id int32 0 252k | repo stringlengths 7 55 | path stringlengths 4 127 | func_name stringlengths 1 88 | original_string stringlengths 75 19.8k | language stringclasses 1
value | code stringlengths 75 19.8k | code_tokens list | docstring stringlengths 3 17.3k | docstring_tokens list | sha stringlengths 40 40 | url stringlengths 87 242 |
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18,300 | tonycpsu/panwid | panwid/scroll.py | Scrollable._adjust_trim_top | def _adjust_trim_top(self, canv, size):
"""Adjust self._trim_top according to self._scroll_action"""
action = self._scroll_action
self._scroll_action = None
maxcol, maxrow = size
trim_top = self._trim_top
canv_rows = canv.rows()
if trim_top < 0:
# Ne... | python | def _adjust_trim_top(self, canv, size):
"""Adjust self._trim_top according to self._scroll_action"""
action = self._scroll_action
self._scroll_action = None
maxcol, maxrow = size
trim_top = self._trim_top
canv_rows = canv.rows()
if trim_top < 0:
# Ne... | [
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18,301 | tonycpsu/panwid | panwid/scroll.py | Scrollable.rows_max | def rows_max(self, size=None, focus=False):
"""Return the number of rows for `size`
If `size` is not given, the currently rendered number of rows is returned.
"""
if size is not None:
ow = self._original_widget
ow_size = self._get_original_widget_size(size)
... | python | def rows_max(self, size=None, focus=False):
"""Return the number of rows for `size`
If `size` is not given, the currently rendered number of rows is returned.
"""
if size is not None:
ow = self._original_widget
ow_size = self._get_original_widget_size(size)
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18,302 | tonycpsu/panwid | panwid/scroll.py | ScrollBar.scrolling_base_widget | def scrolling_base_widget(self):
"""Nearest `original_widget` that is compatible with the scrolling API"""
def orig_iter(w):
while hasattr(w, 'original_widget'):
w = w.original_widget
yield w
yield w
def is_scrolling_widget(w):
... | python | def scrolling_base_widget(self):
"""Nearest `original_widget` that is compatible with the scrolling API"""
def orig_iter(w):
while hasattr(w, 'original_widget'):
w = w.original_widget
yield w
yield w
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18,303 | kyuupichan/aiorpcX | aiorpcx/curio.py | ignore_after | def ignore_after(seconds, coro=None, *args, timeout_result=None):
'''Execute the specified coroutine and return its result. Issue a
cancellation request after seconds have elapsed. When a timeout
occurs, no exception is raised. Instead, timeout_result is
returned.
If coro is None, the result is an ... | python | def ignore_after(seconds, coro=None, *args, timeout_result=None):
'''Execute the specified coroutine and return its result. Issue a
cancellation request after seconds have elapsed. When a timeout
occurs, no exception is raised. Instead, timeout_result is
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18,304 | kyuupichan/aiorpcX | aiorpcx/curio.py | TaskGroup._add_task | def _add_task(self, task):
'''Add an already existing task to the task group.'''
if hasattr(task, '_task_group'):
raise RuntimeError('task is already part of a group')
if self._closed:
raise RuntimeError('task group is closed')
task._task_group = self
if t... | python | def _add_task(self, task):
'''Add an already existing task to the task group.'''
if hasattr(task, '_task_group'):
raise RuntimeError('task is already part of a group')
if self._closed:
raise RuntimeError('task group is closed')
task._task_group = self
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18,305 | kyuupichan/aiorpcX | aiorpcx/curio.py | TaskGroup.next_done | async def next_done(self):
'''Returns the next completed task. Returns None if no more tasks
remain. A TaskGroup may also be used as an asynchronous iterator.
'''
if not self._done and self._pending:
self._done_event.clear()
await self._done_event.wait()
... | python | async def next_done(self):
'''Returns the next completed task. Returns None if no more tasks
remain. A TaskGroup may also be used as an asynchronous iterator.
'''
if not self._done and self._pending:
self._done_event.clear()
await self._done_event.wait()
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18,306 | kyuupichan/aiorpcX | aiorpcx/curio.py | TaskGroup.join | async def join(self):
'''Wait for tasks in the group to terminate according to the wait
policy for the group.
If the join() operation itself is cancelled, all remaining
tasks in the group are also cancelled.
If a TaskGroup is used as a context manager, the join() method
... | python | async def join(self):
'''Wait for tasks in the group to terminate according to the wait
policy for the group.
If the join() operation itself is cancelled, all remaining
tasks in the group are also cancelled.
If a TaskGroup is used as a context manager, the join() method
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18,307 | kyuupichan/aiorpcX | aiorpcx/curio.py | TaskGroup.cancel_remaining | async def cancel_remaining(self):
'''Cancel all remaining tasks.'''
self._closed = True
task_list = list(self._pending)
for task in task_list:
task.cancel()
for task in task_list:
with suppress(CancelledError):
await task | python | async def cancel_remaining(self):
'''Cancel all remaining tasks.'''
self._closed = True
task_list = list(self._pending)
for task in task_list:
task.cancel()
for task in task_list:
with suppress(CancelledError):
await task | [
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18,308 | kyuupichan/aiorpcX | aiorpcx/socks.py | SOCKSProxy._connect_one | async def _connect_one(self, remote_address):
'''Connect to the proxy and perform a handshake requesting a connection.
Return the open socket on success, or the exception on failure.
'''
loop = asyncio.get_event_loop()
for info in await loop.getaddrinfo(str(self.address.host), ... | python | async def _connect_one(self, remote_address):
'''Connect to the proxy and perform a handshake requesting a connection.
Return the open socket on success, or the exception on failure.
'''
loop = asyncio.get_event_loop()
for info in await loop.getaddrinfo(str(self.address.host), ... | [
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18,309 | kyuupichan/aiorpcX | aiorpcx/socks.py | SOCKSProxy._connect | async def _connect(self, remote_addresses):
'''Connect to the proxy and perform a handshake requesting a connection to each address in
addresses.
Return an (open_socket, remote_address) pair on success.
'''
assert remote_addresses
exceptions = []
for remote_addr... | python | async def _connect(self, remote_addresses):
'''Connect to the proxy and perform a handshake requesting a connection to each address in
addresses.
Return an (open_socket, remote_address) pair on success.
'''
assert remote_addresses
exceptions = []
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18,310 | kyuupichan/aiorpcX | aiorpcx/socks.py | SOCKSProxy._detect_proxy | async def _detect_proxy(self):
'''Return True if it appears we can connect to a SOCKS proxy,
otherwise False.
'''
if self.protocol is SOCKS4a:
remote_address = NetAddress('www.apple.com', 80)
else:
remote_address = NetAddress('8.8.8.8', 53)
sock =... | python | async def _detect_proxy(self):
'''Return True if it appears we can connect to a SOCKS proxy,
otherwise False.
'''
if self.protocol is SOCKS4a:
remote_address = NetAddress('www.apple.com', 80)
else:
remote_address = NetAddress('8.8.8.8', 53)
sock =... | [
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18,311 | kyuupichan/aiorpcX | aiorpcx/socks.py | SOCKSProxy.auto_detect_at_host | async def auto_detect_at_host(cls, host, ports, auth):
'''Try to detect a SOCKS proxy on a host on one of the ports.
Calls auto_detect_address for the ports in order. Returning a SOCKSProxy does not
mean it is functioning - for example, it may have no network connectivity.
If no proxy... | python | async def auto_detect_at_host(cls, host, ports, auth):
'''Try to detect a SOCKS proxy on a host on one of the ports.
Calls auto_detect_address for the ports in order. Returning a SOCKSProxy does not
mean it is functioning - for example, it may have no network connectivity.
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18,312 | kyuupichan/aiorpcX | aiorpcx/session.py | Connector.create_connection | async def create_connection(self):
'''Initiate a connection.'''
connector = self.proxy or self.loop
return await connector.create_connection(
self.session_factory, self.host, self.port, **self.kwargs) | python | async def create_connection(self):
'''Initiate a connection.'''
connector = self.proxy or self.loop
return await connector.create_connection(
self.session_factory, self.host, self.port, **self.kwargs) | [
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18,313 | kyuupichan/aiorpcX | aiorpcx/session.py | SessionBase.data_received | def data_received(self, framed_message):
'''Called by asyncio when a message comes in.'''
if self.verbosity >= 4:
self.logger.debug(f'Received framed message {framed_message}')
self.recv_size += len(framed_message)
self.bump_cost(len(framed_message) * self.bw_cost_per_byte)
... | python | def data_received(self, framed_message):
'''Called by asyncio when a message comes in.'''
if self.verbosity >= 4:
self.logger.debug(f'Received framed message {framed_message}')
self.recv_size += len(framed_message)
self.bump_cost(len(framed_message) * self.bw_cost_per_byte)
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18,314 | kyuupichan/aiorpcX | aiorpcx/session.py | SessionBase.pause_writing | def pause_writing(self):
'''Transport calls when the send buffer is full.'''
if not self.is_closing():
self._can_send.clear()
self.transport.pause_reading() | python | def pause_writing(self):
'''Transport calls when the send buffer is full.'''
if not self.is_closing():
self._can_send.clear()
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18,315 | kyuupichan/aiorpcX | aiorpcx/session.py | SessionBase.resume_writing | def resume_writing(self):
'''Transport calls when the send buffer has room.'''
if not self._can_send.is_set():
self._can_send.set()
self.transport.resume_reading() | python | def resume_writing(self):
'''Transport calls when the send buffer has room.'''
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18,316 | kyuupichan/aiorpcX | aiorpcx/session.py | SessionBase.connection_made | def connection_made(self, transport):
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# If the Socks proxy was used then _proxy and _remote_address are already set
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18,317 | kyuupichan/aiorpcX | aiorpcx/session.py | SessionBase.connection_lost | def connection_lost(self, exc):
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Tear down things done in connection_made.'''
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18,318 | kyuupichan/aiorpcX | aiorpcx/session.py | SessionBase.recalc_concurrency | def recalc_concurrency(self):
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'''
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18,319 | kyuupichan/aiorpcX | aiorpcx/session.py | SessionBase.close | async def close(self, *, force_after=30):
'''Close the connection and return when closed.'''
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self.transport.close()
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async with timeout_after(force_after):
await self.closed_event.wait()
except TaskTimeout:
... | python | async def close(self, *, force_after=30):
'''Close the connection and return when closed.'''
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18,320 | kyuupichan/aiorpcX | aiorpcx/session.py | RPCSession.send_request | async def send_request(self, method, args=()):
'''Send an RPC request over the network.'''
message, event = self.connection.send_request(Request(method, args))
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18,321 | kyuupichan/aiorpcX | aiorpcx/session.py | RPCSession.send_notification | async def send_notification(self, method, args=()):
'''Send an RPC notification over the network.'''
message = self.connection.send_notification(Notification(method, args))
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18,322 | kyuupichan/aiorpcX | aiorpcx/session.py | Server.close | async def close(self):
'''Close the listening socket. This does not close any ServerSession
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'''
if self.server:
self.server.close()
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'''Close the listening socket. This does not close any ServerSession
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18,323 | kyuupichan/aiorpcX | aiorpcx/jsonrpc.py | JSONRPC._message_to_payload | def _message_to_payload(cls, message):
'''Returns a Python object or a ProtocolError.'''
try:
return json.loads(message.decode())
except UnicodeDecodeError:
message = 'messages must be encoded in UTF-8'
except json.JSONDecodeError:
message = 'invalid J... | python | def _message_to_payload(cls, message):
'''Returns a Python object or a ProtocolError.'''
try:
return json.loads(message.decode())
except UnicodeDecodeError:
message = 'messages must be encoded in UTF-8'
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18,324 | kyuupichan/aiorpcX | aiorpcx/jsonrpc.py | JSONRPC.batch_message | def batch_message(cls, batch, request_ids):
'''Convert a request Batch to a message.'''
assert isinstance(batch, Batch)
if not cls.allow_batches:
raise ProtocolError.invalid_request(
'protocol does not permit batches')
id_iter = iter(request_ids)
rm = ... | python | def batch_message(cls, batch, request_ids):
'''Convert a request Batch to a message.'''
assert isinstance(batch, Batch)
if not cls.allow_batches:
raise ProtocolError.invalid_request(
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18,325 | kyuupichan/aiorpcX | aiorpcx/jsonrpc.py | JSONRPC.batch_message_from_parts | def batch_message_from_parts(cls, messages):
'''Convert messages, one per batch item, into a batch message. At
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'''
# Comma-separate the messages and wrap the lot in square brackets
middle = b', '.join(messages)
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'''Convert messages, one per batch item, into a batch message. At
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'''
# Comma-separate the messages and wrap the lot in square brackets
middle = b', '.join(messages)
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18,326 | kyuupichan/aiorpcX | aiorpcx/jsonrpc.py | JSONRPC.encode_payload | def encode_payload(cls, payload):
'''Encode a Python object as JSON and convert it to bytes.'''
try:
return json.dumps(payload).encode()
except TypeError:
msg = f'JSON payload encoding error: {payload}'
raise ProtocolError(cls.INTERNAL_ERROR, msg) from None | python | def encode_payload(cls, payload):
'''Encode a Python object as JSON and convert it to bytes.'''
try:
return json.dumps(payload).encode()
except TypeError:
msg = f'JSON payload encoding error: {payload}'
raise ProtocolError(cls.INTERNAL_ERROR, msg) from None | [
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18,327 | kyuupichan/aiorpcX | aiorpcx/jsonrpc.py | JSONRPCAutoDetect.detect_protocol | def detect_protocol(cls, message):
'''Attempt to detect the protocol from the message.'''
main = cls._message_to_payload(message)
def protocol_for_payload(payload):
if not isinstance(payload, dict):
return JSONRPCLoose # Will error
# Obey an explicit "j... | python | def detect_protocol(cls, message):
'''Attempt to detect the protocol from the message.'''
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18,328 | kyuupichan/aiorpcX | aiorpcx/jsonrpc.py | JSONRPCConnection.receive_message | def receive_message(self, message):
'''Call with an unframed message received from the network.
Raises: ProtocolError if the message violates the protocol in
some way. However, if it happened in a response that can be
paired with a request, the ProtocolError is instead set in the
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'''Call with an unframed message received from the network.
Raises: ProtocolError if the message violates the protocol in
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18,329 | kyuupichan/aiorpcX | aiorpcx/jsonrpc.py | JSONRPCConnection.cancel_pending_requests | def cancel_pending_requests(self):
'''Cancel all pending requests.'''
exception = CancelledError()
for _request, event in self._requests.values():
event.result = exception
event.set()
self._requests.clear() | python | def cancel_pending_requests(self):
'''Cancel all pending requests.'''
exception = CancelledError()
for _request, event in self._requests.values():
event.result = exception
event.set()
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18,330 | kyuupichan/aiorpcX | aiorpcx/util.py | is_valid_hostname | def is_valid_hostname(hostname):
'''Return True if hostname is valid, otherwise False.'''
if not isinstance(hostname, str):
raise TypeError('hostname must be a string')
# strip exactly one dot from the right, if present
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if... | python | def is_valid_hostname(hostname):
'''Return True if hostname is valid, otherwise False.'''
if not isinstance(hostname, str):
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# strip exactly one dot from the right, if present
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18,331 | kyuupichan/aiorpcX | aiorpcx/util.py | classify_host | def classify_host(host):
'''Host is an IPv4Address, IPv6Address or a string.
If an IPv4Address or IPv6Address return it. Otherwise convert the string to an
IPv4Address or IPv6Address object if possible and return it. Otherwise return the
original string if it is a valid hostname.
Raise ValueErro... | python | def classify_host(host):
'''Host is an IPv4Address, IPv6Address or a string.
If an IPv4Address or IPv6Address return it. Otherwise convert the string to an
IPv4Address or IPv6Address object if possible and return it. Otherwise return the
original string if it is a valid hostname.
Raise ValueErro... | [
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18,332 | kyuupichan/aiorpcX | aiorpcx/util.py | validate_port | def validate_port(port):
'''Validate port and return it as an integer.
A string, or its representation as an integer, is accepted.'''
if not isinstance(port, (str, int)):
raise TypeError(f'port must be an integer or string: {port}')
if isinstance(port, str) and port.isdigit():
port = in... | python | def validate_port(port):
'''Validate port and return it as an integer.
A string, or its representation as an integer, is accepted.'''
if not isinstance(port, (str, int)):
raise TypeError(f'port must be an integer or string: {port}')
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18,333 | kyuupichan/aiorpcX | aiorpcx/util.py | validate_protocol | def validate_protocol(protocol):
'''Validate a protocol, a string, and return it.'''
if not re.match(PROTOCOL_REGEX, protocol):
raise ValueError(f'invalid protocol: {protocol}')
return protocol.lower() | python | def validate_protocol(protocol):
'''Validate a protocol, a string, and return it.'''
if not re.match(PROTOCOL_REGEX, protocol):
raise ValueError(f'invalid protocol: {protocol}')
return protocol.lower() | [
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18,334 | kyuupichan/aiorpcX | aiorpcx/util.py | is_async_call | def is_async_call(func):
'''inspect.iscoroutinefunction that looks through partials.'''
while isinstance(func, partial):
func = func.func
return inspect.iscoroutinefunction(func) | python | def is_async_call(func):
'''inspect.iscoroutinefunction that looks through partials.'''
while isinstance(func, partial):
func = func.func
return inspect.iscoroutinefunction(func) | [
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18,335 | kyuupichan/aiorpcX | aiorpcx/util.py | Service.from_string | def from_string(cls, string, *, default_func=None):
'''Construct a Service from a string.
If default_func is provided and any ServicePart is missing, it is called with
default_func(protocol, part) to obtain the missing part.
'''
if not isinstance(string, str):
raise ... | python | def from_string(cls, string, *, default_func=None):
'''Construct a Service from a string.
If default_func is provided and any ServicePart is missing, it is called with
default_func(protocol, part) to obtain the missing part.
'''
if not isinstance(string, str):
raise ... | [
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18,336 | monarch-initiative/dipper | dipper/sources/OMIA.py | OMIA.scrub | def scrub(self):
"""
The XML file seems to have mixed-encoding;
we scrub out the control characters
from the file for processing.
i.e.?i
omia.xml:1555328.28: PCDATA invalid Char value 2
<field name="journal">Bulletin et Memoires de la Societe Centrale de Medi... | python | def scrub(self):
"""
The XML file seems to have mixed-encoding;
we scrub out the control characters
from the file for processing.
i.e.?i
omia.xml:1555328.28: PCDATA invalid Char value 2
<field name="journal">Bulletin et Memoires de la Societe Centrale de Medi... | [
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18,337 | monarch-initiative/dipper | dipper/sources/OMIA.py | OMIA.process_associations | def process_associations(self, limit):
"""
Loop through the xml file and process the article-breed, article-phene,
breed-phene, phene-gene associations, and the external links to LIDA.
:param limit:
:return:
"""
myfile = '/'.join((self.rawdir, self.files['data'... | python | def process_associations(self, limit):
"""
Loop through the xml file and process the article-breed, article-phene,
breed-phene, phene-gene associations, and the external links to LIDA.
:param limit:
:return:
"""
myfile = '/'.join((self.rawdir, self.files['data'... | [
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18,338 | monarch-initiative/dipper | dipper/sources/OMIA.py | OMIA._process_article_phene_row | def _process_article_phene_row(self, row):
"""
Linking articles to species-specific phenes.
:param row:
:return:
"""
# article_id, phene_id, added_by
# look up the article in the hashmap
phenotype_id = self.id_hash['phene'].get(row['phene_id'])
ar... | python | def _process_article_phene_row(self, row):
"""
Linking articles to species-specific phenes.
:param row:
:return:
"""
# article_id, phene_id, added_by
# look up the article in the hashmap
phenotype_id = self.id_hash['phene'].get(row['phene_id'])
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18,339 | monarch-initiative/dipper | dipper/sources/OMIA.py | OMIA.filter_keep_phenotype_entry_ids | def filter_keep_phenotype_entry_ids(self, entry):
'''
doubt this should be kept
'''
omim_id = str(entry['mimNumber'])
otype = self.globaltt['obsolete']
if omim_id in self.omim_type:
otype = self.omim_type[omim_id]
if otype == self.globaltt['obs... | python | def filter_keep_phenotype_entry_ids(self, entry):
'''
doubt this should be kept
'''
omim_id = str(entry['mimNumber'])
otype = self.globaltt['obsolete']
if omim_id in self.omim_type:
otype = self.omim_type[omim_id]
if otype == self.globaltt['obs... | [
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18,340 | monarch-initiative/dipper | dipper/sources/ClinVarXML_alpha.py | make_spo | def make_spo(sub, prd, obj):
'''
Decorates the three given strings as a line of ntriples
'''
# To establish string as a curie and expand,
# we use a global curie_map(.yaml)
# sub are allways uri (unless a bnode)
# prd are allways uri (unless prd is 'a')
# should fail loudly if curie do... | python | def make_spo(sub, prd, obj):
'''
Decorates the three given strings as a line of ntriples
'''
# To establish string as a curie and expand,
# we use a global curie_map(.yaml)
# sub are allways uri (unless a bnode)
# prd are allways uri (unless prd is 'a')
# should fail loudly if curie do... | [
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18,341 | monarch-initiative/dipper | dipper/sources/ClinVarXML_alpha.py | write_spo | def write_spo(sub, prd, obj):
'''
write triples to a buffer incase we decide to drop them
'''
rcvtriples.append(make_spo(sub, prd, obj)) | python | def write_spo(sub, prd, obj):
'''
write triples to a buffer incase we decide to drop them
'''
rcvtriples.append(make_spo(sub, prd, obj)) | [
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18,342 | monarch-initiative/dipper | dipper/sources/Decipher.py | Decipher.make_allele_by_consequence | def make_allele_by_consequence(self, consequence, gene_id, gene_symbol):
"""
Given a "consequence" label that describes a variation type,
create an anonymous variant of the specified gene as an instance of
that consequence type.
:param consequence:
:param gene_id:
... | python | def make_allele_by_consequence(self, consequence, gene_id, gene_symbol):
"""
Given a "consequence" label that describes a variation type,
create an anonymous variant of the specified gene as an instance of
that consequence type.
:param consequence:
:param gene_id:
... | [
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18,343 | monarch-initiative/dipper | dipper/sources/EBIGene2Phen.py | EBIGene2Phen.parse | def parse(self, limit: Optional[int]=None):
"""
Here we parse each row of the gene to phenotype file
We create anonymous variants along with their attributes
(allelic requirement, functional consequence)
and connect these to genes and diseases
genes are connected to var... | python | def parse(self, limit: Optional[int]=None):
"""
Here we parse each row of the gene to phenotype file
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and connect these to genes and diseases
genes are connected to var... | [
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18,344 | monarch-initiative/dipper | dipper/sources/EBIGene2Phen.py | EBIGene2Phen._add_gene_disease | def _add_gene_disease(self, row): # ::List getting syntax error here
"""
Parse and add gene variant disease model
Model building happens in _build_gene_disease_model
:param row {List}: single row from DDG2P.csv
:return: None
"""
col = self.files['developmental_... | python | def _add_gene_disease(self, row): # ::List getting syntax error here
"""
Parse and add gene variant disease model
Model building happens in _build_gene_disease_model
:param row {List}: single row from DDG2P.csv
:return: None
"""
col = self.files['developmental_... | [
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18,345 | monarch-initiative/dipper | dipper/sources/EBIGene2Phen.py | EBIGene2Phen._build_gene_disease_model | def _build_gene_disease_model(
self,
gene_id,
relation_id,
disease_id,
variant_label,
consequence_predicate=None,
consequence_id=None,
allelic_requirement=None,
pmids=None):
"""
Builds gene varian... | python | def _build_gene_disease_model(
self,
gene_id,
relation_id,
disease_id,
variant_label,
consequence_predicate=None,
consequence_id=None,
allelic_requirement=None,
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18,346 | monarch-initiative/dipper | dipper/sources/BioGrid.py | BioGrid._get_identifiers | def _get_identifiers(self, limit):
"""
This will process the id mapping file provided by Biogrid.
The file has a very large header, which we scan past,
then pull the identifiers, and make equivalence axioms
:param limit:
:return:
"""
LOG.info("getting i... | python | def _get_identifiers(self, limit):
"""
This will process the id mapping file provided by Biogrid.
The file has a very large header, which we scan past,
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:param limit:
:return:
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18,347 | monarch-initiative/dipper | dipper/models/Evidence.py | Evidence.add_supporting_evidence | def add_supporting_evidence(self, evidence_line, evidence_type=None, label=None):
"""
Add supporting line of evidence node to association id
:param evidence_line: curie or iri, evidence line
:param evidence_type: curie or iri, evidence type if available
:return: None
"""... | python | def add_supporting_evidence(self, evidence_line, evidence_type=None, label=None):
"""
Add supporting line of evidence node to association id
:param evidence_line: curie or iri, evidence line
:param evidence_type: curie or iri, evidence type if available
:return: None
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18,348 | monarch-initiative/dipper | dipper/models/assoc/G2PAssoc.py | G2PAssoc.add_association_to_graph | def add_association_to_graph(self):
"""
Overrides Association by including bnode support
The reified relationship between a genotype (or any genotype part)
and a phenotype is decorated with some provenance information.
This makes the assumption that
both the genotype an... | python | def add_association_to_graph(self):
"""
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The reified relationship between a genotype (or any genotype part)
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18,349 | monarch-initiative/dipper | dipper/sources/MPD.py | MPD.parse | def parse(self, limit=None):
"""
MPD data is delivered in four separate csv files and one xml file,
which we process iteratively and write out as
one large graph.
:param limit:
:return:
"""
if limit is not None:
LOG.info("Only parsing first %s... | python | def parse(self, limit=None):
"""
MPD data is delivered in four separate csv files and one xml file,
which we process iteratively and write out as
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:param limit:
:return:
"""
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18,350 | monarch-initiative/dipper | dipper/sources/MPD.py | MPD._add_g2p_assoc | def _add_g2p_assoc(self, graph, strain_id, sex, assay_id, phenotypes, comment):
"""
Create an association between a sex-specific strain id
and each of the phenotypes.
Here, we create a genotype from the strain,
and a sex-specific genotype.
Each of those genotypes are crea... | python | def _add_g2p_assoc(self, graph, strain_id, sex, assay_id, phenotypes, comment):
"""
Create an association between a sex-specific strain id
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18,351 | monarch-initiative/dipper | dipper/sources/IMPC.py | IMPC.parse | def parse(self, limit=None):
"""
IMPC data is delivered in three separate csv files OR
in one integrated file, each with the same file format.
:param limit:
:return:
"""
if limit is not None:
LOG.info("Only parsing first %s rows fo each file", str(li... | python | def parse(self, limit=None):
"""
IMPC data is delivered in three separate csv files OR
in one integrated file, each with the same file format.
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:return:
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18,352 | monarch-initiative/dipper | dipper/models/Pathway.py | Pathway.addGeneToPathway | def addGeneToPathway(self, gene_id, pathway_id):
"""
When adding a gene to a pathway, we create an intermediate
'gene product' that is involved in
the pathway, through a blank node.
gene_id RO:has_gene_product _gene_product
_gene_product RO:involved_in pathway_id
... | python | def addGeneToPathway(self, gene_id, pathway_id):
"""
When adding a gene to a pathway, we create an intermediate
'gene product' that is involved in
the pathway, through a blank node.
gene_id RO:has_gene_product _gene_product
_gene_product RO:involved_in pathway_id
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18,353 | monarch-initiative/dipper | dipper/models/Pathway.py | Pathway.addComponentToPathway | def addComponentToPathway(self, component_id, pathway_id):
"""
This can be used directly when the component is directly involved in
the pathway. If a transforming event is performed on the component
first, then the addGeneToPathway should be used instead.
:param pathway_id:
... | python | def addComponentToPathway(self, component_id, pathway_id):
"""
This can be used directly when the component is directly involved in
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18,354 | monarch-initiative/dipper | dipper/sources/Source.py | Source.write | def write(self, fmt='turtle', stream=None):
"""
This convenience method will write out all of the graphs
associated with the source.
Right now these are hardcoded to be a single "graph"
and a "src_dataset.ttl" and a "src_test.ttl"
If you do not supply stream='stdout'
... | python | def write(self, fmt='turtle', stream=None):
"""
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18,355 | monarch-initiative/dipper | dipper/sources/Source.py | Source.declareAsOntology | def declareAsOntology(self, graph):
"""
The file we output needs to be declared as an ontology,
including it's version information.
TEC: I am not convinced dipper reformating external data as RDF triples
makes an OWL ontology (nor that it should be considered a goal).
P... | python | def declareAsOntology(self, graph):
"""
The file we output needs to be declared as an ontology,
including it's version information.
TEC: I am not convinced dipper reformating external data as RDF triples
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18,356 | monarch-initiative/dipper | dipper/sources/Source.py | Source.remove_backslash_r | def remove_backslash_r(filename, encoding):
"""
A helpful utility to remove Carriage Return from any file.
This will read a file into memory,
and overwrite the contents of the original file.
TODO: This function may be a liability
:param filename:
:return:
... | python | def remove_backslash_r(filename, encoding):
"""
A helpful utility to remove Carriage Return from any file.
This will read a file into memory,
and overwrite the contents of the original file.
TODO: This function may be a liability
:param filename:
:return:
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18,357 | monarch-initiative/dipper | dipper/sources/Source.py | Source.load_local_translationtable | def load_local_translationtable(self, name):
'''
Load "ingest specific" translation from whatever they called something
to the ontology label we need to map it to.
To facilitate seeing more ontology lables in dipper ingests
a reverse mapping from ontology lables to external strin... | python | def load_local_translationtable(self, name):
'''
Load "ingest specific" translation from whatever they called something
to the ontology label we need to map it to.
To facilitate seeing more ontology lables in dipper ingests
a reverse mapping from ontology lables to external strin... | [
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18,358 | monarch-initiative/dipper | dipper/models/Genotype.py | Genotype.addGene | def addGene(
self, gene_id, gene_label, gene_type=None, gene_description=None
):
''' genes are classes '''
if gene_type is None:
gene_type = self.globaltt['gene']
self.model.addClassToGraph(gene_id, gene_label, gene_type, gene_description)
return | python | def addGene(
self, gene_id, gene_label, gene_type=None, gene_description=None
):
''' genes are classes '''
if gene_type is None:
gene_type = self.globaltt['gene']
self.model.addClassToGraph(gene_id, gene_label, gene_type, gene_description)
return | [
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18,359 | monarch-initiative/dipper | dipper/utils/DipperUtil.py | DipperUtil.get_ncbi_taxon_num_by_label | def get_ncbi_taxon_num_by_label(label):
"""
Here we want to look up the NCBI Taxon id using some kind of label.
It will only return a result if there is a unique hit.
:return:
"""
req = {'db': 'taxonomy', 'retmode': 'json', 'term': label}
req.update(EREQ)
... | python | def get_ncbi_taxon_num_by_label(label):
"""
Here we want to look up the NCBI Taxon id using some kind of label.
It will only return a result if there is a unique hit.
:return:
"""
req = {'db': 'taxonomy', 'retmode': 'json', 'term': label}
req.update(EREQ)
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18,360 | monarch-initiative/dipper | dipper/models/assoc/Association.py | Assoc.set_association_id | def set_association_id(self, assoc_id=None):
"""
This will set the association ID based on the internal parts
of the association.
To be used in cases where an external association identifier
should be used.
:param assoc_id:
:return:
"""
if assoc... | python | def set_association_id(self, assoc_id=None):
"""
This will set the association ID based on the internal parts
of the association.
To be used in cases where an external association identifier
should be used.
:param assoc_id:
:return:
"""
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18,361 | monarch-initiative/dipper | dipper/models/assoc/Association.py | Assoc.make_association_id | def make_association_id(definedby, sub, pred, obj, attributes=None):
"""
A method to create unique identifiers for OBAN-style associations,
based on all the parts of the association
If any of the items is empty or None, it will convert it to blank.
It effectively digests the str... | python | def make_association_id(definedby, sub, pred, obj, attributes=None):
"""
A method to create unique identifiers for OBAN-style associations,
based on all the parts of the association
If any of the items is empty or None, it will convert it to blank.
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18,362 | monarch-initiative/dipper | dipper/utils/romanplus.py | toRoman | def toRoman(num):
"""convert integer to Roman numeral"""
if not 0 < num < 5000:
raise ValueError("number %n out of range (must be 1..4999)", num)
if int(num) != num:
raise TypeError("decimals %n can not be converted", num)
result = ""
for numeral, integer in romanNumeralMap:
... | python | def toRoman(num):
"""convert integer to Roman numeral"""
if not 0 < num < 5000:
raise ValueError("number %n out of range (must be 1..4999)", num)
if int(num) != num:
raise TypeError("decimals %n can not be converted", num)
result = ""
for numeral, integer in romanNumeralMap:
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18,363 | monarch-initiative/dipper | dipper/utils/romanplus.py | fromRoman | def fromRoman(strng):
"""convert Roman numeral to integer"""
if not strng:
raise TypeError('Input can not be blank')
if not romanNumeralPattern.search(strng):
raise ValueError('Invalid Roman numeral: %s', strng)
result = 0
index = 0
for numeral, integer in romanNumeralMap:
... | python | def fromRoman(strng):
"""convert Roman numeral to integer"""
if not strng:
raise TypeError('Input can not be blank')
if not romanNumeralPattern.search(strng):
raise ValueError('Invalid Roman numeral: %s', strng)
result = 0
index = 0
for numeral, integer in romanNumeralMap:
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18,364 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN._process_genotype_backgrounds | def _process_genotype_backgrounds(self, limit=None):
"""
This table provides a mapping of genotypes to background genotypes
Note that the background_id is also a genotype_id.
Makes these triples:
<ZFIN:genotype_id> GENO:has_reference_part <ZFIN:background_id>
<ZFIN:backg... | python | def _process_genotype_backgrounds(self, limit=None):
"""
This table provides a mapping of genotypes to background genotypes
Note that the background_id is also a genotype_id.
Makes these triples:
<ZFIN:genotype_id> GENO:has_reference_part <ZFIN:background_id>
<ZFIN:backg... | [
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<ZFIN:background_id> a GENO:genomic_background
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18,365 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN._process_stages | def _process_stages(self, limit=None):
"""
This table provides mappings between ZFIN stage IDs and ZFS terms,
and includes the starting and ending hours for the developmental stage.
Currently only processing the mapping from the ZFIN stage ID
to the ZFS ID.
:param limit:... | python | def _process_stages(self, limit=None):
"""
This table provides mappings between ZFIN stage IDs and ZFS terms,
and includes the starting and ending hours for the developmental stage.
Currently only processing the mapping from the ZFIN stage ID
to the ZFS ID.
:param limit:... | [
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18,366 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN._process_genes | def _process_genes(self, limit=None):
"""
This table provides the ZFIN gene id, the SO type of the gene,
the gene symbol, and the NCBI Gene ID.
Triples created:
<gene id> a class
<gene id> rdfs:label gene_symbol
<gene id> equivalent class <ncbi_gene_id>
:... | python | def _process_genes(self, limit=None):
"""
This table provides the ZFIN gene id, the SO type of the gene,
the gene symbol, and the NCBI Gene ID.
Triples created:
<gene id> a class
<gene id> rdfs:label gene_symbol
<gene id> equivalent class <ncbi_gene_id>
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18,367 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN._process_features | def _process_features(self, limit=None):
"""
This module provides information for the intrinsic
and extrinsic genotype features of zebrafish.
All items here are 'alterations', and are therefore instances.
sequence alteration ID, SO type, abbreviation, and relationship to
... | python | def _process_features(self, limit=None):
"""
This module provides information for the intrinsic
and extrinsic genotype features of zebrafish.
All items here are 'alterations', and are therefore instances.
sequence alteration ID, SO type, abbreviation, and relationship to
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18,368 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN._process_pubinfo | def _process_pubinfo(self, limit=None):
"""
This will pull the zfin internal publication information,
and map them to their equivalent pmid, and make labels.
Triples created:
<pub_id> is an individual
<pub_id> rdfs:label <pub_label>
<pubmed_id> is an individual
... | python | def _process_pubinfo(self, limit=None):
"""
This will pull the zfin internal publication information,
and map them to their equivalent pmid, and make labels.
Triples created:
<pub_id> is an individual
<pub_id> rdfs:label <pub_label>
<pubmed_id> is an individual
... | [
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<pub_id> rdfs:label <pub_label>
<pubmed_id> is an individual
<pubmed_id> rdfs:label <pub_label>
<pub_id> ... | [
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18,369 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN._process_pub2pubmed | def _process_pub2pubmed(self, limit=None):
"""
This will pull the zfin internal publication to pubmed mappings.
Somewhat redundant with the process_pubinfo method,
but this includes additional mappings.
<pub_id> is an individual
<pub_id> rdfs:label <pub_label>
<p... | python | def _process_pub2pubmed(self, limit=None):
"""
This will pull the zfin internal publication to pubmed mappings.
Somewhat redundant with the process_pubinfo method,
but this includes additional mappings.
<pub_id> is an individual
<pub_id> rdfs:label <pub_label>
<p... | [
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18,370 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN._process_targeting_reagents | def _process_targeting_reagents(self, reagent_type, limit=None):
"""
This method processes the gene targeting knockdown reagents,
such as morpholinos, talens, and crisprs.
We create triples for the reagents and pass the data into a hash map
for use in the pheno_enviro method.
... | python | def _process_targeting_reagents(self, reagent_type, limit=None):
"""
This method processes the gene targeting knockdown reagents,
such as morpholinos, talens, and crisprs.
We create triples for the reagents and pass the data into a hash map
for use in the pheno_enviro method.
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18,371 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN._process_uniprot_ids | def _process_uniprot_ids(self, limit=None):
"""
This method processes the mappings from ZFIN gene IDs to UniProtKB IDs.
Triples created:
<zfin_gene_id> a class
<zfin_gene_id> rdfs:label gene_symbol
<uniprot_id> is an Individual
<uniprot_id> has type <polypeptide... | python | def _process_uniprot_ids(self, limit=None):
"""
This method processes the mappings from ZFIN gene IDs to UniProtKB IDs.
Triples created:
<zfin_gene_id> a class
<zfin_gene_id> rdfs:label gene_symbol
<uniprot_id> is an Individual
<uniprot_id> has type <polypeptide... | [
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18,372 | monarch-initiative/dipper | dipper/sources/ZFIN.py | ZFIN.get_orthology_evidence_code | def get_orthology_evidence_code(self, abbrev):
'''
move to localtt & globltt
'''
# AA Amino acid sequence comparison.
# CE Coincident expression.
# CL Conserved genome location (synteny).
# FC Functional complementation.
# FH Formation of functional he... | python | def get_orthology_evidence_code(self, abbrev):
'''
move to localtt & globltt
'''
# AA Amino acid sequence comparison.
# CE Coincident expression.
# CL Conserved genome location (synteny).
# FC Functional complementation.
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18,373 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._process_diseases | def _process_diseases(self, limit=None):
"""
This method processes the KEGG disease IDs.
Triples created:
<disease_id> is a class
<disease_id> rdfs:label <disease_name>
:param limit:
:return:
"""
LOG.info("Processing diseases")
if self.t... | python | def _process_diseases(self, limit=None):
"""
This method processes the KEGG disease IDs.
Triples created:
<disease_id> is a class
<disease_id> rdfs:label <disease_name>
:param limit:
:return:
"""
LOG.info("Processing diseases")
if self.t... | [
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18,374 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._process_genes | def _process_genes(self, limit=None):
"""
This method processes the KEGG gene IDs.
The label for the gene is pulled as
the first symbol in the list of gene symbols;
the rest are added as synonyms.
The long-form of the gene name is added as a definition.
This is ha... | python | def _process_genes(self, limit=None):
"""
This method processes the KEGG gene IDs.
The label for the gene is pulled as
the first symbol in the list of gene symbols;
the rest are added as synonyms.
The long-form of the gene name is added as a definition.
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18,375 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._process_ortholog_classes | def _process_ortholog_classes(self, limit=None):
"""
This method add the KEGG orthology classes to the graph.
If there's an embedded enzyme commission number,
that is added as an xref.
Triples created:
<orthology_class_id> is a class
<orthology_class_id> has lab... | python | def _process_ortholog_classes(self, limit=None):
"""
This method add the KEGG orthology classes to the graph.
If there's an embedded enzyme commission number,
that is added as an xref.
Triples created:
<orthology_class_id> is a class
<orthology_class_id> has lab... | [
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<orthology_class_id> has label <orthology_symbols>
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18,376 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._process_orthologs | def _process_orthologs(self, raw, limit=None):
"""
This method maps orthologs for a species to the KEGG orthology classes.
Triples created:
<gene_id> is a class
<orthology_class_id> is a class
<assoc_id> has subject <gene_id>
<assoc_id> has object <orthology_cla... | python | def _process_orthologs(self, raw, limit=None):
"""
This method maps orthologs for a species to the KEGG orthology classes.
Triples created:
<gene_id> is a class
<orthology_class_id> is a class
<assoc_id> has subject <gene_id>
<assoc_id> has object <orthology_cla... | [
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18,377 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._process_kegg_disease2gene | def _process_kegg_disease2gene(self, limit=None):
"""
This method creates an association between diseases and
their associated genes. We are being conservative here, and only
processing those diseases for which there is no mapping to OMIM.
Triples created:
<alternate_loc... | python | def _process_kegg_disease2gene(self, limit=None):
"""
This method creates an association between diseases and
their associated genes. We are being conservative here, and only
processing those diseases for which there is no mapping to OMIM.
Triples created:
<alternate_loc... | [
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18,378 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._process_omim2gene | def _process_omim2gene(self, limit=None):
"""
This method maps the OMIM IDs and KEGG gene ID.
Currently split based on the link_type field.
Equivalent link types are mapped as gene XRefs.
Reverse link types are mapped as disease to gene associations.
Original link types a... | python | def _process_omim2gene(self, limit=None):
"""
This method maps the OMIM IDs and KEGG gene ID.
Currently split based on the link_type field.
Equivalent link types are mapped as gene XRefs.
Reverse link types are mapped as disease to gene associations.
Original link types a... | [
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18,379 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._process_genes_kegg2ncbi | def _process_genes_kegg2ncbi(self, limit=None):
"""
This method maps the KEGG human gene IDs
to the corresponding NCBI Gene IDs.
Triples created:
<kegg_gene_id> is a class
<ncbi_gene_id> is a class
<kegg_gene_id> equivalentClass <ncbi_gene_id>
:param ... | python | def _process_genes_kegg2ncbi(self, limit=None):
"""
This method maps the KEGG human gene IDs
to the corresponding NCBI Gene IDs.
Triples created:
<kegg_gene_id> is a class
<ncbi_gene_id> is a class
<kegg_gene_id> equivalentClass <ncbi_gene_id>
:param ... | [
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18,380 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._process_pathway_disease | def _process_pathway_disease(self, limit):
"""
We make a link between the pathway identifiers,
and any diseases associated with them.
Since we model diseases as processes, we make a triple saying that
the pathway may be causally upstream of or within the disease process.
... | python | def _process_pathway_disease(self, limit):
"""
We make a link between the pathway identifiers,
and any diseases associated with them.
Since we model diseases as processes, we make a triple saying that
the pathway may be causally upstream of or within the disease process.
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18,381 | monarch-initiative/dipper | dipper/sources/KEGG.py | KEGG._make_variant_locus_id | def _make_variant_locus_id(self, gene_id, disease_id):
"""
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so we make an anonymous alternate locus,
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"""
We actually want the association between the gene and the disease
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so we make an anonymous alternate locus,
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18,382 | monarch-initiative/dipper | dipper/sources/CTD.py | CTD._fetch_disambiguating_assoc | def _fetch_disambiguating_assoc(self):
"""
For any of the items in the chemical-disease association file that have
ambiguous association types we fetch the disambiguated associations
using the batch query API, and store these in a file. Elsewhere, we can
loop through the file and... | python | def _fetch_disambiguating_assoc(self):
"""
For any of the items in the chemical-disease association file that have
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using the batch query API, and store these in a file. Elsewhere, we can
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18,383 | monarch-initiative/dipper | dipper/sources/CTD.py | CTD._make_association | def _make_association(self, subject_id, object_id, rel_id, pubmed_ids):
"""
Make a reified association given an array of pubmed identifiers.
Args:
:param subject_id id of the subject of the association (gene/chem)
:param object_id id of the object of the association (d... | python | def _make_association(self, subject_id, object_id, rel_id, pubmed_ids):
"""
Make a reified association given an array of pubmed identifiers.
Args:
:param subject_id id of the subject of the association (gene/chem)
:param object_id id of the object of the association (d... | [
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18,384 | monarch-initiative/dipper | dipper/sources/Bgee.py | Bgee.checkIfRemoteIsNewer | def checkIfRemoteIsNewer(self, localfile, remote_size, remote_modify):
"""
Overrides checkIfRemoteIsNewer in Source class
:param localfile: str file path
:param remote_size: str bytes
:param remote_modify: str last modify date in the form 20160705042714
:return: boolean ... | python | def checkIfRemoteIsNewer(self, localfile, remote_size, remote_modify):
"""
Overrides checkIfRemoteIsNewer in Source class
:param localfile: str file path
:param remote_size: str bytes
:param remote_modify: str last modify date in the form 20160705042714
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18,385 | monarch-initiative/dipper | dipper/sources/Bgee.py | Bgee._convert_ftp_time_to_iso | def _convert_ftp_time_to_iso(ftp_time):
"""
Convert datetime in the format 20160705042714 to a datetime object
:return: datetime object
"""
date_time = datetime(
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int(ftp_time[8:10]), int(ftp_time[... | python | def _convert_ftp_time_to_iso(ftp_time):
"""
Convert datetime in the format 20160705042714 to a datetime object
:return: datetime object
"""
date_time = datetime(
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18,386 | monarch-initiative/dipper | dipper/sources/EOM.py | EOM.fetch | def fetch(self, is_dl_forced=False):
'''connection details for DISCO'''
cxn = {}
cxn['host'] = 'nif-db.crbs.ucsd.edu'
cxn['database'] = 'disco_crawler'
cxn['port'] = '5432'
cxn['user'] = config.get_config()['user']['disco']
cxn['password'] = config.get_config()['k... | python | def fetch(self, is_dl_forced=False):
'''connection details for DISCO'''
cxn = {}
cxn['host'] = 'nif-db.crbs.ucsd.edu'
cxn['database'] = 'disco_crawler'
cxn['port'] = '5432'
cxn['user'] = config.get_config()['user']['disco']
cxn['password'] = config.get_config()['k... | [
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18,387 | monarch-initiative/dipper | dipper/sources/EOM.py | EOM.parse | def parse(self, limit=None):
'''
Over ride Source.parse inherited via PostgreSQLSource
'''
if limit is not None:
LOG.info("Only parsing first %s rows of each file", limit)
if self.test_only:
self.test_mode = True
LOG.info("Parsing files...")... | python | def parse(self, limit=None):
'''
Over ride Source.parse inherited via PostgreSQLSource
'''
if limit is not None:
LOG.info("Only parsing first %s rows of each file", limit)
if self.test_only:
self.test_mode = True
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18,388 | monarch-initiative/dipper | dipper/sources/MGI.py | MGI._process_gxd_genotype_view | def _process_gxd_genotype_view(self, limit=None):
"""
This table indicates the relationship between a genotype
and it's background strain. It leverages the Genotype class methods
to do this.
Makes these triples:
<MGI:genotypeid> GENO:has_reference_part <MGI:strainid>
... | python | def _process_gxd_genotype_view(self, limit=None):
"""
This table indicates the relationship between a genotype
and it's background strain. It leverages the Genotype class methods
to do this.
Makes these triples:
<MGI:genotypeid> GENO:has_reference_part <MGI:strainid>
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18,389 | monarch-initiative/dipper | dipper/sources/MGI.py | MGI._process_gxd_genotype_summary_view | def _process_gxd_genotype_summary_view(self, limit=None):
"""
Add the genotype internal id to mgiid mapping to the idhashmap.
Also, add them as individuals to the graph.
We re-format the label to put the background strain in brackets
after the gvc.
We must pass through t... | python | def _process_gxd_genotype_summary_view(self, limit=None):
"""
Add the genotype internal id to mgiid mapping to the idhashmap.
Also, add them as individuals to the graph.
We re-format the label to put the background strain in brackets
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18,390 | monarch-initiative/dipper | dipper/sources/MGI.py | MGI.process_mgi_relationship_transgene_genes | def process_mgi_relationship_transgene_genes(self, limit=None):
"""
Here, we have the relationship between MGI transgene alleles,
and the non-mouse gene ids that are part of them.
We augment the allele with the transgene parts.
:param limit:
:return:
"""
... | python | def process_mgi_relationship_transgene_genes(self, limit=None):
"""
Here, we have the relationship between MGI transgene alleles,
and the non-mouse gene ids that are part of them.
We augment the allele with the transgene parts.
:param limit:
:return:
"""
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18,391 | monarch-initiative/dipper | dipper/graph/RDFGraph.py | RDFGraph._getnode | def _getnode(self, curie): # convention is lowercase names
"""
This is a wrapper for creating a URIRef or Bnode object
with a given a curie or iri as a string.
If an id starts with an underscore, it assigns it to a BNode, otherwise
it creates it with a standard URIRef.
... | python | def _getnode(self, curie): # convention is lowercase names
"""
This is a wrapper for creating a URIRef or Bnode object
with a given a curie or iri as a string.
If an id starts with an underscore, it assigns it to a BNode, otherwise
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18,392 | monarch-initiative/dipper | dipper/models/assoc/D2PAssoc.py | D2PAssoc.add_association_to_graph | def add_association_to_graph(self):
"""
The reified relationship between a disease and a phenotype is decorated
with some provenance information.
This makes the assumption that both the disease and phenotype
are classes.
:param g:
:return:
"""
... | python | def add_association_to_graph(self):
"""
The reified relationship between a disease and a phenotype is decorated
with some provenance information.
This makes the assumption that both the disease and phenotype
are classes.
:param g:
:return:
"""
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18,393 | monarch-initiative/dipper | dipper/sources/Monochrom.py | Monochrom.make_parent_bands | def make_parent_bands(self, band, child_bands):
"""
this will determine the grouping bands that it belongs to, recursively
13q21.31 ==> 13, 13q, 13q2, 13q21, 13q21.3, 13q21.31
:param band:
:param child_bands:
:return:
"""
m = re.match(r'([pq][A-H\d]+(?:... | python | def make_parent_bands(self, band, child_bands):
"""
this will determine the grouping bands that it belongs to, recursively
13q21.31 ==> 13, 13q, 13q2, 13q21, 13q21.3, 13q21.31
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:param child_bands:
:return:
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18,394 | monarch-initiative/dipper | dipper/utils/CurieUtil.py | CurieUtil.get_curie | def get_curie(self, uri):
'''Get a CURIE from a URI '''
prefix = self.get_curie_prefix(uri)
if prefix is not None:
key = self.curie_map[prefix]
return '%s:%s' % (prefix, uri[len(key):len(uri)])
return None | python | def get_curie(self, uri):
'''Get a CURIE from a URI '''
prefix = self.get_curie_prefix(uri)
if prefix is not None:
key = self.curie_map[prefix]
return '%s:%s' % (prefix, uri[len(key):len(uri)])
return None | [
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18,395 | monarch-initiative/dipper | dipper/utils/CurieUtil.py | CurieUtil.get_uri | def get_uri(self, curie):
''' Get a URI from a CURIE '''
if curie is None:
return None
parts = curie.split(':')
if len(parts) == 1:
if curie != '':
LOG.error("Not a properly formed curie: \"%s\"", curie)
return None
prefix = par... | python | def get_uri(self, curie):
''' Get a URI from a CURIE '''
if curie is None:
return None
parts = curie.split(':')
if len(parts) == 1:
if curie != '':
LOG.error("Not a properly formed curie: \"%s\"", curie)
return None
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18,396 | monarch-initiative/dipper | dipper/sources/Coriell.py | Coriell.fetch | def fetch(self, is_dl_forced=False):
"""
Here we connect to the coriell sftp server using private connection
details. They dump bi-weekly files with a timestamp in the filename.
For each catalog, we ping the remote site and pull the most-recently
updated file, renaming it to our... | python | def fetch(self, is_dl_forced=False):
"""
Here we connect to the coriell sftp server using private connection
details. They dump bi-weekly files with a timestamp in the filename.
For each catalog, we ping the remote site and pull the most-recently
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18,397 | monarch-initiative/dipper | dipper/sources/Coriell.py | Coriell._process_collection | def _process_collection(self, collection_id, label, page):
"""
This function will process the data supplied internally
about the repository from Coriell.
Triples:
Repository a ERO:collection
rdf:label Literal(label)
foaf:page Literal(page)
:p... | python | def _process_collection(self, collection_id, label, page):
"""
This function will process the data supplied internally
about the repository from Coriell.
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18,398 | monarch-initiative/dipper | dipper/sources/FlyBase.py | FlyBase._process_genotypes | def _process_genotypes(self, limit):
"""
Add the genotype internal id to flybase mapping to the idhashmap.
Also, add them as individuals to the graph.
Triples created:
<genotype id> a GENO:intrinsic_genotype
<genotype id> rdfs:label "<gvc> [bkgd]"
:param limit:
... | python | def _process_genotypes(self, limit):
"""
Add the genotype internal id to flybase mapping to the idhashmap.
Also, add them as individuals to the graph.
Triples created:
<genotype id> a GENO:intrinsic_genotype
<genotype id> rdfs:label "<gvc> [bkgd]"
:param limit:
... | [
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18,399 | monarch-initiative/dipper | dipper/sources/FlyBase.py | FlyBase._process_stocks | def _process_stocks(self, limit):
"""
Stock definitions.
Here we instantiate them as instances of the given taxon.
:param limit:
:return:
"""
if self.test_mode:
graph = self.testgraph
else:
graph = self.graph
model = Model... | python | def _process_stocks(self, limit):
"""
Stock definitions.
Here we instantiate them as instances of the given taxon.
:param limit:
:return:
"""
if self.test_mode:
graph = self.testgraph
else:
graph = self.graph
model = Model... | [
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Here we instantiate them as instances of the given taxon.
:param limit:
:return: | [
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