = get_territory_currencies(locale.territory)[0]
if prec is None:
pattern, currency_digits = None, True
else:
prec = int(prec)
pattern = locale.currency_formats['standard']
pattern = modify_number_pattern(pattern, frac_prec=(prec, pr... |
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def format_float_field(__, prec, number, locale):
"""Formats a fixed-point field.""" |
format_ = u'0.'
if prec is None:
format_ += u'#' * NUMBER_DECIMAL_DIGITS
else:
format_ += u'0' * int(prec)
pattern = parse_pattern(format_)
return pattern.apply(number, locale) |
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def format_number_field(__, prec, number, locale):
"""Formats a number field.""" |
prec = NUMBER_DECIMAL_DIGITS if prec is None else int(prec)
locale = Locale.parse(locale)
pattern = locale.decimal_formats.get(None)
return pattern.apply(number, locale, force_frac=(prec, prec)) |
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def format_percent_field(__, prec, number, locale):
"""Formats a percent field.""" |
prec = PERCENT_DECIMAL_DIGITS if prec is None else int(prec)
locale = Locale.parse(locale)
pattern = locale.percent_formats.get(None)
return pattern.apply(number, locale, force_frac=(prec, prec)) |
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def format_hexadecimal_field(spec, prec, number, locale):
"""Formats a hexadeciaml field.""" |
if number < 0:
# Take two's complement.
number &= (1 << (8 * int(math.log(-number, 1 << 8) + 1))) - 1
format_ = u'0%d%s' % (int(prec or 0), spec)
return format(number, format_) |
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def delegate(attribute_name, method_names):
""" Decorator factory to delegate methods to an attribute. Decorate a class to map every method in `method_names` to ... |
call_attribute_method = partial(_call_delegated_method, attribute_name)
def decorate(class_):
for method in method_names:
setattr(class_, method, partialmethod(call_attribute_method, method))
return class_
return decorate |
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def prepare_query(query):
""" Prepare a query object for the RAPI. RAPI has lots of curious rules for coercing values. This function operates on dicts in-place a... |
for name in query:
value = query[name]
# None is sent as an empty string.
if value is None:
query[name] = ""
# Booleans are sent as 0 or 1.
elif isinstance(value, bool):
query[name] = int(value)
# XXX shouldn't this just check for basestri... |
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def itemgetters(*args):
""" Get a handful of items from an iterable. """ |
f = itemgetter(*args)
def inner(l):
return [f(x) for x in l]
return inner |
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def stat_container(self, container):
"""Stat container metadata :param container: container name (Container is equivalent to Bucket term in Amazon). """ |
LOG.debug('stat_container() with %s is success.', self.driver)
return self.driver.stat_container(container) |
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def update_container(self, container, metadata, **kwargs):
"""Update container metadata :param container: container name (Container is equivalent to Bucket term ... |
LOG.debug('update_object() with %s is success.', self.driver)
return self.driver.update_container(container, metadata, **kwargs) |
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def stat_object(self, container, obj):
"""Stat object metadata :param container: container name (Container is equivalent to Bucket term in Amazon). :param obj: o... |
LOG.debug('stat_object() with %s is success.', self.driver)
return self.driver.stat_object(container, obj) |
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def delete_object(self, container, obj, **kwargs):
"""Delete object in container :param container: container name (Container is equivalent to Bucket term in Amaz... |
try:
LOG.debug('delete_object() with %s is success.', self.driver)
return self.driver.delete_object(container, obj, **kwargs)
except DriverException as e:
LOG.exception('download_object() with %s raised\
an exception %s.', self.driver, e) |
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def list_container_objects(self, container, prefix=None, delimiter=None):
"""List container objects :param container: container name (Container is equivalent to ... |
LOG.debug('list_container_objects() with %s is success.', self.driver)
return self.driver.list_container_objects(container, prefix, delimiter) |
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def update_object(self, container, obj, metadata, **kwargs):
"""Update object metadata :param container: container name (Container is equivalent to Bucket term i... |
try:
LOG.debug('update_object() with %s is success.', self.driver)
return self.driver.update_object(container, obj,
metadata, **kwargs)
except DriverException as e:
LOG.exception('copy_object() with %s raised\
... |
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def get_path_fields(cls, base=[]):
"""Get object fields used for calculation of django-tutelary object paths. """ |
pfs = []
for pf in cls.TutelaryMeta.path_fields:
if pf == 'pk':
pfs.append(base + ['pk'])
else:
f = cls._meta.get_field(pf)
if isinstance(f, models.ForeignKey):
pfs += get_path_fields(f.target_field.model, base=base + [pf])
else:
... |
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def get_perms_object(obj, action):
"""Get the django-tutelary path for an object, based on the fields listed in ``TutelaryMeta.pfs``. """ |
def get_one(pf):
if isinstance(pf, str):
return pf
else:
return str(reduce(lambda o, f: getattr(o, f), pf, obj))
return Object([get_one(pf) for pf in obj.__class__.TutelaryMeta.pfs]) |
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def permissioned_model(cls, perm_type=None, path_fields=None, actions=None):
"""Function to set up a model for permissioning. Can either be called directly, pass... |
if not issubclass(cls, models.Model):
raise DecoratorException(
'permissioned_model',
"class '" + cls.__name__ + "' is not a Django model"
)
added = False
try:
if not hasattr(cls, 'TutelaryMeta'):
if perm_type is None or path_fields is None or act... |
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def _getArrays(items, attr, defaultValue):
"""Return arrays with equal size of item attributes from a list of sorted "items" for fast and convenient data process... |
arrays = dict([(key, []) for key in attr])
for item in items:
for key in attr:
arrays[key].append(getattr(item, key, defaultValue))
for key in [_ for _ in viewkeys(arrays)]:
arrays[key] = numpy.array(arrays[key])
return arrays |
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def addMsrunContainers(mainContainer, subContainer):
"""Adds the complete content of all specfile entries from the subContainer to the mainContainer. However if ... |
typeToContainer = {'rm': 'rmc', 'ci': 'cic', 'smi': 'smic',
'sai': 'saic', 'si': 'sic'
}
for specfile in subContainer.info:
if specfile in mainContainer.info:
continue
mainContainer.addSpecfile(specfile, subContainer.info[specfile]['pat... |
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def setPath(self, folderpath, specfiles=None):
"""Changes the folderpath of the specified specfiles. The folderpath is used for saving and loading of ``mrc`` fil... |
if specfiles is None:
specfiles = [_ for _ in viewkeys(self.info)]
else:
specfiles = aux.toList(specfiles)
_containerSetPath(self, folderpath, specfiles) |
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def removeSpecfile(self, specfiles):
"""Completely removes the specified specfiles from the ``msrunContainer``. :param specfiles: the name of an ms-run file or a... |
for specfile in aux.toList(specfiles):
for datatypeContainer in ['rmc', 'cic', 'smic', 'saic', 'sic']:
dataContainer = getattr(self, datatypeContainer)
try:
del dataContainer[specfile]
except KeyError:
pass
... |
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def _processDatatypes(self, rm, ci, smi, sai, si):
"""Helper function that returns a list of datatype strings, depending on the parameters boolean value. :param ... |
datatypes = list()
for datatype, value in [('rm', rm), ('ci', ci), ('smi', smi),
('sai', sai), ('si', si)]:
if value:
datatypes.append(datatype)
return datatypes |
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def save(self, specfiles=None, rm=False, ci=False, smi=False, sai=False, si=False, compress=True, path=None):
"""Writes the specified datatypes to ``mrc`` files ... |
if specfiles is None:
specfiles = [_ for _ in viewkeys(self.info)]
else:
specfiles = aux.toList(specfiles)
datatypes = self._processDatatypes(rm, ci, smi, sai, si)
if len(datatypes) == 0:
datatypes = ['rm', 'ci', 'smi', 'sai', 'si']
for specf... |
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def _writeRmc(self, filelike, specfile):
"""Writes the ``.rmc`` container entry of the specified specfile as an human readable and pretty formatted xml string. :... |
xmlString = ETREE.tostring(self.rmc[specfile], pretty_print=True)
filelike.write(xmlString) |
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def load(self, specfiles=None, rm=False, ci=False, smi=False, sai=False, si=False):
"""Import the specified datatypes from ``mrc`` files on the hard disk. :param... |
if specfiles is None:
specfiles = [_ for _ in viewkeys(self.info)]
else:
specfiles = aux.toList(specfiles)
#Select only specfiles which are present in the ``self.info``.
selectedSpecfiles = list()
for specfile in specfiles:
if specfile not in... |
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def jsonHook(encoded):
"""Custom JSON decoder that allows construction of a new ``Ci`` instance from a decoded JSON object. :param encoded: a JSON decoded object... |
if '__Ci__' in encoded:
return Ci._fromJSON(encoded['__Ci__'])
elif '__MzmlProduct__' in encoded:
return MzmlProduct._fromJSON(encoded['__MzmlProduct__'])
elif '__MzmlPrecursor__' in encoded:
return MzmlPrecursor._fromJSON(encoded['__MzmlPrecursor__'])
... |
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def jsonHook(encoded):
"""Custom JSON decoder that allows construction of a new ``Smi`` instance from a decoded JSON object. :param encoded: a JSON decoded objec... |
if '__Smi__' in encoded:
return Smi._fromJSON(encoded['__Smi__'])
elif '__MzmlScan__' in encoded:
return MzmlScan._fromJSON(encoded['__MzmlScan__'])
elif '__MzmlProduct__' in encoded:
return MzmlProduct._fromJSON(encoded['__MzmlProduct__'])
elif '__Mz... |
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def removeSpecfile(self, specfiles):
"""Completely removes the specified specfiles from the ``SiiContainer``. :param specfiles: the name of an ms-run file or a l... |
for specfile in aux.toList(specfiles):
del self.container[specfile]
del self.info[specfile] |
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def save(self, specfiles=None, compress=True, path=None):
"""Writes the specified specfiles to ``siic`` files on the hard disk. .. note:: If ``.save()`` is calle... |
if specfiles is None:
specfiles = [_ for _ in viewkeys(self.info)]
else:
specfiles = aux.toList(specfiles)
for specfile in specfiles:
if specfile not in self.info:
warntext = 'Error while calling "SiiContainer.save()": "%s" is'\
... |
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def calcMz(self, specfiles=None, guessCharge=True, obsMzKey='obsMz'):
"""Calculate the exact mass for ``Sii`` elements from the ``Sii.peptide`` sequence. :param ... |
#TODO: important to test function, since changes were made
_calcMass = maspy.peptidemethods.calcPeptideMass
_calcMzFromMass = maspy.peptidemethods.calcMzFromMass
_massProton = maspy.constants.atomicMassProton
_guessCharge = lambda mass, mz: round(mass / (mz - _massProton), 0)
... |
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def _writeContainer(self, filelike, specfile, compress):
"""Writes the ``self.container`` entry of the specified specfile to the ``fic`` format. :param filelike:... |
aux.writeJsonZipfile(filelike, self.container[specfile],
compress=compress
) |
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def load(self, specfiles=None):
"""Imports the specified ``fic`` files from the hard disk. :param specfiles: the name of an ms-run file or a list of names. If No... |
if specfiles is None:
specfiles = [_ for _ in viewkeys(self.info)]
else:
specfiles = aux.toList(specfiles)
for specfile in specfiles:
if specfile not in self.info:
warntext = 'Error while calling "FiContainer.load()": "%s" is'\
... |
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