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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/manager.py | AsperaTransferCoordinatorController.free_processed_queue | def free_processed_queue(self):
''' call the Aspera sdk to freeup resources '''
with self._lock:
if len(self._processed_coordinators) > 0:
for _coordinator in self._processed_coordinators:
_coordinator.free_resources()
self._processed_coord... | python | def free_processed_queue(self):
''' call the Aspera sdk to freeup resources '''
with self._lock:
if len(self._processed_coordinators) > 0:
for _coordinator in self._processed_coordinators:
_coordinator.free_resources()
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/manager.py | AsperaTransferCoordinatorController.is_stop | def is_stop(self):
''' has either of the stop processing flags been set '''
if len(self._processed_coordinators) > 0:
self.free_processed_queue()
return self._cancel_called or self._processing_stop | python | def is_stop(self):
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if len(self._processed_coordinators) > 0:
self.free_processed_queue()
return self._cancel_called or self._processing_stop | [
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/manager.py | AsperaTransferCoordinatorController._process_waiting_queue | def _process_waiting_queue(self):
''' thread to processes the waiting queue
fetches transfer spec
then calls start transfer
ensures that max ascp is not exceeded '''
logger.info("Queue processing thread started")
while not self.is_stop():
self._pro... | python | def _process_waiting_queue(self):
''' thread to processes the waiting queue
fetches transfer spec
then calls start transfer
ensures that max ascp is not exceeded '''
logger.info("Queue processing thread started")
while not self.is_stop():
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/manager.py | AsperaTransferCoordinatorController.clear_waiting_coordinators | def clear_waiting_coordinators(self, cancel=False):
''' remove all entries from waiting queue or cancell all in waiting queue '''
with self._lockw:
if cancel:
for _coordinator in self._waiting_transfer_coordinators:
_coordinator.notify_cancelled("Clear Wai... | python | def clear_waiting_coordinators(self, cancel=False):
''' remove all entries from waiting queue or cancell all in waiting queue '''
with self._lockw:
if cancel:
for _coordinator in self._waiting_transfer_coordinators:
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/manager.py | AsperaTransferCoordinatorController.cancel | def cancel(self, *args, **kwargs):
""" Cancel all queue items - then attempt to cancel all in progress items """
self._cancel_called = True
self.clear_waiting_coordinators(cancel=True)
super(AsperaTransferCoordinatorController, self).cancel(*args, **kwargs) | python | def cancel(self, *args, **kwargs):
""" Cancel all queue items - then attempt to cancel all in progress items """
self._cancel_called = True
self.clear_waiting_coordinators(cancel=True)
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/manager.py | AsperaTransferCoordinatorController.wait | def wait(self):
""" Wait until all in progress and queued items are processed """
self._wait_called = True
while self.tracked_coordinator_count() > 0 or \
self.waiting_coordinator_count() > 0:
time.sleep(1)
super(AsperaTransferCoordinatorController, self).... | python | def wait(self):
""" Wait until all in progress and queued items are processed """
self._wait_called = True
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time.sleep(1)
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SuperCowPowers/workbench | workbench/workers/view_zip.py | ViewZip.execute | def execute(self, input_data):
''' Execute the ViewZip worker '''
# Just a small check to make sure we haven't been called on the wrong file type
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferFuture.set_exception | def set_exception(self, exception):
"""Sets the exception on the future."""
if not self.is_done():
raise TransferNotDoneError(
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self._coordinator.set_exception(exception, override=Tru... | python | def set_exception(self, exception):
"""Sets the exception on the future."""
if not self.is_done():
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferListener.transferReporter | def transferReporter(self, xferId, message):
''' the callback method used by the Aspera sdk during transfer
to notify progress, error or successful completion
'''
if self.is_stopped():
return True
_asp_message = AsperaMessage(message)
if not _asp_message... | python | def transferReporter(self, xferId, message):
''' the callback method used by the Aspera sdk during transfer
to notify progress, error or successful completion
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if self.is_stopped():
return True
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferListener.start_transfer | def start_transfer(self):
''' pass the transfer spec to the Aspera sdk and start the transfer '''
try:
if not self.is_done():
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''' pass the transfer spec to the Aspera sdk and start the transfer '''
try:
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferListener.is_running | def is_running(self, is_stopped):
''' check whether a transfer is currently running '''
if is_stopped and self.is_stopped():
return False
return faspmanager2.isRunning(self.get_transfer_id()) | python | def is_running(self, is_stopped):
''' check whether a transfer is currently running '''
if is_stopped and self.is_stopped():
return False
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferListener.is_stopped | def is_stopped(self, is_stopping=True):
''' check whether a transfer is stopped or is being stopped '''
if is_stopping:
return self._is_stopped or self._is_stopping
return self._is_stopped | python | def is_stopped(self, is_stopping=True):
''' check whether a transfer is stopped or is being stopped '''
if is_stopping:
return self._is_stopped or self._is_stopping
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferListener._modify_transfer | def _modify_transfer(self, option, value=0):
''' call Apsera sdk modify an in progress eg pause/resume
allowed values defined in enumAsperaModifyTransfer class '''
_ret = False
try:
if self.is_running(True):
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''' call Apsera sdk modify an in progress eg pause/resume
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_ret = False
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferListener.stop | def stop(self, free_resource=False):
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cancel - stop an in progress transfer
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self._... | python | def stop(self, free_resource=False):
''' send a stop transfer request to the Aspera sdk, can be done for:
cancel - stop an in progress transfer
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferListener.free_resources | def free_resources(self):
''' call stop to free up resources '''
if not self.is_stopped():
logger.info("Freeing resources: %s" % self.get_transfer_id())
self.stop(True) | python | def free_resources(self):
''' call stop to free up resources '''
if not self.is_stopped():
logger.info("Freeing resources: %s" % self.get_transfer_id())
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaMessage.extract_message_value | def extract_message_value(self, name):
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name += ":"
assert(self._message)
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if _start >= 0:
_start += len(name) + 1
_end = self._message.find("\n", _start)
... | python | def extract_message_value(self, name):
''' search message to find and extract a named value '''
name += ":"
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if _start >= 0:
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaSession._set_status | def _set_status(self, status, ex=None):
''' set session status - eg failed, success --
valid values contained in enumAsperaControllerStatus class '''
self._status = status
logger.debug("Set status(%s) for %s" % (self._status, self.session_id))
self.set_done()
if ex:
... | python | def _set_status(self, status, ex=None):
''' set session status - eg failed, success --
valid values contained in enumAsperaControllerStatus class '''
self._status = status
logger.debug("Set status(%s) for %s" % (self._status, self.session_id))
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaSession.set_bytes_transferred | def set_bytes_transferred(self, bytes_transferred):
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_changed = False
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaSession.set_exception | def set_exception(self, exception):
''' set the exception message and set the status to failed '''
logger.error("%s : %s" % (exception.__class__.__name__, str(exception)))
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logger.error("%s : %s" % (exception.__class__.__name__, str(exception)))
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaSession.wait | def wait(self):
''' wait for the done event to be set - no timeout'''
self._done_event.wait(MAXINT)
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self._done_event.wait(MAXINT)
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.cancel | def cancel(self, msg='', exc_type=CancelledError):
"""Cancels the TransferFuture
:param msg: The message to attach to the cancellation
:param exc_type: The type of exception to set for the cancellation
"""
_ret = False
if not self.is_done():
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"""Cancels the TransferFuture
:param msg: The message to attach to the cancellation
:param exc_type: The type of exception to set for the cancellation
"""
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator._update_session_count | def _update_session_count(self, type=0, actutal_session_count=0):
''' update the session/ascp count
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.result | def result(self, raise_exception=True):
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.notify_init | def notify_init(self):
''' run the queed callback for just the first session only '''
_session_count = len(self._sessions)
self._update_session_count(1, _session_count)
if _session_count == 1:
self._run_queued_callbacks() | python | def notify_init(self):
''' run the queed callback for just the first session only '''
_session_count = len(self._sessions)
self._update_session_count(1, _session_count)
if _session_count == 1:
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.notify_done | def notify_done(self, error=False, run_done_callbacks=True):
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then run the done callbacks
'''
if error:
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.notify_progress | def notify_progress(self):
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_total = 0
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_total += _session.bytes_transferred
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... | python | def notify_progress(self):
''' only call the progress callback if total has changed
or PROGRESS_MSGS_SEND_ALL is set '''
_total = 0
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.notify_exception | def notify_exception(self, exception, run_done_callbacks=True):
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logger.error("%s : %s" % (exception.__class__.__name__, str(exception)))
self._exception = exception
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# ... | python | def notify_exception(self, exception, run_done_callbacks=True):
''' set the exception message, stop transfer if running and set the done event '''
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.is_success | def is_success(self):
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.set_transfer_spec | def set_transfer_spec(self):
''' run the function to set the transfer spec on error set associated exception '''
_ret = False
try:
self._args.transfer_spec_func(self._args)
_ret = True
except Exception as ex:
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''' run the function to set the transfer spec on error set associated exception '''
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator._add_subscribers_for_type | def _add_subscribers_for_type(self, callback_type, subscribers, callbacks, **kwargs):
''' add a done/queued/progress callback to the appropriate list '''
for subscriber in subscribers:
callback_name = 'on_' + callback_type
if hasattr(subscriber, callback_name):
_f... | python | def _add_subscribers_for_type(self, callback_type, subscribers, callbacks, **kwargs):
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for subscriber in subscribers:
callback_name = 'on_' + callback_type
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.add_done_callback | def add_done_callback(self, function, **kwargs):
"""Add a done callback to be invoked when transfer is complete """
with self._callbacks_lock:
_function = functools.partial(function, **kwargs)
self._done_callbacks.append(_function) | python | def add_done_callback(self, function, **kwargs):
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator.add_subscribers | def add_subscribers(self, subscribers, **kwargs):
""" Add a callbacks to be invoked during transfer """
if subscribers:
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self._ad... | python | def add_subscribers(self, subscribers, **kwargs):
""" Add a callbacks to be invoked during transfer """
if subscribers:
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self._add_subscribers_for_type(
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/futures.py | AsperaTransferCoordinator._run_queued_callbacks | def _run_queued_callbacks(self):
''' run the init/quued calback when the trasnfer is initiated on apsera '''
for callback in self._queued_callbacks:
try:
callback()
except Exception as ex:
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''' run the init/quued calback when the trasnfer is initiated on apsera '''
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'''
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for callback in self._done_callbacks:
try:
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''' Run the callbacks and remove the callbacks from the internal
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'''
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yfpeng/bioc | bioc/bioc.py | BioCAnnotation.total_span | def total_span(self) -> BioCLocation:
"""The total span of this annotation. Discontinued locations will be merged."""
if not self.locations:
raise ValueError('BioCAnnotation must have at least one location')
start = min(l.offset for l in self.locations)
end = max(l.end for l ... | python | def total_span(self) -> BioCLocation:
"""The total span of this annotation. Discontinued locations will be merged."""
if not self.locations:
raise ValueError('BioCAnnotation must have at least one location')
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yfpeng/bioc | bioc/bioc.py | BioCRelation.get_node | def get_node(self, role: str, default=None) -> BioCNode:
"""
Get the first node with role
Args:
role: role
default: node returned instead of raising StopIteration
Returns:
the first node with role
"""
return next((node for node in sel... | python | def get_node(self, role: str, default=None) -> BioCNode:
"""
Get the first node with role
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role: role
default: node returned instead of raising StopIteration
Returns:
the first node with role
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yfpeng/bioc | bioc/bioc.py | BioCPassage.get_sentence | def get_sentence(self, offset: int) -> BioCSentence or None:
"""
Gets sentence with specified offset
Args:
offset: sentence offset
Return:
the sentence with specified offset
"""
for sentence in self.sentences:
if sentence.offset == of... | python | def get_sentence(self, offset: int) -> BioCSentence or None:
"""
Gets sentence with specified offset
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offset: sentence offset
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the sentence with specified offset
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yfpeng/bioc | bioc/bioc.py | BioCDocument.get_passage | def get_passage(self, offset: int) -> BioCPassage or None:
"""
Gets passage
Args:
offset: passage offset
Return:
the passage with specified offset
"""
for passage in self.passages:
if passage.offset == offset:
return p... | python | def get_passage(self, offset: int) -> BioCPassage or None:
"""
Gets passage
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offset: passage offset
Return:
the passage with specified offset
"""
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yfpeng/bioc | bioc/bioc.py | BioCDocument.of | def of(cls, *passages: BioCPassage):
"""
Returns a collection passages
"""
if len(passages) <= 0:
raise ValueError("There has to be at least one passage.")
c = BioCDocument()
for passage in passages:
if passage is None:
raise ValueE... | python | def of(cls, *passages: BioCPassage):
"""
Returns a collection passages
"""
if len(passages) <= 0:
raise ValueError("There has to be at least one passage.")
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yfpeng/bioc | bioc/bioc.py | BioCCollection.of | def of(cls, *documents: BioCDocument):
"""
Returns a collection documents
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"""
Returns a collection documents
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SuperCowPowers/workbench | workbench/clients/pe_sim_graph.py | add_it | def add_it(workbench, file_list, labels):
"""Add the given file_list to workbench as samples, also add them as nodes.
Args:
workbench: Instance of Workbench Client.
file_list: list of files.
labels: labels for the nodes.
Returns:
A list of md5s.
"""
md5s = []
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workbench: Instance of Workbench Client.
file_list: list of files.
labels: labels for the nodes.
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SuperCowPowers/workbench | workbench/clients/pe_sim_graph.py | jaccard_sims | def jaccard_sims(feature_list):
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SuperCowPowers/workbench | workbench/clients/pe_sim_graph.py | jaccard_sim | def jaccard_sim(features1, features2):
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Args:
features1: list of PE Symbols.
features2: list of PE Symbols.
Returns:
Returns an int.
"""
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try:
return ... | python | def jaccard_sim(features1, features2):
"""Compute similarity between two sets using Jaccard similarity.
Args:
features1: list of PE Symbols.
features2: list of PE Symbols.
Returns:
Returns an int.
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SuperCowPowers/workbench | workbench/clients/pe_sim_graph.py | run | def run():
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args = client_helper.grab_server_args()
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yfpeng/bioc | bioc/utils.py | pad_char | def pad_char(text: str, width: int, char: str = '\n') -> str:
"""Pads a text until length width."""
dis = width - len(text)
if dis < 0:
raise ValueError
if dis > 0:
text += char * dis
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"""Pads a text until length width."""
dis = width - len(text)
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raise ValueError
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yfpeng/bioc | bioc/utils.py | get_text | def get_text(obj) -> Tuple[int, str]:
"""
Return text with its offset in the document
Args:
obj: BioCDocument, BioCPassage, or BioCSentence
Returns:
offset, text
"""
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"""
Return text with its offset in the document
Args:
obj: BioCDocument, BioCPassage, or BioCSentence
Returns:
offset, text
"""
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yfpeng/bioc | bioc/utils.py | pretty_print | def pretty_print(source, dest):
"""
Pretty print the XML file
"""
parser = etree.XMLParser(remove_blank_text=True)
if not isinstance(source, str):
source = str(source)
tree = etree.parse(source, parser)
docinfo = tree.docinfo
with open(dest, 'wb') as fp:
fp.writ... | python | def pretty_print(source, dest):
"""
Pretty print the XML file
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SuperCowPowers/workbench | workbench/workers/pe_indicators.py | PEIndicators._search_within_pe_warnings | def _search_within_pe_warnings(self, matches):
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SuperCowPowers/workbench | workbench/workers/pe_indicators.py | PEIndicators._search_for_import_symbols | def _search_for_import_symbols(self, matches):
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yfpeng/bioc | bioc/biocitertools.py | annotations | def annotations(obj: BioCCollection or BioCDocument or BioCPassage or BioCSentence,
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Get all annotations in document id.
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yfpeng/bioc | bioc/biocitertools.py | sentences | def sentences(obj: BioCCollection or BioCDocument or BioCPassage) \
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yfpeng/bioc | bioc/biocxml/encoder.py | dump | def dump(collection: BioCCollection, fp, pretty_print: bool = True):
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Serialize ``collection`` as a BioC formatted stream to ``fp``.
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collection: the BioC collection
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Serialize ``collection`` as a BioC formatted stream to ``fp``.
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collection: the BioC collection
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yfpeng/bioc | bioc/biocxml/encoder.py | dumps | def dumps(collection: BioCCollection, pretty_print: bool = True) -> str:
"""
Serialize ``collection`` to a BioC formatted ``str``.
Args:
collection: the BioC collection
pretty_print: enables formatted XML
Returns:
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"""
doc = etree.Elem... | python | def dumps(collection: BioCCollection, pretty_print: bool = True) -> str:
"""
Serialize ``collection`` to a BioC formatted ``str``.
Args:
collection: the BioC collection
pretty_print: enables formatted XML
Returns:
a BioC formatted ``str``
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yfpeng/bioc | bioc/biocxml/encoder.py | encode_location | def encode_location(location: BioCLocation):
"""Encode a single location."""
return etree.Element('location',
{'offset': str(location.offset), 'length': str(location.length)}) | python | def encode_location(location: BioCLocation):
"""Encode a single location."""
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yfpeng/bioc | bioc/biocxml/encoder.py | encode_relation | def encode_relation(relation: BioCRelation):
"""Encode a single relation."""
tree = etree.Element('relation', {'id': relation.id})
encode_infons(tree, relation.infons)
for node in relation.nodes:
tree.append(encode_node(node))
return tree | python | def encode_relation(relation: BioCRelation):
"""Encode a single relation."""
tree = etree.Element('relation', {'id': relation.id})
encode_infons(tree, relation.infons)
for node in relation.nodes:
tree.append(encode_node(node))
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yfpeng/bioc | bioc/biocxml/encoder.py | encode_annotation | def encode_annotation(annotation):
"""Encode a single annotation."""
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encode_infons(tree, annotation.infons)
for location in annotation.locations:
tree.append(encode_location(location))
etree.SubElement(tree, 'text').text = annot... | python | def encode_annotation(annotation):
"""Encode a single annotation."""
tree = etree.Element('annotation', {'id': annotation.id})
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tree.append(encode_location(location))
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yfpeng/bioc | bioc/biocxml/encoder.py | encode_sentence | def encode_sentence(sentence):
"""Encode a single sentence."""
tree = etree.Element('sentence')
encode_infons(tree, sentence.infons)
etree.SubElement(tree, 'offset').text = str(sentence.offset)
if sentence.text:
etree.SubElement(tree, 'text').text = sentence.text
for ann in senten... | python | def encode_sentence(sentence):
"""Encode a single sentence."""
tree = etree.Element('sentence')
encode_infons(tree, sentence.infons)
etree.SubElement(tree, 'offset').text = str(sentence.offset)
if sentence.text:
etree.SubElement(tree, 'text').text = sentence.text
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yfpeng/bioc | bioc/biocxml/encoder.py | encode_passage | def encode_passage(passage):
"""Encode a single passage."""
tree = etree.Element('passage')
encode_infons(tree, passage.infons)
etree.SubElement(tree, 'offset').text = str(passage.offset)
if passage.text:
etree.SubElement(tree, 'text').text = passage.text
for sen in passage.senten... | python | def encode_passage(passage):
"""Encode a single passage."""
tree = etree.Element('passage')
encode_infons(tree, passage.infons)
etree.SubElement(tree, 'offset').text = str(passage.offset)
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yfpeng/bioc | bioc/biocxml/encoder.py | encode_document | def encode_document(document):
"""Encode a single document."""
tree = etree.Element('document')
etree.SubElement(tree, 'id').text = document.id
encode_infons(tree, document.infons)
for passage in document.passages:
tree.append(encode_passage(passage))
for ann in document.annotatio... | python | def encode_document(document):
"""Encode a single document."""
tree = etree.Element('document')
etree.SubElement(tree, 'id').text = document.id
encode_infons(tree, document.infons)
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yfpeng/bioc | bioc/biocxml/encoder.py | encode_collection | def encode_collection(collection):
"""Encode a single collection."""
tree = etree.Element('collection')
etree.SubElement(tree, 'source').text = collection.source
etree.SubElement(tree, 'date').text = collection.date
etree.SubElement(tree, 'key').text = collection.key
encode_infons(tree, co... | python | def encode_collection(collection):
"""Encode a single collection."""
tree = etree.Element('collection')
etree.SubElement(tree, 'source').text = collection.source
etree.SubElement(tree, 'date').text = collection.date
etree.SubElement(tree, 'key').text = collection.key
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yfpeng/bioc | bioc/biocxml/encoder.py | BioCXMLEncoder.default | def default(self, obj):
"""Implement this method in a subclass such that it returns a tree for ``o``."""
if isinstance(obj, BioCDocument):
return encode_document(obj)
if isinstance(obj, BioCCollection):
return encode_collection(obj)
raise TypeError(f'Object ... | python | def default(self, obj):
"""Implement this method in a subclass such that it returns a tree for ``o``."""
if isinstance(obj, BioCDocument):
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if isinstance(obj, BioCCollection):
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yfpeng/bioc | bioc/biocxml/encoder.py | BioCXMLDocumentWriter.write_collection_info | def write_collection_info(self, collection: BioCCollection):
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elem = etree.Element('source')
elem.text = collection.source
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yfpeng/bioc | bioc/biocxml/encoder.py | BioCXMLDocumentWriter.write_document | def write_document(self, document: BioCDocument):
"""Encode and write a single document."""
tree = self.encoder.encode(document)
self.__writer.send(tree) | python | def write_document(self, document: BioCDocument):
"""Encode and write a single document."""
tree = self.encoder.encode(document)
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SuperCowPowers/workbench | workbench/clients/customer_report.py | run | def run():
"""This client generates customer reports on all the samples in workbench."""
# Grab server args
args = client_helper.grab_server_args()
# Start up workbench connection
workbench = zerorpc.Client(timeout=300, heartbeat=60)
workbench.connect('tcp://'+args['server']+':'+args['port... | python | def run():
"""This client generates customer reports on all the samples in workbench."""
# Grab server args
args = client_helper.grab_server_args()
# Start up workbench connection
workbench = zerorpc.Client(timeout=300, heartbeat=60)
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IBM/ibm-cos-sdk-python-s3transfer | ibm_s3transfer/aspera/utils.py | check_io_access | def check_io_access(ioobj, access, is_file=False):
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_objtype = "File" if is_file else "Direct... | python | def check_io_access(ioobj, access, is_file=False):
''' check if a file/folder exists and has a given IO access '''
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yfpeng/bioc | bioc/validator.py | validate | def validate(collection, onerror: Callable[[str, List], None] = None):
"""Validate BioC data structure."""
BioCValidator(onerror).validate(collection) | python | def validate(collection, onerror: Callable[[str, List], None] = None):
"""Validate BioC data structure."""
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yfpeng/bioc | bioc/validator.py | BioCValidator.validate_doc | def validate_doc(self, document: BioCDocument):
"""Validate a single document."""
annotations = []
annotations.extend(document.annotations)
annotations.extend(document.relations)
for passage in document.passages:
annotations.extend(passage.annotations)
ann... | python | def validate_doc(self, document: BioCDocument):
"""Validate a single document."""
annotations = []
annotations.extend(document.annotations)
annotations.extend(document.relations)
for passage in document.passages:
annotations.extend(passage.annotations)
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yfpeng/bioc | bioc/validator.py | BioCValidator.validate | def validate(self, collection: BioCCollection):
"""Validate a single collection."""
for document in collection.documents:
self.validate_doc(document) | python | def validate(self, collection: BioCCollection):
"""Validate a single collection."""
for document in collection.documents:
self.validate_doc(document) | [
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SuperCowPowers/workbench | workbench/clients/pe_indexer.py | run | def run():
"""This client pushes PE Files -> ELS Indexer."""
# Grab server args
args = client_helper.grab_server_args()
# Start up workbench connection
workbench = zerorpc.Client(timeout=300, heartbeat=60)
workbench.connect('tcp://'+args['server']+':'+args['port'])
# Test out PEFile -... | python | def run():
"""This client pushes PE Files -> ELS Indexer."""
# Grab server args
args = client_helper.grab_server_args()
# Start up workbench connection
workbench = zerorpc.Client(timeout=300, heartbeat=60)
workbench.connect('tcp://'+args['server']+':'+args['port'])
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SuperCowPowers/workbench | workbench/workers/mem_procdump.py | MemoryImageProcDump.execute | def execute(self, input_data):
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adapter = RekallAdapter()
adapter.set_plugin_name(self.plugin_name)
# Create a temporary directory and run this plugin from there
with self.goto_temp_directory():
# R... | python | def execute(self, input_data):
''' Execute method '''
# Spin up the rekall adapter
adapter = RekallAdapter()
adapter.set_plugin_name(self.plugin_name)
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SuperCowPowers/workbench | workbench/workers/pe_features.py | convert_to_utf8 | def convert_to_utf8(string):
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SuperCowPowers/workbench | workbench/workers/pe_features.py | PEFileWorker.extract_features_using_pefile | def extract_features_using_pefile(self, pef):
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SuperCowPowers/workbench | workbench/server/bro/bro_log_reader.py | BroLogReader.read_log | def read_log(self, logfile):
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Usage:
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for row in rows:
do something with row
Args:
logfile: The Bro Log file.
"""... | python | def read_log(self, logfile):
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Usage:
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do something with row
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logfile: The Bro Log file.
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SuperCowPowers/workbench | workbench/server/bro/bro_log_reader.py | BroLogReader._cast_dict | def _cast_dict(self, data_dict):
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Args:
data_dict: dictionary containing bro log data.
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... | python | def _cast_dict(self, data_dict):
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SuperCowPowers/workbench | workbench/clients/zip_file_extraction.py | run | def run():
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args = client_helper.grab_server_args()
# Start up workbench connection
workbench = zerorpc.Client(timeout=300, heartbeat=60)
workbench.connect('tcp://'+args['server']+':'+args['port'])
# ... | python | def run():
"""This client shows workbench extacting files from a zip file."""
# Grab server args
args = client_helper.grab_server_args()
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workbench = zerorpc.Client(timeout=300, heartbeat=60)
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SuperCowPowers/workbench | workbench/workers/vt_query.py | VTQuery.execute | def execute(self, input_data):
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md5 = input_data['meta']['md5']
response = requests.get('http://www.virustotal.com/vtapi/v2/file/report',
params={'apikey':self.apikey,'resource':md5, 'allinfo':1})
# Make sure we got a js... | python | def execute(self, input_data):
''' Execute the VTQuery worker '''
md5 = input_data['meta']['md5']
response = requests.get('http://www.virustotal.com/vtapi/v2/file/report',
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SuperCowPowers/workbench | workbench/workers/pe_peid.py | get_peid_db | def get_peid_db():
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db_path = os.path.join(my_dir, 'peid_userdb.txt')
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SuperCowPowers/workbench | workbench/workers/pe_peid.py | PEIDWorker.execute | def execute(self, input_data):
''' Execute the PEIDWorker '''
raw_bytes = input_data['sample']['raw_bytes']
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pefile_handle = pefile.PE(data=raw_bytes, fast_load=False)
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SuperCowPowers/workbench | workbench/workers/pe_peid.py | PEIDWorker.peid_features | def peid_features(self, pefile_handle):
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peid_match = self.peid_sigs.match(pefile_handle)
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SuperCowPowers/workbench | workbench/clients/pcap_report.py | run | def run():
"""This client pulls PCAP files for building report.
Returns:
A list with `view_pcap` , `meta` and `filename` objects.
"""
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args = client_helper.grab_server_args()
# Start up workbench connection
WORKBENCH = zero... | python | def run():
"""This client pulls PCAP files for building report.
Returns:
A list with `view_pcap` , `meta` and `filename` objects.
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global WORKBENCH
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SuperCowPowers/workbench | workbench/clients/pcap_report.py | show_files | def show_files(md5):
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'''Renders template with `view` of the md5.'''
if not WORKBENCH:
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SuperCowPowers/workbench | workbench/clients/pcap_report.py | show_md5_view | def show_md5_view(md5):
'''Renders template with `stream_sample` of the md5.'''
if not WORKBENCH:
return flask.redirect('/')
md5_view = WORKBENCH.stream_sample(md5)
return flask.render_template('templates/md5_view.html', md5_view=list(md5_view), md5=md5) | python | def show_md5_view(md5):
'''Renders template with `stream_sample` of the md5.'''
if not WORKBENCH:
return flask.redirect('/')
md5_view = WORKBENCH.stream_sample(md5)
return flask.render_template('templates/md5_view.html', md5_view=list(md5_view), md5=md5) | [
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SuperCowPowers/workbench | workbench/workers/timeout_corner/pe_features_df.py | PEFeaturesDF.execute | def execute(self, input_data):
"""This worker puts the output of pe_features into a dictionary of dataframes"""
if 'sample' in input_data:
print 'Warning: PEFeaturesDF is supposed to be called on a sample_set'
self.samples.append(input_data['sample']['md5'])
else:
... | python | def execute(self, input_data):
"""This worker puts the output of pe_features into a dictionary of dataframes"""
if 'sample' in input_data:
print 'Warning: PEFeaturesDF is supposed to be called on a sample_set'
self.samples.append(input_data['sample']['md5'])
else:
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SuperCowPowers/workbench | workbench/server/neo_db.py | NeoDB.add_node | def add_node(self, node_id, name, labels):
"""Add the node with name and labels.
Args:
node_id: Id for the node.
name: Name for the node.
labels: Label for the node.
Raises:
NotImplementedError: When adding labels is not supported.
"""
... | python | def add_node(self, node_id, name, labels):
"""Add the node with name and labels.
Args:
node_id: Id for the node.
name: Name for the node.
labels: Label for the node.
Raises:
NotImplementedError: When adding labels is not supported.
"""
... | [
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