INSTRUCTION stringlengths 1 8.43k | RESPONSE stringlengths 75 104k |
|---|---|
Returns a dict mapping kernel names to resource directories. | def find_kernel_specs(self):
"""Returns a dict mapping kernel names to resource directories."""
# let real installed kernels overwrite envs with the same name:
# this is the same order as the get_kernel_spec way, which also prefers
# kernels from the jupyter dir over env kernels.
... |
Returns a dict mapping kernel names and resource directories. | def get_all_specs(self):
"""Returns a dict mapping kernel names and resource directories.
"""
# This is new in 4.1 -> https://github.com/jupyter/jupyter_client/pull/93
specs = self.get_all_kernel_specs_for_envs()
specs.update(super(EnvironmentKernelSpecManager, self).get_all_spec... |
Returns a: class: KernelSpec instance for the given kernel_name. | def get_kernel_spec(self, kernel_name):
"""Returns a :class:`KernelSpec` instance for the given kernel_name.
Raises :exc:`NoSuchKernel` if the given kernel name is not found.
"""
try:
return super(EnvironmentKernelSpecManager,
self).get_kernel_spec(k... |
Transliterate serbian cyrillic string of characters to latin string of characters.: param string_to_transliterate: The cyrillic string to transliterate into latin characters.: param lang_code: Indicates the cyrillic language code we are translating from. Defaults to Serbian ( sr ).: return: A string of latin characters... | def to_latin(string_to_transliterate, lang_code='sr'):
''' Transliterate serbian cyrillic string of characters to latin string of characters.
:param string_to_transliterate: The cyrillic string to transliterate into latin characters.
:param lang_code: Indicates the cyrillic language code we are translating ... |
Transliterate serbian latin string of characters to cyrillic string of characters.: param string_to_transliterate: The latin string to transliterate into cyrillic characters.: param lang_code: Indicates the cyrillic language code we are translating to. Defaults to Serbian ( sr ).: return: A string of cyrillic character... | def to_cyrillic(string_to_transliterate, lang_code='sr'):
''' Transliterate serbian latin string of characters to cyrillic string of characters.
:param string_to_transliterate: The latin string to transliterate into cyrillic characters.
:param lang_code: Indicates the cyrillic language code we are translati... |
Parses the incoming bytestream as XML and returns the resulting data. | def parse(self, stream, media_type=None, parser_context=None):
"""
Parses the incoming bytestream as XML and returns the resulting data.
"""
assert etree, 'XMLParser requires defusedxml to be installed'
parser_context = parser_context or {}
encoding = parser_context.get(... |
convert the xml element into the corresponding python object | def _xml_convert(self, element):
"""
convert the xml `element` into the corresponding python object
"""
children = list(element)
if len(children) == 0:
return self._type_convert(element.text)
else:
# if the fist child tag is list-item means all c... |
Converts the value returned by the XMl parse into the equivalent Python type | def _type_convert(self, value):
"""
Converts the value returned by the XMl parse into the equivalent
Python type
"""
if value is None:
return value
try:
return datetime.datetime.strptime(value, '%Y-%m-%d %H:%M:%S')
except ValueError:
... |
Renders data into serialized XML. | def render(self, data, accepted_media_type=None, renderer_context=None):
"""
Renders `data` into serialized XML.
"""
if data is None:
return ''
stream = StringIO()
xml = SimplerXMLGenerator(stream, self.charset)
xml.startDocument()
xml.startE... |
Open a connection to the device. | def open(self):
"""Open a connection to the device."""
device_type = 'cisco_ios'
if self.transport == 'telnet':
device_type = 'cisco_ios_telnet'
self.device = ConnectHandler(device_type=device_type,
host=self.hostname,
... |
Write temp file and for use with inline config and SCP. | def _create_tmp_file(config):
"""Write temp file and for use with inline config and SCP."""
tmp_dir = tempfile.gettempdir()
rand_fname = py23_compat.text_type(uuid.uuid4())
filename = os.path.join(tmp_dir, rand_fname)
with open(filename, 'wt') as fobj:
fobj.write(conf... |
Transfer file to remote device for either merge or replace operations | def _load_candidate_wrapper(self, source_file=None, source_config=None, dest_file=None,
file_system=None):
"""
Transfer file to remote device for either merge or replace operations
Returns (return_status, msg)
"""
return_status = False
msg... |
SCP file to device filesystem defaults to candidate_config. | def load_replace_candidate(self, filename=None, config=None):
"""
SCP file to device filesystem, defaults to candidate_config.
Return None or raise exception
"""
self.config_replace = True
return_status, msg = self._load_candidate_wrapper(source_file=filename,
... |
SCP file to remote device. | def load_merge_candidate(self, filename=None, config=None):
"""
SCP file to remote device.
Merge configuration in: copy <file> running-config
"""
self.config_replace = False
return_status, msg = self._load_candidate_wrapper(source_file=filename,
... |
Special handler for hostname change on commit operation. | def _commit_hostname_handler(self, cmd):
"""Special handler for hostname change on commit operation."""
current_prompt = self.device.find_prompt().strip()
terminating_char = current_prompt[-1]
pattern = r"[>#{}]\s*$".format(terminating_char)
# Look exclusively for trailing patter... |
If replacement operation perform configure replace for the entire config. | def commit_config(self):
"""
If replacement operation, perform 'configure replace' for the entire config.
If merge operation, perform copy <file> running-config.
"""
# Always generate a rollback config on commit
self._gen_rollback_cfg()
if self.config_replace:
... |
Set candidate_cfg to current running - config. Erase the merge_cfg file. | def discard_config(self):
"""Set candidate_cfg to current running-config. Erase the merge_cfg file."""
discard_candidate = 'copy running-config {}'.format(self._gen_full_path(self.candidate_cfg))
discard_merge = 'copy null: {}'.format(self._gen_full_path(self.merge_cfg))
self._disable_co... |
Transfer file to remote device. | def _xfer_file(self, source_file=None, source_config=None, dest_file=None, file_system=None,
TransferClass=FileTransfer):
"""Transfer file to remote device.
By default, this will use Secure Copy if self.inline_transfer is set, then will use
Netmiko InlineTransfer method to tr... |
Generate full file path on remote device. | def _gen_full_path(self, filename, file_system=None):
"""Generate full file path on remote device."""
if file_system is None:
return '{}/{}'.format(self.dest_file_system, filename)
else:
if ":" not in file_system:
raise ValueError("Invalid file_system spec... |
Save a configuration that can be used for rollback. | def _gen_rollback_cfg(self):
"""Save a configuration that can be used for rollback."""
cfg_file = self._gen_full_path(self.rollback_cfg)
cmd = 'copy running-config {}'.format(cfg_file)
self._disable_confirm()
self.device.send_command_expect(cmd)
self._enable_confirm() |
Check that the file exists on remote device using full path. | def _check_file_exists(self, cfg_file):
"""
Check that the file exists on remote device using full path.
cfg_file is full path i.e. flash:/file_name
For example
# dir flash:/candidate_config.txt
Directory of flash:/candidate_config.txt
33 -rw- 5592 Dec... |
Obtain the full interface name from the abbreviated name. | def _expand_interface_name(self, interface_brief):
"""
Obtain the full interface name from the abbreviated name.
Cache mappings in self.interface_map.
"""
if self.interface_map.get(interface_brief):
return self.interface_map.get(interface_brief)
command = 'sh... |
IOS implementation of get_lldp_neighbors. | def get_lldp_neighbors(self):
"""IOS implementation of get_lldp_neighbors."""
lldp = {}
command = 'show lldp neighbors'
output = self._send_command(command)
# Check if router supports the command
if '% Invalid input' in output:
return {}
# Process th... |
IOS implementation of get_lldp_neighbors_detail. | def get_lldp_neighbors_detail(self, interface=''):
"""
IOS implementation of get_lldp_neighbors_detail.
Calls get_lldp_neighbors.
"""
lldp = {}
lldp_neighbors = self.get_lldp_neighbors()
# Filter to specific interface
if interface:
lldp_data ... |
Return a set of facts from the devices. | def get_facts(self):
"""Return a set of facts from the devices."""
# default values.
vendor = u'Cisco'
uptime = -1
serial_number, fqdn, os_version, hostname, domain_name = ('Unknown',) * 5
# obtain output from device
show_ver = self._send_command('show version')
... |
Get interface details. | def get_interfaces(self):
"""
Get interface details.
last_flapped is not implemented
Example Output:
{ u'Vlan1': { 'description': u'N/A',
'is_enabled': True,
'is_up': True,
'last_flapped': -1.0,
... |
Get interface ip details. | def get_interfaces_ip(self):
"""
Get interface ip details.
Returns a dict of dicts
Example Output:
{ u'FastEthernet8': { 'ipv4': { u'10.66.43.169': { 'prefix_length': 22}}},
u'Loopback555': { 'ipv4': { u'192.168.1.1': { 'prefix_length': 24}},
... |
Convert string time to seconds. | def bgp_time_conversion(bgp_uptime):
"""
Convert string time to seconds.
Examples
00:14:23
00:13:40
00:00:21
00:00:13
00:00:49
1d11h
1d17h
1w0d
8w5d
1y28w
never
"""
bgp_uptime = bgp_uptime.st... |
BGP neighbor information. | def get_bgp_neighbors(self):
"""BGP neighbor information.
Currently no VRF support. Supports both IPv4 and IPv6.
"""
supported_afi = ['ipv4', 'ipv6']
bgp_neighbor_data = dict()
bgp_neighbor_data['global'] = {}
# get summary output from device
cmd_bgp_al... |
Get environment facts. | def get_environment(self):
"""
Get environment facts.
power and fan are currently not implemented
cpu is using 1-minute average
cpu hard-coded to cpu0 (i.e. only a single CPU)
"""
environment = {}
cpu_cmd = 'show proc cpu'
mem_cmd = 'show memory s... |
Get arp table information. | def get_arp_table(self):
"""
Get arp table information.
Return a list of dictionaries having the following set of keys:
* interface (string)
* mac (string)
* ip (string)
* age (float)
For example::
[
{
... |
Execute a list of commands and return the output in a dictionary format using the command as the key. | def cli(self, commands):
"""
Execute a list of commands and return the output in a dictionary format using the command
as the key.
Example input:
['show clock', 'show calendar']
Output example:
{ 'show calendar': u'22:02:01 UTC Thu Feb 18 2016',
's... |
Returns a lists of dictionaries. Each dictionary represents an entry in the MAC Address Table having the following keys * mac ( string ) * interface ( string ) * vlan ( int ) * active ( boolean ) * static ( boolean ) * moves ( int ) * last_move ( float ) | def get_mac_address_table(self):
"""
Returns a lists of dictionaries. Each dictionary represents an entry in the MAC Address
Table, having the following keys
* mac (string)
* interface (string)
* vlan (int)
* active (boolean)
* static (... |
Executes traceroute on the device and returns a dictionary with the result. | def traceroute(self, destination, source=C.TRACEROUTE_SOURCE,
ttl=C.TRACEROUTE_TTL, timeout=C.TRACEROUTE_TIMEOUT, vrf=C.TRACEROUTE_VRF):
"""
Executes traceroute on the device and returns a dictionary with the result.
:param destination: Host or IP Address of the destination
... |
Implementation of get_config for IOS. | def get_config(self, retrieve='all'):
"""Implementation of get_config for IOS.
Returns the startup or/and running configuration as dictionary.
The keys of the dictionary represent the type of configuration
(startup or running). The candidate is always empty string,
since IOS doe... |
Set the range of the accelerometer to the provided value. Range value should be one of these constants: - ADXL345_RANGE_2_G = +/ - 2G - ADXL345_RANGE_4_G = +/ - 4G - ADXL345_RANGE_8_G = +/ - 8G - ADXL345_RANGE_16_G = +/ - 16G | def set_range(self, value):
"""Set the range of the accelerometer to the provided value. Range value
should be one of these constants:
- ADXL345_RANGE_2_G = +/-2G
- ADXL345_RANGE_4_G = +/-4G
- ADXL345_RANGE_8_G = +/-8G
- ADXL345_RANGE_16_G = +/-16G
... |
Read the current value of the accelerometer and return it as a tuple of signed 16 - bit X Y Z axis values. | def read(self):
"""Read the current value of the accelerometer and return it as a tuple
of signed 16-bit X, Y, Z axis values.
"""
raw = self._device.readList(ADXL345_REG_DATAX0, 6)
return struct.unpack('<hhh', raw) |
Stops interrupts on all boards. Only required when using: func: digital_read and: func: digital_write. | def deinit(bus=DEFAULT_SPI_BUS,
chip_select=DEFAULT_SPI_CHIP_SELECT):
"""Stops interrupts on all boards. Only required when using
:func:`digital_read` and :func:`digital_write`.
:param bus: SPI bus /dev/spidev<bus>.<chipselect> (default: {bus})
:type bus: int
:param chip_select: SPI chip... |
Writes the value to the input pin specified. | def digital_write(pin_num, value, hardware_addr=0):
"""Writes the value to the input pin specified.
.. note:: This function is for familiarality with users of other types of
IO board. Consider accessing the ``output_pins`` attribute of a
PiFaceDigital object:
>>> pfd = PiFaceDigital(hardw... |
Writes the value to the input pullup specified. | def digital_write_pullup(pin_num, value, hardware_addr=0):
"""Writes the value to the input pullup specified.
.. note:: This function is for familiarality with users of other types of
IO board. Consider accessing the ``gppub`` attribute of a
PiFaceDigital object:
>>> pfd = PiFaceDigital(h... |
Returns this computers IP address as a string. | def get_my_ip():
"""Returns this computers IP address as a string."""
ip = subprocess.check_output(GET_IP_CMD, shell=True).decode('utf-8')[:-1]
return ip.strip() |
Sets the output port value to new_value defaults to old_value. | def set_output_port(self, new_value, old_value=0):
"""Sets the output port value to new_value, defaults to old_value."""
print("Setting output port to {}.".format(new_value))
port_value = old_value
try:
port_value = int(new_value) # dec
except ValueError:
... |
Wrap the calls the url with the given arguments. | def _request_api(self, **kwargs):
"""Wrap the calls the url, with the given arguments.
:param str url: Url to call with the given arguments
:param str method: [POST | GET] Method to use on the request
:param int status: Expected status code
"""
_url = kwargs.get('url')
... |
Get info about a user based on his id. | def get_infos_with_id(self, uid):
"""Get info about a user based on his id.
:return: JSON
"""
_logid = uid
_user_info_url = USER_INFO_URL.format(logid=_logid)
return self._request_api(url=_user_info_url).json() |
Get the current activities of user. | def get_current_activities(self, login=None, **kwargs):
"""Get the current activities of user.
Either use the `login` param, or the client's login if unset.
:return: JSON
"""
_login = kwargs.get(
'login',
login or self._login
)
_activity_... |
Get the current notifications of a user. | def get_notifications(self, login=None, **kwargs):
"""Get the current notifications of a user.
:return: JSON
"""
_login = kwargs.get(
'login',
login or self._login
)
_notif_url = NOTIF_URL.format(login=_login)
return self._request_api(url... |
Get a user s grades on a single promotion based on his login. | def get_grades(self, login=None, promotion=None, **kwargs):
"""Get a user's grades on a single promotion based on his login.
Either use the `login` param, or the client's login if unset.
:return: JSON
"""
_login = kwargs.get(
'login',
login or self._logi... |
Get a user s picture. | def get_picture(self, login=None, **kwargs):
"""Get a user's picture.
:param str login: Login of the user to check
:return: JSON
"""
_login = kwargs.get(
'login',
login or self._login
)
_activities_url = PICTURE_URL.format(login=_login)
... |
Get a user s project. | def get_projects(self, **kwargs):
"""Get a user's project.
:param str login: User's login (Default: self._login)
:return: JSON
"""
_login = kwargs.get('login', self._login)
search_url = SEARCH_URL.format(login=_login)
return self._request_api(url=search_url).jso... |
Get the related activities of a project. | def get_activities_for_project(self, module=None, **kwargs):
"""Get the related activities of a project.
:param str module: Stages of a given module
:return: JSON
"""
_module_id = kwargs.get('module', module)
_activities_url = ACTIVITIES_URL.format(module_id=_module_id)... |
Get groups for activity. | def get_group_for_activity(self, module=None, project=None, **kwargs):
"""Get groups for activity.
:param str module: Base module
:param str module: Project which contains the group requested
:return: JSON
"""
_module_id = kwargs.get('module', module)
_project_i... |
Get users by promotion id. | def get_students(self, **kwargs):
"""Get users by promotion id.
:param int promotion: Promotion ID
:return: JSON
"""
_promotion_id = kwargs.get('promotion')
_url = PROMOTION_URL.format(promo_id=_promotion_id)
return self._request_api(url=_url).json() |
Get a user s log events. | def get_log_events(self, login=None, **kwargs):
"""Get a user's log events.
:param str login: User's login (Default: self._login)
:return: JSON
"""
_login = kwargs.get(
'login',
login
)
log_events_url = GSA_EVENTS_URL.format(login=_login)... |
Get a user s events. | def get_events(self, login=None, start_date=None, end_date=None, **kwargs):
"""Get a user's events.
:param str login: User's login (Default: self._login)
:param str start_date: Start date
:param str end_date: To date
:return: JSON
"""
_login = kwargs.get(
... |
Get a user s logs. | def get_logs(self, login=None, **kwargs):
"""Get a user's logs.
:param str login: User's login (Default: self._login)
:return: JSON
"""
_login = kwargs.get(
'login',
login
)
log_events_url = GSA_LOGS_URL.format(login=_login)
retur... |
Process headers dict to return the format class ( not the instance ) | def negotiate(cls, headers):
""" Process headers dict to return the format class
(not the instance)
"""
# set lower keys
headers = {k.lower(): v for k, v in headers.items()}
accept = headers.get('accept', "*/*")
parsed_accept = accept.split(";")
pars... |
Registers a collector | def register(self, collector):
""" Registers a collector"""
if not isinstance(collector, Collector):
raise TypeError(
"Can't register instance, not a valid type of collector")
if collector.name in self.collectors:
raise ValueError("Collector already exist... |
Add works like replace but only previously pushed metrics with the same name ( and the same job and instance ) will be replaced. ( It uses HTTP method POST to push to the Pushgateway. ) | def add(self, registry):
""" Add works like replace, but only previously pushed metrics with the
same name (and the same job and instance) will be replaced.
(It uses HTTP method 'POST' to push to the Pushgateway.)
"""
# POST
payload = self.formatter.marshall(regis... |
Push triggers a metric collection and pushes all collected metrics to the Pushgateway specified by addr Note that all previously pushed metrics with the same job and instance will be replaced with the metrics pushed by this call. ( It uses HTTP method PUT to push to the Pushgateway. ) | def replace(self, registry):
""" Push triggers a metric collection and pushes all collected metrics
to the Pushgateway specified by addr
Note that all previously pushed metrics with the same job and
instance will be replaced with the metrics pushed by this call.
(... |
Marshalls a collector and returns the storage/ transfer format in a tuple this tuple has reprensentation format per element. | def marshall_lines(self, collector):
""" Marshalls a collector and returns the storage/transfer format in
a tuple, this tuple has reprensentation format per element.
"""
if isinstance(collector, collectors.Counter):
exec_method = self._format_counter
elif isinsta... |
Marshalls a full registry ( various collectors ) | def marshall(self, registry):
"""Marshalls a full registry (various collectors)"""
blocks = []
for i in registry.get_all():
blocks.append(self.marshall_collector(i))
# Sort? used in tests
blocks = sorted(blocks)
# Needs EOF
blocks.append("")
... |
Returns bytes | def marshall(self, registry):
"""Returns bytes"""
result = b""
for i in registry.get_all():
# Each message needs to be prefixed with a varint with the size of
# the message (MetrycType)
# https://github.com/matttproud/golang_protobuf_extensions/blob/master/ex... |
Gathers the metrics | def gather_data(registry):
"""Gathers the metrics"""
# Get the host name of the machine
host = socket.gethostname()
# Create our collectors
trig_metric = Gauge("trigonometry_example",
"Various trigonometry examples.",
{'host': host})
# register ... |
Sets a value in the container | def set_value(self, labels, value):
""" Sets a value in the container"""
if labels:
self._label_names_correct(labels)
with mutex:
self.values[labels] = value |
Raise exception ( ValueError ) if labels not correct | def _label_names_correct(self, labels):
"""Raise exception (ValueError) if labels not correct"""
for k, v in labels.items():
# Check reserved labels
if k in RESTRICTED_LABELS_NAMES:
raise ValueError("Labels not correct")
# Check prefixes
... |
Returns a list populated by tuples of 2 elements first one is a dict with all the labels and the second elemnt is the value of the metric itself | def get_all(self):
""" Returns a list populated by tuples of 2 elements, first one is
a dict with all the labels and the second elemnt is the value
of the metric itself
"""
with mutex:
items = self.values.items()
result = []
for k, v in items:... |
Add adds the given value to the Gauge. ( The value can be negative resulting in a decrease of the Gauge. ) | def add(self, labels, value):
""" Add adds the given value to the Gauge. (The value can be
negative, resulting in a decrease of the Gauge.)
"""
try:
current = self.get_value(labels)
except KeyError:
current = 0
self.set_value(labels, current ... |
Add adds a single observation to the summary. | def add(self, labels, value):
"""Add adds a single observation to the summary."""
if type(value) not in (float, int):
raise TypeError("Summary only works with digits (int, float)")
# We have already a lock for data but not for the estimator
with mutex:
try:
... |
Get gets the data in the form of 0. 5 0. 9 and 0. 99 percentiles. Also you get sum and count all in a dict | def get(self, labels):
""" Get gets the data in the form of 0.5, 0.9 and 0.99 percentiles. Also
you get sum and count, all in a dict
"""
return_data = {}
# We have already a lock for data but not for the estimator
with mutex:
e = self.get_value(labels)
... |
Gathers the metrics | def gather_data(registry):
"""Gathers the metrics"""
# Get the host name of the machine
host = socket.gethostname()
# Create our collectors
ram_metric = Gauge("memory_usage_bytes", "Memory usage in bytes.",
{'host': host})
cpu_metric = Gauge("cpu_usage_percent", "CPU usa... |
Gathers the metrics | def gather_data(registry):
"""Gathers the metrics"""
# Get the host name of the machine
host = socket.gethostname()
# Create our collectors
io_metric = Summary("write_file_io_example",
"Writing io file in disk example.",
{'host': host})
# regist... |
Returns the first child that matches the given name and attributes. | def get_child(self, name, attribs=None):
"""
Returns the first child that matches the given name and
attributes.
"""
if name == '.':
if attribs is None or len(attribs) == 0:
return self
if attribs == self.attribs:
return sel... |
Creates the given node regardless of whether or not it already exists. Returns the new node. | def create(self, path, data=None):
"""
Creates the given node, regardless of whether or not it already
exists.
Returns the new node.
"""
node = self.current[-1]
path = self._splitpath(path)
n_items = len(path)
for n, item in enumerate(path):
... |
Creates the given node if it does not exist. Returns the ( new or existing ) node. | def add(self, path, data=None, replace=False):
"""
Creates the given node if it does not exist.
Returns the (new or existing) node.
"""
node = self.current[-1]
for item in self._splitpath(path):
tag, attribs = self._splittag(item)
next_node = node.... |
Creates the given attribute and sets it to the given value. Returns the ( new or existing ) node to which the attribute was added. | def add_attribute(self, path, name, value):
"""
Creates the given attribute and sets it to the given value.
Returns the (new or existing) node to which the attribute was added.
"""
node = self.add(path)
node.attribs.append((name, value))
return node |
Creates and enters the given node regardless of whether it already exists. Returns the new node. | def open(self, path):
"""
Creates and enters the given node, regardless of whether it already
exists.
Returns the new node.
"""
self.current.append(self.create(path))
return self.current[-1] |
Enters the given node. Creates it if it does not exist. Returns the node. | def enter(self, path):
"""
Enters the given node. Creates it if it does not exist.
Returns the node.
"""
self.current.append(self.add(path))
return self.current[-1] |
Given a converter ( as returned by compile () ) this function reads the given input file and converts it to the requested output format. | def generate(converter, input_file, format='xml', encoding='utf8'):
"""
Given a converter (as returned by compile()), this function reads
the given input file and converts it to the requested output format.
Supported output formats are 'xml', 'yaml', 'json', or 'none'.
:type converter: compiler.C... |
Like generate () but writes the output to the given output file instead. | def generate_to_file(converter,
input_file,
output_file,
format='xml',
in_encoding='utf8',
out_encoding='utf8'):
"""
Like generate(), but writes the output to the given output file
instead.
:type c... |
Like generate () but reads the input from a string instead of from a file. | def generate_string(converter, input, format='xml'):
"""
Like generate(), but reads the input from a string instead of
from a file.
:type converter: compiler.Context
:param converter: The compiled converter.
:type input: str
:param input: The string to convert.
:type format: str
... |
Like generate () but reads the input from a string instead of from a file and writes the output to the given output file. | def generate_string_to_file(converter,
input,
output_file,
format='xml',
out_encoding='utf8'):
"""
Like generate(), but reads the input from a string instead of
from a file, and writes the output ... |
A very simple cron - like parser to determine if ( cron - like ) string is valid for this date and time. | def is_now(s, dt=None):
'''
A very simple cron-like parser to determine, if (cron-like) string is valid for this date and time.
@input:
s = cron-like string (minute, hour, day of month, month, day of week)
dt = datetime to use as reference time, defaults to now
@output: boolean of result... |
A parser to check whether a ( cron - like ) string has been true during a certain time period. Useful for applications which cannot check every minute or need to catch up during a restart. | def has_been(s, since, dt=None):
'''
A parser to check whether a (cron-like) string has been true during a certain time period.
Useful for applications which cannot check every minute or need to catch up during a restart.
@input:
s = cron-like string (minute, hour, day of month, month, day of we... |
Area under the precision - recall curve | def auprc(y_true, y_pred):
"""Area under the precision-recall curve
"""
y_true, y_pred = _mask_value_nan(y_true, y_pred)
return skm.average_precision_score(y_true, y_pred) |
Get tid of the best trial | def best_trial_tid(self, rank=0):
"""Get tid of the best trial
rank=0 means the best model
rank=1 means second best
...
"""
candidates = [t for t in self.trials
if t['result']['status'] == STATUS_OK]
if len(candidates) == 0:
retu... |
Extends the original object in order to inject checking for stalled jobs and killing them if they are running for too long | def count_by_state_unsynced(self, arg):
"""Extends the original object in order to inject checking
for stalled jobs and killing them if they are running for too long
"""
if self.kill_timeout is not None:
self.delete_running(self.kill_timeout)
return super(KMongoTrials... |
Plot the loss curves | def plot_history(self, tid, scores=["loss", "f1", "accuracy"],
figsize=(15, 3)):
"""Plot the loss curves"""
history = self.train_history(tid)
import matplotlib.pyplot as plt
fig = plt.figure(figsize=figsize)
for i, score in enumerate(scores):
plt... |
Load saved keras model of the trial. | def load_model(self, tid, custom_objects=None):
"""Load saved keras model of the trial.
If tid = None, get the best model
Not applicable for trials ran in cross validion (i.e. not applicable
for `CompileFN.cv_n_folds is None`
"""
if tid is None:
tid = self.b... |
Number of ok trials () | def n_ok(self):
"""Number of ok trials()
"""
if len(self.trials) == 0:
return 0
else:
return np.sum(np.array(self.statuses()) == "ok") |
Return a list of results with ok status | def get_ok_results(self, verbose=True):
"""Return a list of results with ok status
"""
if len(self.trials) == 0:
return []
not_ok = np.where(np.array(self.statuses()) != "ok")[0]
if len(not_ok) > 0 and verbose:
print("{0}/{1} trials were not ok.".format(... |
Common wrapper for the authentication modules. * Parses the request before passing it on to the authentication module. * Sets pyoidc cookie if authentication succeeds. * Redirects the user to complete the authentication. * Allows the user to retry authentication if it fails.: param verifier: authentication module | def VerifierMiddleware(verifier):
"""Common wrapper for the authentication modules.
* Parses the request before passing it on to the authentication module.
* Sets 'pyoidc' cookie if authentication succeeds.
* Redirects the user to complete the authentication.
* Allows the user to ret... |
Common wrapper for the underlying pyoidc library functions. Reads GET params and POST data before passing it on the library and converts the response from oic. utils. http_util to wsgi.: param func: underlying library function | def pyoidcMiddleware(func):
"""Common wrapper for the underlying pyoidc library functions.
Reads GET params and POST data before passing it on the library and
converts the response from oic.utils.http_util to wsgi.
:param func: underlying library function
"""
def wrapper(environ, start_response... |
Convert an oic. utils. http_util instance to Flask. | def resp2flask(resp):
"""Convert an oic.utils.http_util instance to Flask."""
if isinstance(resp, Redirect) or isinstance(resp, SeeOther):
code = int(resp.status.split()[0])
raise cherrypy.HTTPRedirect(resp.message, code)
return resp.message, resp.status, resp.headers |
Add all authentication methods specified in the configuration. | def setup_authentication_methods(authn_config, template_env):
"""Add all authentication methods specified in the configuration."""
routing = {}
ac = AuthnBroker()
for authn_method in authn_config:
cls = make_cls_from_name(authn_method["class"])
instance = cls(template_env=template_env, *... |
Setup the OpenID Connect Provider endpoints. | def setup_endpoints(provider):
"""Setup the OpenID Connect Provider endpoints."""
app_routing = {}
endpoints = [
AuthorizationEndpoint(
pyoidcMiddleware(provider.authorization_endpoint)),
TokenEndpoint(
pyoidcMiddleware(provider.token_endpoint)),
UserinfoEndpo... |
Handle webfinger requests. | def _webfinger(provider, request, **kwargs):
"""Handle webfinger requests."""
params = urlparse.parse_qs(request)
if params["rel"][0] == OIC_ISSUER:
wf = WebFinger()
return Response(wf.response(params["resource"][0], provider.baseurl),
headers=[("Content-Type", "appli... |
Converts a dictionary of keyword arguments into a tuple of SQL select statements and the list of SQL arguments | def featuresQuery(self, **kwargs):
"""
Converts a dictionary of keyword arguments into a tuple
of SQL select statements and the list of SQL arguments
"""
# TODO: Optimize by refactoring out string concatenation
sql = ""
sql_rows = "SELECT * FROM FEATURE WHERE id >... |
Perform a full features query in database. | def searchFeaturesInDb(
self, startIndex=0, maxResults=None,
referenceName=None, start=None, end=None,
parentId=None, featureTypes=None,
name=None, geneSymbol=None):
"""
Perform a full features query in database.
:param startIndex: int representin... |
Fetch feature by featureID. | def getFeatureById(self, featureId):
"""
Fetch feature by featureID.
:param featureId: the FeatureID as found in GFF3 records
:return: dictionary representing a feature object,
or None if no match is found.
"""
sql = "SELECT * FROM FEATURE WHERE id = ?"
... |
Returns the representation of this FeatureSet as the corresponding ProtocolElement. | def toProtocolElement(self):
"""
Returns the representation of this FeatureSet as the corresponding
ProtocolElement.
"""
gaFeatureSet = protocol.FeatureSet()
gaFeatureSet.id = self.getId()
gaFeatureSet.dataset_id = self.getParentContainer().getId()
gaFeatu... |
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