Search is not available for this dataset
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def elasticsearch(line):
'''
>>> import pprint
>>> input_line = '[2017-08-30T06:27:19,158] [WARN ][o.e.m.j.JvmGcMonitorService] [Glsuj_2] [gc][296816] overhead, spent [1.2s] collecting in the last [1.3s]'
>>> output_line = elasticsearch(input_line)
>>> pprint.pprint(output_line)
{'data': {'garba... |
def elasticsearch_ispartial_log(line):
'''
>>> line1 = ' [2018-04-03T00:22:38,048][DEBUG][o.e.c.u.c.QueueResizingEsThreadPoolExecutor] [search17/search]: there were [2000] tasks in [809ms], avg task time [28.4micros], EWMA task execution [790nanos], [35165.36 tasks/s], optimal queue is [35165], current capacit... |
def get(self, attr, default=None):
"""Get an attribute defined by this session"""
attrs = self.body.get('attributes') or {}
return attrs.get(attr, default) |
def get_all(self, cat):
"""
if data can't found in cache then it will be fetched from db,
parsed and stored to cache for each lang_code.
:param cat: cat of catalog data
:return:
"""
return self._get_from_local_cache(cat) or self._get_from_cache(cat) or self._get... |
def _fill_get_item_cache(self, catalog, key):
"""
get from redis, cache locally then return
:param catalog: catalog name
:param key:
:return:
"""
lang = self._get_lang()
keylist = self.get_all(catalog)
self.ITEM_CACHE[lang][catalog] = dict([(i['va... |
def run(self, host, port, debug=True, validate_requests=True):
"""Utility method to quickly get a server up and running.
:param debug: turns on Werkzeug debugger, code reloading, and full
logging.
:param validate_requests: whether or not to ensure that requests are
sent ... |
def dispatch_request(self, body):
"""Given a parsed JSON request object, call the correct Intent, Launch,
or SessionEnded function.
This function is called after request parsing and validaion and will
raise a `ValueError` if an unknown request type comes in.
:param body: JSON o... |
def intent(self, intent_name):
"""Decorator to register a handler for the given intent.
The decorated function can either take 0 or 2 arguments. If two are
specified, it will be provided a dictionary of `{slot_name: value}` and
a :py:class:`alexandra.session.Session` instance.
... |
def set_password(self, raw_password):
"""
Kullanıcı şifresini encrypt ederek set eder.
Args:
raw_password (str)
"""
self.password = pbkdf2_sha512.encrypt(raw_password, rounds=10000,
salt_size=10) |
def encrypt_password(self):
""" encrypt password if not already encrypted """
if self.password and not self.password.startswith('$pbkdf2'):
self.set_password(self.password) |
def send_notification(self, title, message, typ=1, url=None, sender=None):
"""
sends message to users private mq exchange
Args:
title:
message:
sender:
url:
typ:
"""
self.created_channels.channel.add_message(
... |
def send_client_cmd(self, data, cmd=None, via_queue=None):
"""
Send arbitrary cmd and data to client
if queue name passed by "via_queue" parameter,
that queue will be used instead of users private exchange.
Args:
data: dict
cmd: string
via_que... |
def seek(self, offset):
"""
shifts on a given number of record in the original file
:param offset: number of record
"""
if self._shifts:
if 0 <= offset < len(self._shifts):
current_pos = self._file.tell()
new_pos = self._shifts[offset]
... |
def tell(self):
"""
:return: number of records processed from the original file
"""
if self._shifts:
t = self._file.tell()
if t == self._shifts[0]:
return 0
elif t == self._shifts[-1]:
return len(self._shifts) - 1
... |
def assign_yourself(self):
"""
Assigning the workflow to itself.
The selected job is checked to see if there is an assigned role.
If it does not have a role assigned to it, it takes the job to itself
and displays a message that the process is successful.
... |
def select_role(self):
"""
The workflow method to be assigned to the person with the same role and unit as the user.
.. code-block:: python
# request:
{
'task_inv_key': string,
}
"""
roles = [(m.key,... |
def send_workflow(self):
"""
With the workflow instance and the task invitation is assigned a role.
"""
task_invitation = TaskInvitation.objects.get(self.task_invitation_key)
wfi = task_invitation.instance
select_role = self.input['form']['select_role']
if wfi.cur... |
def select_postponed_date(self):
"""
The time intervals at which the workflow is to be extended are determined.
.. code-block:: python
# request:
{
'task_inv_key': string,
}
"""
_form = forms.Jso... |
def save_date(self):
"""
Invitations with the same workflow status are deleted.
Workflow instance and invitation roles change.
"""
task_invitation = TaskInvitation.objects.get(self.task_invitation_key)
wfi = task_invitation.instance
if wfi.current_actor.e... |
def suspend(self):
"""
If there is a role assigned to the workflow and
it is the same as the user, it can drop the workflow.
If it does not exist, it can not do anything.
.. code-block:: python
# request:
{
'task_inv_ke... |
def on_home_row(self, location=None):
"""
Finds out if the piece is on the home row.
:return: bool for whether piece is on home row or not
"""
location = location or self.location
return (self.color == color.white and location.rank == 1) or \
(self.color =... |
def would_move_be_promotion(self, location=None):
"""
Finds if move from current get_location would result in promotion
:type: location: Location
:rtype: bool
"""
location = location or self.location
return (location.rank == 1 and self.color == color.black) or \
... |
def square_in_front(self, location=None):
"""
Finds square directly in front of Pawn
:type: location: Location
:rtype: Location
"""
location = location or self.location
return location.shift_up() if self.color == color.white else location.shift_down() |
def forward_moves(self, position):
"""
Finds possible moves one step and two steps in front
of Pawn.
:type: position: Board
:rtype: list
"""
if position.is_square_empty(self.square_in_front(self.location)):
"""
If square in front is empty ... |
def _one_diagonal_capture_square(self, capture_square, position):
"""
Adds specified diagonal as a capture move if it is one
"""
if self.contains_opposite_color_piece(capture_square, position):
if self.would_move_be_promotion():
for move in self.create_promot... |
def capture_moves(self, position):
"""
Finds out all possible capture moves
:rtype: list
"""
try:
right_diagonal = self.square_in_front(self.location.shift_right())
for move in self._one_diagonal_capture_square(right_diagonal, position):
y... |
def on_en_passant_valid_location(self):
"""
Finds out if pawn is on enemy center rank.
:rtype: bool
"""
return (self.color == color.white and self.location.rank == 4) or \
(self.color == color.black and self.location.rank == 3) |
def _is_en_passant_valid(self, opponent_pawn_location, position):
"""
Finds if their opponent's pawn is next to this pawn
:rtype: bool
"""
try:
pawn = position.piece_at_square(opponent_pawn_location)
return pawn is not None and \
isinstanc... |
def add_one_en_passant_move(self, direction, position):
"""
Yields en_passant moves in given direction if it is legal.
:type: direction: function
:type: position: Board
:rtype: gen
"""
try:
if self._is_en_passant_valid(direction(self.location), positi... |
def en_passant_moves(self, position):
"""
Finds possible en passant moves.
:rtype: list
"""
# if pawn is not on a valid en passant get_location then return None
if self.on_en_passant_valid_location():
for move in itertools.chain(self.add_one_en_passant_move(... |
def possible_moves(self, position):
"""
Finds out the locations of possible moves given board.Board position.
:pre get_location is on board and piece at specified get_location on position
:type: position: Board
:rtype: list
"""
for move in itertools.chain(self.fo... |
def main():
"""
Main method
"""
print("Creating a new game...")
new_game = Game(Human(color.white), Human(color.black))
result = new_game.play()
print("Result is ", result) |
def respond(text=None, ssml=None, attributes=None, reprompt_text=None,
reprompt_ssml=None, end_session=True):
""" Build a dict containing a valid response to an Alexa request.
If speech output is desired, either of `text` or `ssml` should
be specified.
:param text: Plain text speech output... |
def reprompt(text=None, ssml=None, attributes=None):
"""Convenience method to save a little bit of typing for the common case of
reprompting the user. Simply calls :py:func:`alexandra.util.respond` with
the given arguments and holds the session open.
One of either the `text` or `ssml` should be provide... |
def validate_request_timestamp(req_body, max_diff=150):
"""Ensure the request's timestamp doesn't fall outside of the
app's specified tolerance.
Returns True if this request is valid, False otherwise.
:param req_body: JSON object parsed out of the raw POST data of a request.
:param max_diff: Maxim... |
def validate_request_certificate(headers, data):
"""Ensure that the certificate and signature specified in the
request headers are truely from Amazon and correctly verify.
Returns True if certificate verification succeeds, False otherwise.
:param headers: Dictionary (or sufficiently dictionary-like) m... |
def _get_certificate(cert_url):
"""Download and validate a specified Amazon PEM file."""
global _cache
if cert_url in _cache:
cert = _cache[cert_url]
if cert.has_expired():
_cache = {}
else:
return cert
url = urlparse(cert_url)
host = url.netloc.lowe... |
def is_processed(self, db_versions):
"""Check if version is already applied in the database.
:param db_versions:
"""
return self.number in (v.number for v in db_versions if v.date_done) |
def is_noop(self):
"""Check if version is a no operation version.
"""
has_operations = [mode.pre_operations or mode.post_operations
for mode in self._version_modes.values()]
has_upgrade_addons = [mode.upgrade_addons or mode.remove_addons
... |
def _get_version_mode(self, mode=None):
"""Return a VersionMode for a mode name.
When the mode is None, we are working with the 'base' mode.
"""
version_mode = self._version_modes.get(mode)
if not version_mode:
version_mode = self._version_modes[mode] = VersionMode(n... |
def add_operation(self, operation_type, operation, mode=None):
"""Add an operation to the version
:param mode: Name of the mode in which the operation is executed
:type mode: str
:param operation_type: one of 'pre', 'post'
:type operation_type: str
:param operation: the ... |
def add_backup_operation(self, backup, mode=None):
"""Add a backup operation to the version.
:param backup: To either add or skip the backup
:type backup: Boolean
:param mode: Name of the mode in which the operation is executed
For now, backups are mode-independent
... |
def pre_operations(self, mode=None):
""" Return pre-operations only for the mode asked """
version_mode = self._get_version_mode(mode=mode)
return version_mode.pre_operations |
def post_operations(self, mode=None):
""" Return post-operations only for the mode asked """
version_mode = self._get_version_mode(mode=mode)
return version_mode.post_operations |
def upgrade_addons_operation(self, addons_state, mode=None):
""" Return merged set of main addons and mode's addons """
installed = set(a.name for a in addons_state
if a.state in ('installed', 'to upgrade'))
base_mode = self._get_version_mode()
addons_list = base... |
def copy(self):
"""
get copy of object
:return: ReactionContainer
"""
return type(self)(reagents=[x.copy() for x in self.__reagents], meta=self.__meta.copy(),
products=[x.copy() for x in self.__products],
reactants=[x.copy() fo... |
def implicify_hydrogens(self):
"""
remove explicit hydrogens if possible
:return: number of removed hydrogens
"""
total = 0
for ml in (self.__reagents, self.__reactants, self.__products):
for m in ml:
if hasattr(m, 'implicify_hydrogens'):
... |
def reset_query_marks(self):
"""
set or reset hyb and neighbors marks to atoms.
"""
for ml in (self.__reagents, self.__reactants, self.__products):
for m in ml:
if hasattr(m, 'reset_query_marks'):
m.reset_query_marks()
self.flush_ca... |
def compose(self):
"""
get CGR of reaction
reagents will be presented as unchanged molecules
:return: CGRContainer
"""
rr = self.__reagents + self.__reactants
if rr:
if not all(isinstance(x, (MoleculeContainer, CGRContainer)) for x in rr):
... |
def calculate2d(self, force=True):
"""
recalculate 2d coordinates. currently rings can be calculated badly.
:param force: ignore existing coordinates of atoms
"""
for ml in (self.__reagents, self.__reactants, self.__products):
for m in ml:
m.calculate... |
def fix_positions(self):
"""
fix coordinates of molecules in reaction
"""
shift_x = 0
for m in self.__reactants:
max_x = self.__fix_positions(m, shift_x, 0)
shift_x = max_x + 1
arrow_min = shift_x
if self.__reagents:
for m in s... |
def get_role_keys(cls, unit_key):
"""
:param unit_key: Parent unit key
:return: role keys of subunits
"""
stack = Role.objects.filter(unit_id=unit_key).values_list('key', flatten=True)
for unit_key in cls.objects.filter(parent_id=unit_key).values_list('key', flatten=True)... |
def get_permissions(self):
"""
Permissions of the user.
Returns:
List of Permission objects.
"""
user_role = self.last_login_role() if self.last_login_role_key else self.role_set[0].role
return user_role.get_permissions() |
def get_permissions(self):
"""
Soyut role ait Permission nesnelerini bulur ve code değerlerini
döner.
Returns:
list: Permission code değerleri
"""
return [p.permission.code for p in self.Permissions if p.permission.code] |
def add_permission(self, perm):
"""
Soyut Role Permission nesnesi tanımlamayı sağlar.
Args:
perm (object):
"""
self.Permissions(permission=perm)
PermissionCache.flush()
self.save() |
def add_permission_by_name(self, code, save=False):
"""
Adds a permission with given name.
Args:
code (str): Code name of the permission.
save (bool): If False, does nothing.
"""
if not save:
return ["%s | %s" % (p.name, p.code) for p in
... |
def send_notification(self, title, message, typ=1, url=None, sender=None):
"""
sends a message to user of this role's private mq exchange
"""
self.user.send_notification(title=title, message=message, typ=typ, url=url,
sender=sender) |
def would_move_be_promotion(self):
"""
Finds if move from current location would be a promotion
"""
return (self._end_loc.rank == 0 and not self.color) or \
(self._end_loc.rank == 7 and self.color) |
def connect(self, receiver, sender=None, weak=True, dispatch_uid=None):
"""
Connect receiver to sender for signal.
Arguments:
receiver
A function or an instance method which is to receive signals.
Receivers must be hashable objects.
... |
def disconnect(self, receiver=None, sender=None, dispatch_uid=None):
"""
Disconnect receiver from sender for signal.
If weak references are used, disconnect need not be called. The receiver
will be remove from dispatch automatically.
Arguments:
receiver
... |
def migrate(config):
"""Perform a migration according to config.
:param config: The configuration to be applied
:type config: Config
"""
webapp = WebApp(config.web_host, config.web_port,
custom_maintenance_file=config.web_custom_html)
webserver = WebServer(webapp)
webse... |
def main():
"""Parse the command line and run :func:`migrate`."""
parser = get_args_parser()
args = parser.parse_args()
config = Config.from_parse_args(args)
migrate(config) |
def get_permissions(cls):
"""
Generates permissions for all CrudView based class methods.
Returns:
List of Permission objects.
"""
perms = []
for kls_name, kls in cls.registry.items():
for method_name in cls.__dict__.keys():
if met... |
def _get_object_menu_models():
"""
we need to create basic permissions
for only CRUD enabled models
"""
from pyoko.conf import settings
enabled_models = []
for entry in settings.OBJECT_MENU.values():
for mdl in entry:
if 'wf' not in mdl:
enabled_models.app... |
def add(cls, code_name, name='', description=''):
"""
create a custom permission
"""
if code_name not in cls.registry:
cls.registry[code_name] = (code_name, name or code_name, description)
return code_name |
def get_mapping(self, other):
"""
get self to other mapping
"""
m = next(self._matcher(other).isomorphisms_iter(), None)
if m:
return {v: k for k, v in m.items()} |
def get_substructure_mapping(self, other, limit=1):
"""
get self to other substructure mapping
:param limit: number of matches. if 0 return iterator for all possible; if 1 return dict or None;
if > 1 return list of dicts
"""
i = self._matcher(other).subgraph_isomorph... |
def from_string(cls, alg_str):
"""
Creates a location from a two character string consisting of
the file then rank written in algebraic notation.
Examples: e4, b5, a7
:type: alg_str: str
:rtype: Location
"""
try:
return cls(int(alg_s... |
def shift(self, direction):
"""
Shifts in direction provided by ``Direction`` enum.
:type: direction: Direction
:rtype: Location
"""
try:
if direction == Direction.UP:
return self.shift_up()
elif direction == Direction.DOWN:
... |
def shift_up(self, times=1):
"""
Finds Location shifted up by 1
:rtype: Location
"""
try:
return Location(self._rank + times, self._file)
except IndexError as e:
raise IndexError(e) |
def shift_down(self, times=1):
"""
Finds Location shifted down by 1
:rtype: Location
"""
try:
return Location(self._rank - times, self._file)
except IndexError as e:
raise IndexError(e) |
def shift_right(self, times=1):
"""
Finds Location shifted right by 1
:rtype: Location
"""
try:
return Location(self._rank, self._file + times)
except IndexError as e:
raise IndexError(e) |
def shift_left(self, times=1):
"""
Finds Location shifted left by 1
:rtype: Location
"""
try:
return Location(self._rank, self._file - times)
except IndexError as e:
raise IndexError(e) |
def shift_up_right(self, times=1):
"""
Finds Location shifted up right by 1
:rtype: Location
"""
try:
return Location(self._rank + times, self._file + times)
except IndexError as e:
raise IndexError(e) |
def shift_up_left(self, times=1):
"""
Finds Location shifted up left by 1
:rtype: Location
"""
try:
return Location(self._rank + times, self._file - times)
except IndexError as e:
raise IndexError(e) |
def shift_down_right(self, times=1):
"""
Finds Location shifted down right by 1
:rtype: Location
"""
try:
return Location(self._rank - times, self._file + times)
except IndexError as e:
raise IndexError(e) |
def shift_down_left(self, times=1):
"""
Finds Location shifted down left by 1
:rtype: Location
"""
try:
return Location(self._rank - times, self._file - times)
except IndexError as e:
raise IndexError(e) |
def standardize(self):
"""
standardize functional groups
:return: number of found groups
"""
self.reset_query_marks()
seen = set()
total = 0
for n, atom in self.atoms():
if n in seen:
continue
for k, center in centr... |
def get_staged_files():
"""Get all files staged for the current commit.
"""
proc = subprocess.Popen(('git', 'status', '--porcelain'),
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
out, _ = proc.communicate()
staged_files = modified_re.findall... |
def runserver(host=None, port=None):
"""
Run Tornado server
"""
host = host or os.getenv('HTTP_HOST', '0.0.0.0')
port = port or os.getenv('HTTP_PORT', '9001')
zioloop = ioloop.IOLoop.instance()
# setup pika client:
pc = QueueManager(zioloop)
app.pc = pc
pc.connect()
app.list... |
def open(self):
"""
Called on new websocket connection.
"""
sess_id = self._get_sess_id()
if sess_id:
self.application.pc.websockets[self._get_sess_id()] = self
self.write_message(json.dumps({"cmd": "status", "status": "open"}))
else:
s... |
def on_message(self, message):
"""
called on new websocket message,
"""
log.debug("WS MSG for %s: %s" % (self._get_sess_id(), message))
self.application.pc.redirect_incoming_message(self._get_sess_id(), message, self.request) |
def _handle_headers(self):
"""
Do response processing
"""
origin = self.request.headers.get('Origin')
if not settings.DEBUG:
if origin in settings.ALLOWED_ORIGINS or not origin:
self.set_header('Access-Control-Allow-Origin', origin)
else:
... |
def post(self, view_name):
"""
login handler
"""
sess_id = None
input_data = {}
# try:
self._handle_headers()
# handle input
input_data = json_decode(self.request.body) if self.request.body else {}
input_data['path'] = view_name
#... |
def load_formatter_fn(formatter):
'''
>>> load_formatter_fn('logagg.formatters.basescript') #doctest: +ELLIPSIS
<function basescript at 0x...>
'''
obj = util.load_object(formatter)
if not hasattr(obj, 'ispartial'):
obj.ispartial = util.ispartial
return obj |
def _remove_redundancy(self, log):
"""Removes duplicate data from 'data' inside log dict and brings it
out.
>>> lc = LogCollector('file=/path/to/log_file.log:formatter=logagg.formatters.basescript', 30)
>>> log = {'id' : 46846876, 'type' : 'log',
... 'data' : {'a' : 1, ... |
def validate_log_format(self, log):
'''
>>> lc = LogCollector('file=/path/to/file.log:formatter=logagg.formatters.basescript', 30)
>>> incomplete_log = {'data' : {'x' : 1, 'y' : 2},
... 'raw' : 'Not all keys present'}
>>> lc.validate_log_format(incomplete_log... |
def assign_default_log_values(self, fpath, line, formatter):
'''
>>> lc = LogCollector('file=/path/to/log_file.log:formatter=logagg.formatters.basescript', 30)
>>> from pprint import pprint
>>> formatter = 'logagg.formatters.mongodb'
>>> fpath = '/var/log/mongodb/mongodb.log'
... |
def _scan_fpatterns(self, state):
'''
For a list of given fpatterns, this starts a thread
collecting log lines from file
>>> os.path.isfile = lambda path: path == '/path/to/log_file.log'
>>> lc = LogCollector('file=/path/to/log_file.log:formatter=logagg.formatters.basescript', 3... |
def get_links(self, **kw):
"""
Prepare links of form by mimicing pyoko's get_links method's result
Args:
**kw:
Returns: list of link dicts
"""
links = [a for a in dir(self) if isinstance(getattr(self, a), Model)
and not a.startswith('_mode... |
def set_data(self, data):
"""
Fills form with data
Args:
data (dict): Data to assign form fields.
Returns:
Self. Form object.
"""
for name in self._fields:
setattr(self, name, data.get(name))
return self |
def serialize(self):
"""
Converts the form/model into JSON ready dicts/lists compatible
with `Ulakbus-UI API`_.
Example:
.. code-block:: json
{
"forms": {
"constraints": {},
"model": {
... |
def _cache_form_details(self, form):
"""
Caches some form details to lates process and validate incoming (response) form data
Args:
form: form dict
"""
cache = FormCache()
form['model']['form_key'] = cache.form_id
form['model']['form_name'] = self.__c... |
def _parse_msg_for_mongodb(self, msgs):
'''
>>> mdbf = MongoDBForwarder('no_host', '27017', 'deadpool',
... 'chimichanga', 'logs', 'collection')
>>> log = [{u'data': {u'_': {u'file': u'log.py',
... u'fn': u'start',
... ... |
def _tag_and_field_maker(self, event):
'''
>>> idbf = InfluxDBForwarder('no_host', '8086', 'deadpool',
... 'chimichanga', 'logs', 'collection')
>>> log = {u'data': {u'_': {u'file': u'log.py',
... u'fn': u'start',
... ... |
def _parse_msg_for_influxdb(self, msgs):
'''
>>> from logagg.forwarders import InfluxDBForwarder
>>> idbf = InfluxDBForwarder('no_host', '8086', 'deadpool',
... 'chimichanga', 'logs', 'collection')
>>> valid_log = [{u'data': {u'_force_this_as_field': ... |
def get_input(source, files, threads=4, readtype="1D",
combine="simple", names=None, barcoded=False):
"""Get input and process accordingly.
Data can be:
- a uncompressed, bgzip, bzip2 or gzip compressed fastq file
- a uncompressed, bgzip, bzip2 or gzip compressed fasta file
- a rich f... |
def combine_dfs(dfs, names, method):
"""Combine dataframes.
Combination is either done simple by just concatenating the DataFrames
or performs tracking by adding the name of the dataset as a column."""
if method == "track":
res = list()
for df, identifier in zip(dfs, names):
... |
def calculate_start_time(df):
"""Calculate the star_time per read.
Time data is either
a "time" (in seconds, derived from summary files) or
a "timestamp" (in UTC, derived from fastq_rich format)
and has to be converted appropriately in a datetime format time_arr
For both the time_zero is the m... |
def parser_from_buffer(cls, fp):
"""Construct YamlParser from a file pointer."""
yaml = YAML(typ="safe")
return cls(yaml.load(fp)) |
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