def encode_worker(
realtime_vocoder: RealtimeVocoder,
time_length: float,
extra_time: float,
queue_input: Queue,
queue_output: Queue,
acquired_lock: Lock,
):
logger = logging.getLogger('encode')
init_logger(logger)
logger.info('encode worker')
stream = EncodeStream(vocoder=realtime_vocoder)
stream_wrapper = StreamWrapper(stream=stream, extra_time=extra_time)
acquired_lock.release()
start_time = extra_time
while True:
item: Item = queue_input.get()
start = time.time()
wave: numpy.ndarray = item.item
stream.add(start_time=start_time, data=wave)
start_time += time_length
feature_wrapper: AcousticFeatureWrapper = stream_wrapper.process_next(
time_length=time_length)
item.item = feature_wrapper
queue_output.put(item)
logger.debug(f'{item.index}: {time.time() - start}')
def f(lock: Lock, i: int):
lock.acquire()
try:
print('hello world', i)
print('hello world', i + 1)
finally:
lock.release()
def __init__(self):
self._reader, self._writer = Pipe(duplex=False)
self._rlock = Lock()
if sys.platform == 'win32':
self._wlock = None
else:
self._wlock = Lock()
self._make_methods()
def __init__(self, pid):
Daemon.__init__(self, pid)
# Reddit https://praw.readthedocs.io/en/stable/pages/comment_parsing.html
self.reddit = {}
self.default_subs = 'pollster_bot'
self.bot_name = 'pollster_bot'
self.version = '1.0'
self.touched_comment_ids = []
# create logger
self.logger = logging.getLogger('Pollster_Bot')
self.logger.setLevel(logging.INFO)
# File handler set to DEBUG
fh = logging.FileHandler(filename=os.path.join(
os.path.dirname(__file__), 'PollsterBotLog.txt'))
fh.setLevel(logging.DEBUG)
# create console handler and set level to debug
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
# create formatter
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# add formatter to ch
ch.setFormatter(formatter)
fh.setFormatter(formatter)
# add ch, fh to logger
self.logger.addHandler(ch)
self.logger.addHandler(fh)
self.lock = Lock()
self.logger.info('Starting Pollster Bot ver. ' + self.version)
# Huffington post http://elections.huffingtonpost.com/pollster/api
self.uri = 'http://elections.huffingtonpost.com/pollster/api/charts.json'
# Set states
self.states = {}
self.states = self.load_json_file('data/states.json')
# phrases
phrases = self.load_json_file('data/phrases.json')
self.greetings = phrases['greeting']
self.winning = phrases['winning']
self.losing = phrases['losing']
# keywords to call the pollster bot
self.keywords = self.load_json_file('data/keywords.json')['keywords']
# subs
subs = self.load_json_file('data/subs.json')['subs']
for sub in subs:
self.default_subs += '+' + sub
self.log_in_credentials = self.load_json_file(
'data/login_credentials.json')
def decode_worker(
realtime_vocoder: RealtimeVocoder,
time_length: float,
extra_time: float,
vocoder_buffer_size: int,
out_audio_chunk: int,
output_silent_threshold: float,
queue_input: Queue,
queue_output: Queue,
acquired_lock: Lock,
):
logger = logging.getLogger('decode')
init_logger(logger)
logging.info('decode worker')
realtime_vocoder.create_synthesizer(
buffer_size=vocoder_buffer_size,
number_of_pointers=16,
)
stream = DecodeStream(vocoder=realtime_vocoder)
stream_wrapper = StreamWrapper(stream=stream, extra_time=extra_time)
acquired_lock.release()
start_time = extra_time
wave_fragment = numpy.empty(0)
while True:
item: Item = queue_input.get()
start = time.time()
feature: AcousticFeature = item.item
stream.add(
start_time=start_time,
data=feature,
)
start_time += time_length
wave = stream_wrapper.process_next(time_length=time_length)
wave_fragment = numpy.concatenate([wave_fragment, wave])
if len(wave_fragment) >= out_audio_chunk:
wave, wave_fragment = wave_fragment[:
out_audio_chunk], wave_fragment[
out_audio_chunk:]
power = librosa.core.power_to_db(numpy.abs(
librosa.stft(wave))**2).mean()
if power < -output_silent_threshold:
wave = None # pass
else:
wave = None
item.item = wave
queue_output.put(item)
logger.debug(f'{item.index}: {time.time() - start}')
class AudioOutputLoop(Thread):
def __init__(self, audioDevice, sampleRate = 44100, bufferSize = 512):
Thread.__init__(self, name = "AudioOutputLoop")
self._lock = Lock()
self._isRunning = False
self._audioDevice = audioDevice
self._bufferSize = bufferSize
self._sampleRate = sampleRate
self._maxTimePerBlockInSec = bufferSize / sampleRate
pygame.mixer.init(deviceName = audioDevice.name, frequency = sampleRate, buffer = bufferSize)
self._channel = pygame.mixer.find_channel()
self.testWave = wave.open("./tests/resources/test.wav", "r")
self.totalFrames = self.testWave.getnframes()
self.allsamples = self.testWave.readframes(self.totalFrames)
self._byteArray = bytearray(self._bufferSize * 2)
self.numFrames = 0
logger.info("Mixer initialized")
def terminate(self):
pygame.mixer.quit()
def run(self):
logger.debug("AudioOutputLoop started")
self._isRunning = True
while self._isRunning:
startTime = clock()
self._lock.acquire(True)
# do cool stuff here
if self.numFrames + self._bufferSize > self.totalFrames:
self._isRunning = False
else:
startFrame = self.numFrames
endFrame = startFrame + self._bufferSize * 2
bytesOut = bytes(self.allsamples[startFrame:endFrame])
sound = pygame.mixer.Sound(self.allsamples[startFrame:endFrame])
self._channel.play(sound)
self.numFrames += self._bufferSize * 2
stopTime = clock()
timeInBlockInSec = (stopTime - startTime)
sleepTime = self._maxTimePerBlockInSec - timeInBlockInSec
if sleepTime < 0:
logger.warn("Audio dropout!")
else:
logger.info("CPU: %f", 100 * timeInBlockInSec / self._maxTimePerBlockInSec)
sleep(sleepTime)
self._lock.release()
def __init__(self, maxsize = 0):
if maxsize <= 0:
maxsize = _multiprocessing.SemLock.SEM_VALUE_MAX
self._maxsize = maxsize
self._reader, self._writer = Pipe(duplex=False)
self._rlock = Lock()
self._opid = os.getpid()
if sys.platform == 'win32':
self._wlock = None
else:
self._wlock = Lock()
self._sem = BoundedSemaphore(maxsize)
self._after_fork()
if sys.platform != 'win32':
register_after_fork(self, Queue._after_fork)
return
def __init__(self, delegate, pollIntervalInMs = 25):
Thread.__init__(self, name = "MidiEventLoop")
self._lock = Lock()
self._isRunning = False
self.delegate = delegate
self._pollInterval = pollIntervalInMs / 1000
self.devices = None
self.midiMappings = MidiMappingTable(PathFinder.findUserFile('midimappings.sql'))
def convert_worker(
acoustic_converter: AcousticConverter,
super_resolution: SuperResolution,
time_length: float,
extra_time: float,
input_silent_threshold: float,
queue_input: Queue,
queue_output: Queue,
acquired_lock: Lock,
):
logger = logging.getLogger('convert')
init_logger(logger)
logging.info('convert worker')
chainer.global_config.enable_backprop = False
chainer.global_config.train = False
stream = ConvertStream(voice_changer=VoiceChanger(
super_resolution=super_resolution,
acoustic_converter=acoustic_converter,
threshold=input_silent_threshold,
))
stream_wrapper = StreamWrapper(stream=stream, extra_time=extra_time)
acquired_lock.release()
start_time = extra_time
while True:
item: Item = queue_input.get()
start = time.time()
in_feature: AcousticFeatureWrapper = item.item
stream.add(
start_time=start_time,
data=in_feature,
)
start_time += time_length
out_feature = stream_wrapper.process_next(time_length=time_length)
item.item = out_feature
queue_output.put(item)
logger.debug(f'{item.index}: {time.time() - start}')
def test_get_instance_with_concurrent_mode(self, mr_lock: LockFactory):
try:
_lock = mr_lock.get_instance()
except ValueError as ve:
assert "FeatureMode is None. Please configure it as one of 'multirunnable.mode.FeatureMode'." in str(
ve), "It should set the FeatureMode first."
mr_lock.feature_mode = FeatureMode.Concurrent
_lock = mr_lock.get_instance()
from threading import Lock
assert _lock is not None and isinstance(_lock, type(Lock(
))) is True, "This type of Lock instance should be 'threading.Lock'."
def __init__(self, maxsize = 0):
if maxsize <= 0:
maxsize = _multiprocessing.SemLock.SEM_VALUE_MAX
self._maxsize = maxsize
self._reader, self._writer = Pipe(duplex=False)
self._rlock = Lock()
self._opid = os.getpid()
if sys.platform == 'win32':
self._wlock = None
else:
self._wlock = Lock()
self._sem = BoundedSemaphore(maxsize)
self._after_fork()
if sys.platform != 'win32':
register_after_fork(self, Queue._after_fork)
def __init__(self, maxsize=0):
if maxsize <= 0:
maxsize = 2147483647L
self._maxsize = maxsize
self._reader, self._writer = Pipe(duplex=False)
self._rlock = Lock()
self._opid = os.getpid()
if sys.platform == 'win32':
self._wlock = None
else:
self._wlock = Lock()
self._sem = BoundedSemaphore(maxsize)
self._after_fork()
if sys.platform != 'win32':
register_after_fork(self, Queue._after_fork)
class MidiEventLoop(Thread):
def __init__(self, delegate, pollIntervalInMs = 25):
Thread.__init__(self, name = "MidiEventLoop")
self._lock = Lock()
self._isRunning = False
self.delegate = delegate
self._pollInterval = pollIntervalInMs / 1000
self.devices = None
self.midiMappings = MidiMappingTable(PathFinder.findUserFile('midimappings.sql'))
def quit(self):
self._lock.acquire(True)
if self.devices is not None:
self.devices.closeAll()
self._isRunning = False
self._lock.release()
logger.info("Closed all MIDI devices")
def run(self):
# Initialize is done here so as not to block the main thread
self.devices = MidiDeviceList()
self.devices.openAll()
logger.debug("MidiEventLoop started")
self._isRunning = True
while self._isRunning:
self._lock.acquire(True)
for device in self.devices.openedInputs():
while device.poll():
self._parseEvent(device.readEvents())
self._lock.release()
sleep(self._pollInterval)
pygame.midi.quit()
def _parseEvent(self, eventList):
eventData = eventList[0][0]
midiEvent = MidiEvent(eventData[0], eventData[1], eventData[2], eventList[0][1])
self.midiMappings.process(midiEvent, self.delegate)
def __init__(self, audioDevice, sampleRate = 44100, bufferSize = 512):
Thread.__init__(self, name = "AudioOutputLoop")
self._lock = Lock()
self._isRunning = False
self._audioDevice = audioDevice
self._bufferSize = bufferSize
self._sampleRate = sampleRate
self._maxTimePerBlockInSec = bufferSize / sampleRate
pygame.mixer.init(deviceName = audioDevice.name, frequency = sampleRate, buffer = bufferSize)
self._channel = pygame.mixer.find_channel()
self.testWave = wave.open("./tests/resources/test.wav", "r")
self.totalFrames = self.testWave.getnframes()
self.allsamples = self.testWave.readframes(self.totalFrames)
self._byteArray = bytearray(self._bufferSize * 2)
self.numFrames = 0
logger.info("Mixer initialized")
#!/usr/bin/env python
# coding=utf-8
# Python 3.6
from multiprocessing.synchronize import Lock
from PIL import Image
from utils import *
pathlock = Lock() # type: Lock
class TextureConvert(object):
def __init__(self):
self.args = get_args()
self.tool = "PVRTexToolCLI"
pass
def execute(self):
print("BuildTool excute >")
pass
def get_texture_format(self, option, exists_alpha=True):
args = get_args()
if args.convert_tool == "PVRTexToolCLI":
if option == "ETC1":
return "ETC1"
elif option == "ETC2":
if exists_alpha:
return "ETC2_RGBA"
else:
return "ETC2_RGB"
elif args.convert_tool == "etctool":
def process(self,
artifact: Artifact,
discovery: Dict[str, DiscoveryState],
objects: List[Artifact],
lock: LockT) -> List[Artifact]:
new_artifacts: List[Artifact] = []
new_discovery: Dict[str, DiscoveryState] = {}
new_objects: List[Artifact] = []
# Identify tasks that are completely new
if (artifact.state is New
and artifact.filetype is Unknown):
# Use the pathmap list to work out the
# filetype and starting state
new_artifact = None
for pathmap in self._pathmaps:
if artifact.location in pathmap:
new_artifact = Artifact(artifact.location,
pathmap.filetype,
pathmap.state)
# Assuming we found a match and were able
# to create the artifact, return it so that
# it can be added to the queue
if new_artifact is not None:
# Also store its hash in the file database
file_info = FileInfoDatabase(self._database)
file_info.add_file_info(artifact.location,
new_artifact.hash)
new_artifacts.append(new_artifact)
elif artifact.state is Analysed:
# Work out whether this artifact needs to be
# included in the build or not - if any of its
# definitions are mentioned in the (shared)
# discovery mapping, or if it is defining
# the target of the build then it should be included
# TODO: Looping through a list of what could
# eventually contain every unit/symbol in the build has
# the potential to become an issue for performance.
# Longer term we probably want to drop using the shared
# discovery array in favour of database lookups
required = False
for definition in artifact.defines:
# Is this the target?
if (definition == self.target
or definition in discovery):
required = True
break
if required:
# Update the discovery list to indicate that
# the definitions from this Artifact are present
# (but not yet compiled)
for definition in artifact.defines:
if definition not in discovery:
new_discovery[definition] = DiscoveryState.SEEN
# Now check whether the Artifact's dependencies
# have already been seen and compiled
compiled = [False]*len(artifact.depends_on)
for idep, dependency in enumerate(artifact.depends_on):
# Only applies to str dependencies
if isinstance(dependency, Path):
continue
if dependency in discovery:
# Are the dependencies compiled?
if discovery[dependency] == DiscoveryState.COMPILED:
compiled[idep] = True
else:
# If the dependency isn't in the list at all yet
# then add an entry so the system knows we are
# expecting it later (for the above check)
new_discovery[dependency] = DiscoveryState.AWARE_OF
# If the dependencies are satisfied (or there weren't
# any) then this file can be compiled now
if len(compiled) == 0 or all(compiled):
for definition in artifact.defines:
task = self._taskmap[(artifact.filetype,
artifact.state)]
new_artifacts.extend(task.run([artifact]))
new_discovery[definition] = DiscoveryState.COMPILED
else:
# If the dependencies weren't all satisfied then
# back on the queue for another pass later
new_artifacts.append(artifact)
else:
# If it wasn't required it could be later, so
# put it back on the queue, unless the target
# has been compiled, in which case it wasn't
# needed at all!
if (self._target not in discovery
or discovery[self._target] != DiscoveryState.COMPILED):
new_artifacts.append(artifact)
elif artifact.state is Compiled:
# Begin populating the list for linking
new_objects.append(artifact)
# But do not return a new artifact - this object
# is "done" as far as the processing is concerned
# But, if this is the file containing the target
# that means everything must have been compiled
# by this point; so we can do the linking step
if self._target in artifact.defines:
task = self._taskmap[(artifact.filetype,
artifact.state)]
new_artifacts.extend(task.run(objects + [artifact]))
elif artifact.state is Linked:
# Nothing to do at present with the final linked
# executable, but included here for completeness
pass
else:
# If the object specifies any paths in its dependencies
# then these must exist before it can be processed
# TODO: This needs more thorough logic and to come from
# the database eventually
ready = True
for dependency in artifact.depends_on:
if isinstance(dependency, Path):
if not dependency.exists():
ready = False
if ready:
# An artifact with a filetype and state set
# will have an appropriate task that should
# be used to run it (though unlike the old
# implementation this is probably returning
# the instance of the Task not the class)
if ((artifact.filetype, artifact.state)
in self._taskmap):
task = self._taskmap[(artifact.filetype,
artifact.state)]
new_artifacts.extend(task.run([artifact]))
else:
new_artifacts.append(artifact)
# Update shared arrays
lock.acquire()
objects.extend(new_objects)
for key, value in new_discovery.items():
discovery[key] = value
lock.release()
return new_artifacts
def __init__(self):
self._events = []
self._lock = Lock()
# limitations under the License.
import logging
import uuid
from configparser import NoOptionError
import nexusproto.DataTile_pb2 as nexusproto
import numpy as np
from cassandra.auth import PlainTextAuthProvider
from cassandra.cqlengine import columns, connection, CQLEngineException
from cassandra.cqlengine.models import Model
from cassandra.policies import TokenAwarePolicy, DCAwareRoundRobinPolicy, WhiteListRoundRobinPolicy
from multiprocessing.synchronize import Lock
from nexusproto.serialization import from_shaped_array
INIT_LOCK = Lock(ctx=None)
logger = logging.getLogger(__name__)
class NexusTileData(Model):
__table_name__ = 'sea_surface_temp'
tile_id = columns.UUID(primary_key=True)
tile_blob = columns.Blob()
__nexus_tile = None
def _get_nexus_tile(self):
if self.__nexus_tile is None:
self.__nexus_tile = nexusproto.TileData.FromString(self.tile_blob)
from ObexSender.ObexSender import ObexSender
import ProximusAgent
from ProximusAgent import ProximusAgent
import getopt
#from encodings.punycode import adapt
def DeviceFound(address, properties):
if not queue.has_key(address):
queue[address] = properties
#print "# Queued %s Name: %s" % (address, properties["Name"])
manager = bluez.Manager('gobject')
adapter = manager.DefaultAdapter()
queueLock = Lock()
queue = {}
logger = None
def MePropertyChanged(name, value):
global adapter
global logger
if (logger != None):
logger.debug("# - property changed (%s: %s)" % (name, value))
if (name == "Discovering"):
if (value == 1):
if (logger != None):
logger.debug("# - queue sleep 10")
time.sleep(10)
queueLock.acquire()
class Queue(object):
def __init__(self, maxsize = 0):
if maxsize <= 0:
maxsize = _multiprocessing.SemLock.SEM_VALUE_MAX
self._maxsize = maxsize
self._reader, self._writer = Pipe(duplex=False)
self._rlock = Lock()
self._opid = os.getpid()
if sys.platform == 'win32':
self._wlock = None
else:
self._wlock = Lock()
self._sem = BoundedSemaphore(maxsize)
self._after_fork()
if sys.platform != 'win32':
register_after_fork(self, Queue._after_fork)
return
def __getstate__(self):
assert_spawning(self)
return (self._maxsize,
self._reader,
self._writer,
self._rlock,
self._wlock,
self._sem,
self._opid)
def __setstate__(self, state):
self._maxsize, self._reader, self._writer, self._rlock, self._wlock, self._sem, self._opid = state
self._after_fork()
def _after_fork(self):
debug('Queue._after_fork()')
self._notempty = threading.Condition(threading.Lock())
self._buffer = collections.deque()
self._thread = None
self._jointhread = None
self._joincancelled = False
self._closed = False
self._close = None
self._send = self._writer.send
self._recv = self._reader.recv
self._poll = self._reader.poll
return
def put(self, obj, block = True, timeout = None):
if not not self._closed:
raise AssertionError
raise self._sem.acquire(block, timeout) or Full
self._notempty.acquire()
try:
if self._thread is None:
self._start_thread()
self._buffer.append(obj)
self._notempty.notify()
finally:
self._notempty.release()
return
def get(self, block = True, timeout = None):
if block and timeout is None:
self._rlock.acquire()
try:
res = self._recv()
self._sem.release()
return res
finally:
self._rlock.release()
else:
if block:
deadline = time.time() + timeout
if not self._rlock.acquire(block, timeout):
raise Empty
try:
if block:
timeout = deadline - time.time()
if timeout < 0 or not self._poll(timeout):
raise Empty
elif not self._poll():
raise Empty
res = self._recv()
self._sem.release()
return res
finally:
self._rlock.release()
return
def qsize(self):
return self._maxsize - self._sem._semlock._get_value()
def empty(self):
return not self._poll()
def full(self):
return self._sem._semlock._is_zero()
def get_nowait(self):
return self.get(False)
def put_nowait(self, obj):
return self.put(obj, False)
def close(self):
self._closed = True
self._reader.close()
if self._close:
self._close()
def join_thread(self):
debug('Queue.join_thread()')
if not self._closed:
raise AssertionError
self._jointhread and self._jointhread()
def cancel_join_thread(self):
debug('Queue.cancel_join_thread()')
self._joincancelled = True
try:
self._jointhread.cancel()
except AttributeError:
pass
def _start_thread(self):
debug('Queue._start_thread()')
self._buffer.clear()
self._thread = threading.Thread(target=Queue._feed, args=(self._buffer,
self._notempty,
self._send,
self._wlock,
self._writer.close), name='QueueFeederThread')
self._thread.daemon = True
debug('doing self._thread.start()')
self._thread.start()
debug('... done self._thread.start()')
if not self._joincancelled:
self._jointhread = Finalize(self._thread, Queue._finalize_join, [weakref.ref(self._thread)], exitpriority=-5)
self._close = Finalize(self, Queue._finalize_close, [self._buffer, self._notempty], exitpriority=10)
@staticmethod
def _finalize_join(twr):
debug('joining queue thread')
thread = twr()
if thread is not None:
thread.join()
debug('... queue thread joined')
else:
debug('... queue thread already dead')
return
@staticmethod
def _finalize_close(buffer, notempty):
debug('telling queue thread to quit')
notempty.acquire()
try:
buffer.append(_sentinel)
notempty.notify()
finally:
notempty.release()
@staticmethod
def _feed(buffer, notempty, send, writelock, close):
debug('starting thread to feed data to pipe')
from .util import is_exiting
nacquire = notempty.acquire
nrelease = notempty.release
nwait = notempty.wait
bpopleft = buffer.popleft
sentinel = _sentinel
if sys.platform != 'win32':
wacquire = writelock.acquire
wrelease = writelock.release
else:
wacquire = None
try:
while 1:
nacquire()
try:
if not buffer:
nwait()
finally:
nrelease()
try:
while 1:
obj = bpopleft()
if obj is sentinel:
debug('feeder thread got sentinel -- exiting')
close()
return
if wacquire is None:
send(obj)
else:
wacquire()
try:
send(obj)
finally:
wrelease()
except IndexError:
pass
except Exception as e:
try:
if is_exiting():
info('error in queue thread: %s', e)
else:
import traceback
traceback.print_exc()
except Exception:
pass
return
class Queue(object):
def __init__(self, maxsize=0):
if maxsize <= 0:
maxsize = _multiprocessing.SemLock.SEM_VALUE_MAX
self._maxsize = maxsize
self._reader, self._writer = Pipe(duplex=False)
self._rlock = Lock()
self._opid = os.getpid()
if sys.platform == 'win32':
self._wlock = None
else:
self._wlock = Lock()
self._sem = BoundedSemaphore(maxsize)
self._after_fork()
if sys.platform != 'win32':
register_after_fork(self, Queue._after_fork)
def __getstate__(self):
assert_spawning(self)
return (self._maxsize, self._reader, self._writer, self._rlock,
self._wlock, self._sem, self._opid)
def __setstate__(self, state):
(self._maxsize, self._reader, self._writer, self._rlock, self._wlock,
self._sem, self._opid) = state
self._after_fork()
def _after_fork(self):
debug('Queue._after_fork()')
self._notempty = threading.Condition(threading.Lock())
self._buffer = collections.deque()
self._thread = None
self._jointhread = None
self._joincancelled = False
self._closed = False
self._close = None
self._send = self._writer.send
self._recv = self._reader.recv
self._poll = self._reader.poll
def put(self, obj, block=True, timeout=None):
assert not self._closed
if not self._sem.acquire(block, timeout):
raise Full
self._notempty.acquire()
try:
if self._thread is None:
self._start_thread()
self._buffer.append(obj)
self._notempty.notify()
finally:
self._notempty.release()
def get(self, block=True, timeout=None):
if block and timeout is None:
self._rlock.acquire()
try:
res = self._recv()
self._sem.release()
return res
finally:
self._rlock.release()
else:
if block:
deadline = time.time() + timeout
if not self._rlock.acquire(block, timeout):
raise Empty
try:
if not self._poll(block and (deadline - time.time()) or 0.0):
raise Empty
res = self._recv()
self._sem.release()
return res
finally:
self._rlock.release()
def qsize(self):
# Raises NotImplementError on Mac OSX because of broken sem_getvalue()
return self._maxsize - self._sem._semlock._get_value()
def empty(self):
return not self._poll()
def full(self):
return self._sem._semlock._is_zero()
def get_nowait(self):
return self.get(False)
def put_nowait(self, obj):
return self.put(obj, False)
def close(self):
self._closed = True
self._reader.close()
if self._close:
self._close()
def join_thread(self):
debug('Queue.join_thread()')
assert self._closed
if self._jointhread:
self._jointhread()
def cancel_join_thread(self):
debug('Queue.cancel_join_thread()')
self._joincancelled = True
try:
self._jointhread.cancel()
except AttributeError:
pass
def _start_thread(self):
debug('Queue._start_thread()')
# Start thread which transfers data from buffer to pipe
self._buffer.clear()
self._thread = threading.Thread(target=Queue._feed,
args=(self._buffer, self._notempty,
self._send, self._wlock,
self._writer.close),
name='QueueFeederThread')
self._thread.daemon = True
debug('doing self._thread.start()')
self._thread.start()
debug('... done self._thread.start()')
# On process exit we will wait for data to be flushed to pipe.
#
# However, if this process created the queue then all
# processes which use the queue will be descendants of this
# process. Therefore waiting for the queue to be flushed
# is pointless once all the child processes have been joined.
created_by_this_process = (self._opid == os.getpid())
if not self._joincancelled and not created_by_this_process:
self._jointhread = Finalize(self._thread,
Queue._finalize_join,
[weakref.ref(self._thread)],
exitpriority=-5)
# Send sentinel to the thread queue object when garbage collected
self._close = Finalize(self,
Queue._finalize_close,
[self._buffer, self._notempty],
exitpriority=10)
@staticmethod
def _finalize_join(twr):
debug('joining queue thread')
thread = twr()
if thread is not None:
thread.join()
debug('... queue thread joined')
else:
debug('... queue thread already dead')
@staticmethod
def _finalize_close(buffer, notempty):
debug('telling queue thread to quit')
notempty.acquire()
try:
buffer.append(_sentinel)
notempty.notify()
finally:
notempty.release()
@staticmethod
def _feed(buffer, notempty, send, writelock, close):
debug('starting thread to feed data to pipe')
from .util import is_exiting
nacquire = notempty.acquire
nrelease = notempty.release
nwait = notempty.wait
bpopleft = buffer.popleft
sentinel = _sentinel
if sys.platform != 'win32':
wacquire = writelock.acquire
wrelease = writelock.release
else:
wacquire = None
try:
while 1:
nacquire()
try:
if not buffer:
nwait()
finally:
nrelease()
try:
while 1:
obj = bpopleft()
if obj is sentinel:
debug('feeder thread got sentinel -- exiting')
close()
return
if wacquire is None:
send(obj)
else:
wacquire()
try:
send(obj)
finally:
wrelease()
except IndexError:
pass
except Exception, e:
# Since this runs in a daemon thread the resources it uses
# may be become unusable while the process is cleaning up.
# We ignore errors which happen after the process has
# started to cleanup.
try:
if is_exiting():
info('error in queue thread: %s', e)
else:
import traceback
traceback.print_exc()
except Exception:
pass
class Queue(object):
def __init__(self, maxsize=0):
if maxsize <= 0:
maxsize = _multiprocessing.SemLock.SEM_VALUE_MAX
self._maxsize = maxsize
self._reader, self._writer = Pipe(duplex=False)
self._rlock = Lock()
self._opid = os.getpid()
if sys.platform == 'win32':
self._wlock = None
else:
self._wlock = Lock()
self._sem = BoundedSemaphore(maxsize)
self._after_fork()
if sys.platform != 'win32':
register_after_fork(self, Queue._after_fork)
def __getstate__(self):
assert_spawning(self)
return (self._maxsize, self._reader, self._writer,
self._rlock, self._wlock, self._sem, self._opid)
def __setstate__(self, state):
(self._maxsize, self._reader, self._writer,
self._rlock, self._wlock, self._sem, self._opid) = state
self._after_fork()
def _after_fork(self):
debug('Queue._after_fork()')
self._notempty = threading.Condition(threading.Lock())
self._buffer = collections.deque()
self._thread = None
self._jointhread = None
self._joincancelled = False
self._closed = False
self._close = None
self._send = self._writer.send
self._recv = self._reader.recv
self._poll = self._reader.poll
def put(self, obj, block=True, timeout=None):
assert not self._closed
if not self._sem.acquire(block, timeout):
raise Full
self._notempty.acquire()
try:
if self._thread is None:
self._start_thread()
self._buffer.append(obj)
self._notempty.notify()
finally:
self._notempty.release()
def get(self, block=True, timeout=None):
if block and timeout is None:
self._rlock.acquire()
try:
res = self._recv()
self._sem.release()
return res
finally:
self._rlock.release()
else:
if block:
deadline = time.time() + timeout
if not self._rlock.acquire(block, timeout):
raise Empty
try:
if not self._poll(block and (deadline-time.time()) or 0.0):
raise Empty
res = self._recv()
self._sem.release()
return res
finally:
self._rlock.release()
def qsize(self):
# Raises NotImplementedError on Mac OSX because of broken sem_getvalue()
return self._maxsize - self._sem._semlock._get_value()
def empty(self):
return not self._poll()
def full(self):
return self._sem._semlock._is_zero()
def get_nowait(self):
return self.get(False)
def put_nowait(self, obj):
return self.put(obj, False)
def close(self):
self._closed = True
self._reader.close()
if self._close:
self._close()
def join_thread(self):
debug('Queue.join_thread()')
assert self._closed
if self._jointhread:
self._jointhread()
def cancel_join_thread(self):
debug('Queue.cancel_join_thread()')
self._joincancelled = True
try:
self._jointhread.cancel()
except AttributeError:
pass
def _start_thread(self):
debug('Queue._start_thread()')
# Start thread which transfers data from buffer to pipe
self._buffer.clear()
self._thread = threading.Thread(
target=Queue._feed,
args=(self._buffer, self._notempty, self._send,
self._wlock, self._writer.close),
name='QueueFeederThread'
)
self._thread.daemon = True
debug('doing self._thread.start()')
self._thread.start()
debug('... done self._thread.start()')
# On process exit we will wait for data to be flushed to pipe.
#
# However, if this process created the queue then all
# processes which use the queue will be descendants of this
# process. Therefore waiting for the queue to be flushed
# is pointless once all the child processes have been joined.
created_by_this_process = (self._opid == os.getpid())
if not self._joincancelled and not created_by_this_process:
self._jointhread = Finalize(
self._thread, Queue._finalize_join,
[weakref.ref(self._thread)],
exitpriority=-5
)
# Send sentinel to the thread queue object when garbage collected
self._close = Finalize(
self, Queue._finalize_close,
[self._buffer, self._notempty],
exitpriority=10
)
@staticmethod
def _finalize_join(twr):
debug('joining queue thread')
thread = twr()
if thread is not None:
thread.join()
debug('... queue thread joined')
else:
debug('... queue thread already dead')
@staticmethod
def _finalize_close(buffer, notempty):
debug('telling queue thread to quit')
notempty.acquire()
try:
buffer.append(_sentinel)
notempty.notify()
finally:
notempty.release()
@staticmethod
def _feed(buffer, notempty, send, writelock, close):
debug('starting thread to feed data to pipe')
from .util import is_exiting
nacquire = notempty.acquire
nrelease = notempty.release
nwait = notempty.wait
bpopleft = buffer.popleft
sentinel = _sentinel
if sys.platform != 'win32':
wacquire = writelock.acquire
wrelease = writelock.release
else:
wacquire = None
try:
while 1:
nacquire()
try:
if not buffer:
nwait()
finally:
nrelease()
try:
while 1:
obj = bpopleft()
if obj is sentinel:
debug('feeder thread got sentinel -- exiting')
close()
return
if wacquire is None:
send(obj)
else:
wacquire()
try:
send(obj)
finally:
wrelease()
except IndexError:
pass
except Exception as e:
# Since this runs in a daemon thread the resources it uses
# may be become unusable while the process is cleaning up.
# We ignore errors which happen after the process has
# started to cleanup.
try:
if is_exiting():
info('error in queue thread: %s', e)
else:
import traceback
traceback.print_exc()
except Exception:
pass
def main(argv=None): # IGNORE:C0111
'''Command line options.'''
if argv is None:
argv = sys.argv
else:
sys.argv.extend(argv)
parser = ArgumentParser(formatter_class=RawDescriptionHelpFormatter)
parser.add_argument("-v",
"--verbose",
dest="verbose",
action="count",
help="set verbosity level [default: %(default)s]")
# parser.add_argument("-dir", "--structs_dir", required = True )
parser.add_argument("-db", "--database_name", default='pdb')
parser.add_argument("-host", "--db_host", default='127.0.0.1')
parser.add_argument("--procesados",
default='/tmp/pdbs_dist_procesados.txt')
parser.add_argument("--domains",
default='/data/databases/pdb/processed/dns_pdbs.tlb')
parser.add_argument(
"--seqs", default='/data/databases/pdb/processed/pdb_seq_res.fasta')
parser.add_argument("--pdbs", default='/data/databases/pdb/')
parser.add_argument(
"--distances",
default='/data/databases/pdb/processed/distances.tbl',
help=
"Final output: table with atom distances between residues and ligands. Only for distances less than 'dist' parameter"
)
parser.add_argument("--dist", default=5)
parser.add_argument(
"--pdbs_with_drug",
default='/data/databases/pdb/processed/pdbs_with_drug.txt',
help="Output: list of PDB codes with an associated ligand")
args = parser.parse_args()
if not os.path.exists(args.pdbs):
sys.stderr.write(
"%s not found. Specify where is pdbs/divided directory" %
(parser.pdbs))
sys.exit(1)
PDB_PATH = args.pdbs
CONTACT_DIST = args.dist
pdbs_with_drug_path = args.pdbs_with_drug
if not os.path.exists(os.path.dirname(args.pdbs_with_drug)):
sys.stderr.write("can't %s create %s. Set pdbs_with_drug correctly" %
(pdbs_with_drug_path))
sys.exit(1)
if not os.path.exists(os.path.dirname(args.distances)):
sys.stderr.write("can't %s create %s. Set distances correctly" %
(args.distances))
sys.exit(1)
pdbs_procesados_path = args.procesados
print(
"In %s the processed pdbs are kept, if the file is deleted, the process starts from scratch "
% pdbs_procesados_path)
print("Outputs: '%s' and '%s' " % (pdbs_with_drug_path, args.distances))
pdbs_procesados = []
if os.path.exists(pdbs_procesados_path):
with open(pdbs_procesados_path) as handle:
pdbs_procesados = [x.strip() for x in handle.readlines()]
pdbs_procesados = {x: 1 for x in pdbs_procesados}
pdbs_iterator = PDBsIterator(pdb_dir=args.pdbs)
def not_processed_iter():
for pdb, pdb_path in pdbs_iterator:
if pdb not in pdbs_procesados:
yield [pdb, pdb_path]
DNsPDBs = args.domains
if not os.path.exists(DNsPDBs):
seqs_from_pdb = args.seqs
if not os.path.exists(seqs_from_pdb):
sys.stderr.write(
"%s does not exists and %s not found. Specify where it is." %
(DNsPDBs, seqs_from_pdb))
sys.exit(1)
sys.stderr.write(
"%s not found. You can create it with the following command: \n" %
DNsPDBs)
sys.stderr.write(
"hmmscan --cut_tc --domtblout dns_pdbs.tlb --acc -o pdb_seq_res.hmm Pfam-A.hmm seqs_from_pdb.fasta"
)
sys.exit(1)
drugcompounds = [
x for x, y in compound_type.items() if y in ["DRUG", "COFACTOR"]
]
othercompounds = [
x for x, y in compound_type.items()
if y in ["METAL", "SUGAR", "NUCLEOTIDE", "LIPID"]
]
aminoacidcompounds = [
x for x, y in compound_type.items() if y in ["MODIFIED", "RESIDUE"]
]
drugcompounds = othercompounds + drugcompounds
pdbs_with_drug_path = "/data/databases/pdb/processed/pdbs_with_drug.txt"
_log.info("proceced pdbs: %i" % len(pdbs_procesados))
ppb = CaPPBuilder()
p = PDBParser(PERMISSIVE=1, QUIET=1)
pdbs_with_drug = []
if os.path.exists(pdbs_with_drug_path):
_log.info("pdbs with drugs already loaded")
with open(pdbs_with_drug_path) as handle:
for x in handle.readlines():
pdbs_with_drug.append(x.strip())
else:
with open(pdbs_with_drug_path, "a") as handle:
_log.info("pdbs with drugs will be loaded")
pdbs = list(pdbs_iterator)
for pdb, file_path in tqdm(pdbs):
try:
if pdb not in pdbs_with_drug:
structure = p.get_structure(pdb, file_path)
for res in structure.get_residues():
if res.resname in drugcompounds:
pdbs_with_drug.append(pdb)
handle.write(pdb + "\n")
handle.flush()
break
except Exception as ex:
print(str(ex))
# import re
# dns_table = re.sub(r" +", "\t","\n".join( [str(i) + "\t" + x for i,x in enumerate(open('/data/databases/pdb/processed/dns_pdbs.tlb').readlines()) if not x.startswith("#") ]) )
if not os.path.exists(DNsPDBs + "2"):
cols = [
"target_name", "accession", "tlen", "query_name", "accession2",
"qlen", "E-value", "score1", "bias1", "#", "of", "c-Evalue",
"i-Evalue", "score2", "bias2", "from1", "to1", "from2", "to2",
"from3", "to3", "acc"
]
_log.info("correcting hmmer-pdb output")
regexp = re.compile(" +")
items = []
for x in tqdm(open(DNsPDBs).readlines()):
if not x.startswith("#"):
line = regexp.split(x)
items.append(line[0:len(cols)])
# record = {c: line[i] for i, c in enumerate(cols)}
df_hmm = pd.DataFrame.from_records(items, columns=cols)
# df_hmm = df = pd.read_table('/data/databases/pdb/processed/dns_pdbs.tlb', index_col=None, header=None, delimiter=r"\s+",comment="#",names=cols)
# df_hmm = df_hmm.dropna()
df_hmm = df_hmm[["accession", "query_name", "from3", "to3"]]
df_hmm.to_csv(DNsPDBs + "2")
df_hmm["pdb"] = map(lambda x: x.split("_")[0].lower().strip(),
df_hmm["query_name"])
df_hmm["chain"] = map(lambda x: x.split("_")[1].upper().strip(),
df_hmm["query_name"])
df_hmm["start_res"] = map(lambda x: x.split("_")[2].upper().strip(),
df_hmm["query_name"])
df_hmm["end_res"] = map(lambda x: x.split("_")[3].upper().strip(),
df_hmm["query_name"])
else:
df_hmm = pd.read_csv(DNsPDBs + "2")
df_hmm["pdb"] = map(lambda x: x.split("_")[0].lower().strip(),
df_hmm["query_name"])
df_hmm["chain"] = map(lambda x: x.split("_")[1].upper().strip(),
df_hmm["query_name"])
df_hmm["start_res"] = map(lambda x: x.split("_")[2].upper().strip(),
df_hmm["query_name"])
df_hmm["end_res"] = map(lambda x: x.split("_")[3].upper().strip(),
df_hmm["query_name"])
print(len(df_hmm))
lock = Lock()
def centeroid(arr):
length = len(arr)
sum_x = np.sum([x.coord[0] for x in arr])
sum_y = np.sum([x.coord[1] for x in arr])
sum_z = np.sum([x.coord[2] for x in arr])
return sum_x / length, sum_y / length, sum_z / length
def residues_near_drug(drug_centroid, aa_residues):
residues_near = []
for r in aa_residues:
for a in list(r):
dist = a - Struct(coord=drug_centroid)
if dist > 20:
break
if dist < 10:
residues_near.append(r)
break
return residues_near
def juan(pdb_raw):
try:
pepe(pdb_raw)
except Exception:
traceback.print_exc()
finally:
with lock:
pdbs_procesados.append(pdb_raw)
with open(pdbs_procesados_path, "a") as handle:
handle.write(pdb_raw + "\n")
def pepe(pdb):
ppb = CaPPBuilder()
p = PDBParser(PERMISSIVE=1, QUIET=1)
path_dir = PDB_PATH + "/" + pdb[1:3].lower() + "/"
path = path_dir + "pdb" + pdb.lower() + ".ent"
model = list(p.get_structure('X', path))[0]
for chain_obj in list(model):
chain = chain_obj.id
hmm_residues = {}
pdb_seq = list(model[chain].get_residues())
if pdb_seq:
hmm_contacts = {}
hmm_residues = {}
hmms = df_hmm[(df_hmm["pdb"] == pdb)
& (df_hmm["chain"] == chain) &
(df_hmm["start_res"] == str(pdb_seq[0].id[1]))]
for j, hmm in hmms.iterrows():
try:
hmm_start = int(hmm["from3"]) - 1
hmm_end = int(hmm["to3"]) - 1
hmm_chain_name = "_".join(
map(str, [
hmm["accession"].split(".")[0], hmm["chain"],
pdb_seq[hmm_start].id[1],
pdb_seq[hmm_end].id[1]
]))
hmm_contacts[hmm_chain_name] = []
hmm_residues.update({
res.id[1]: hmm_chain_name
for res in pdb_seq[hmm_start:hmm_end]
})
except IndexError:
print(pdb, hmm["accession"], hmm["chain"], hmm_start,
hmm_end, pdb_seq)
aa_residues = []
drug_molecules = []
for res_obj in chain_obj.get_residues():
if res_obj.resname in drugcompounds:
drug_molecules.append(res_obj)
elif res_obj.resname in aminoacidcompounds:
aa_residues.append(res_obj)
for res_drug_obj in drug_molecules:
drug_centroid = centeroid(list(res_drug_obj))
near_residues = residues_near_drug(drug_centroid, aa_residues)
for drug_atom in list(res_drug_obj):
for near_residue in near_residues:
for residue_atom in list(near_residue):
distance = (residue_atom - drug_atom)
if distance > 20:
break
if distance < CONTACT_DIST:
with open(args.distances, "a") as handle:
hmm_name = hmm_residues[
near_residue.id[1]] if near_residue.id[
1] in hmm_residues else "NoDn"
fields = [
pdb, chain, hmm_name,
near_residue.id[1],
near_residue.resname,
residue_atom.serial_number,
res_drug_obj.id[1],
res_drug_obj.resname,
drug_atom.serial_number, distance
]
handle.write("\t".join(map(str, fields)) +
"\n")
_log.info("processing distances file")
for x in tqdm(set(pdbs_with_drug)):
if x not in pdbs_procesados:
juan(x)
# pool = ThreadPool(1)
# pool.map(juan, set(pdbs_with_drug) - set(pdbs_procesados))
print("Finished!!!")
# limitations under the License.
import logging
import uuid
from ConfigParser import NoOptionError
import nexusproto.DataTile_pb2 as nexusproto
import numpy as np
from cassandra.auth import PlainTextAuthProvider
from cassandra.cqlengine import columns, connection, CQLEngineException
from cassandra.cqlengine.models import Model
from cassandra.policies import TokenAwarePolicy, DCAwareRoundRobinPolicy, WhiteListRoundRobinPolicy
from multiprocessing.synchronize import Lock
from nexusproto.serialization import from_shaped_array
INIT_LOCK = Lock()
logger = logging.getLogger(__name__)
class NexusTileData(Model):
__table_name__ = 'sea_surface_temp'
tile_id = columns.UUID(primary_key=True)
tile_blob = columns.Blob()
__nexus_tile = None
def _get_nexus_tile(self):
if self.__nexus_tile is None:
self.__nexus_tile = nexusproto.TileData.FromString(self.tile_blob)
return self.__nexus_tile
class Queue(object):
def __init__(self, maxsize = 0):
if maxsize <= 0:
maxsize = _multiprocessing.SemLock.SEM_VALUE_MAX
self._maxsize = maxsize
self._reader, self._writer = Pipe(duplex=False)
self._rlock = Lock()
self._opid = os.getpid()
if sys.platform == 'win32':
self._wlock = None
else:
self._wlock = Lock()
self._sem = BoundedSemaphore(maxsize)
self._after_fork()
if sys.platform != 'win32':
register_after_fork(self, Queue._after_fork)
return
def __getstate__(self):
assert_spawning(self)
return (self._maxsize,
self._reader,
self._writer,
self._rlock,
self._wlock,
self._sem,
self._opid)
def __setstate__(self, state):
self._maxsize, self._reader, self._writer, self._rlock, self._wlock, self._sem, self._opid = state
self._after_fork()
def _after_fork(self):
debug('Queue._after_fork()')
self._notempty = threading.Condition(threading.Lock())
self._buffer = collections.deque()
self._thread = None
self._jointhread = None
self._joincancelled = False
self._closed = False
self._close = None
self._send = self._writer.send
self._recv = self._reader.recv
self._poll = self._reader.poll
return
def put(self, obj, block = True, timeout = None):
if not not self._closed:
raise AssertionError
raise self._sem.acquire(block, timeout) or Full
self._notempty.acquire()
try:
if self._thread is None:
self._start_thread()
self._buffer.append(obj)
self._notempty.notify()
finally:
self._notempty.release()
return
def get(self, block = True, timeout = None):
if block and timeout is None:
self._rlock.acquire()
try:
res = self._recv()
self._sem.release()
return res
finally:
self._rlock.release()
else:
if block:
deadline = time.time() + timeout
if not self._rlock.acquire(block, timeout):
raise Empty
try:
if block:
timeout = deadline - time.time()
if timeout < 0 or not self._poll(timeout):
raise Empty
elif not self._poll():
raise Empty
res = self._recv()
self._sem.release()
return res
finally:
self._rlock.release()
return
def qsize(self):
return self._maxsize - self._sem._semlock._get_value()
def empty(self):
return not self._poll()
def full(self):
return self._sem._semlock._is_zero()
def get_nowait(self):
return self.get(False)
def put_nowait(self, obj):
return self.put(obj, False)
def close(self):
self._closed = True
self._reader.close()
if self._close:
self._close()
def join_thread(self):
debug('Queue.join_thread()')
if not self._closed:
raise AssertionError
self._jointhread and self._jointhread()
def cancel_join_thread(self):
debug('Queue.cancel_join_thread()')
self._joincancelled = True
try:
self._jointhread.cancel()
except AttributeError:
pass
def _start_thread(self):
debug('Queue._start_thread()')
self._buffer.clear()
self._thread = threading.Thread(target=Queue._feed, args=(self._buffer,
self._notempty,
self._send,
self._wlock,
self._writer.close), name='QueueFeederThread')
self._thread.daemon = True
debug('doing self._thread.start()')
self._thread.start()
debug('... done self._thread.start()')
if not self._joincancelled:
self._jointhread = Finalize(self._thread, Queue._finalize_join, [weakref.ref(self._thread)], exitpriority=-5)
self._close = Finalize(self, Queue._finalize_close, [self._buffer, self._notempty], exitpriority=10)
@staticmethod
def _finalize_join(twr):
debug('joining queue thread')
thread = twr()
if thread is not None:
thread.join()
debug('... queue thread joined')
else:
debug('... queue thread already dead')
return
@staticmethod
def _finalize_close(buffer, notempty):
debug('telling queue thread to quit')
notempty.acquire()
try:
buffer.append(_sentinel)
notempty.notify()
finally:
notempty.release()
@staticmethod
def _feed(buffer, notempty, send, writelock, close):
debug('starting thread to feed data to pipe')
from .util import is_exiting
nacquire = notempty.acquire
nrelease = notempty.release
nwait = notempty.wait
bpopleft = buffer.popleft
sentinel = _sentinel
if sys.platform != 'win32':
wacquire = writelock.acquire
wrelease = writelock.release
else:
wacquire = None
try:
while 1:
nacquire()
try:
if not buffer:
nwait()
finally:
nrelease()
try:
while 1:
obj = bpopleft()
if obj is sentinel:
debug('feeder thread got sentinel -- exiting')
close()
return
if wacquire is None:
send(obj)
else:
wacquire()
try:
send(obj)
finally:
wrelease()
except IndexError:
pass
except Exception as e:
try:
if is_exiting():
info('error in queue thread: %s', e)
else:
import traceback
traceback.print_exc()
except Exception:
pass
return
def Lock():
"""
Returns a non-recursive lock object
"""
from multiprocessing.synchronize import Lock
return Lock()
#! -*- coding: utf-8 -*-
from rpccore.gen import Links
from thrift.server import TServer
from thrift.transport import TSocket
from thrift.transport import TTransport
from thrift.protocol import TBinaryProtocol
from multiprocessing.synchronize import Lock
_lock = Lock()
class LinksHandler(Links.InterFace):
DEFAULT_PORT = 9990
def getStand(self, predicate, pendings):
try:
_lock.acquire()
print "do something"
return
finally:
_lock.release()
handler = LinksHandler()
processor = Links.Processor(handler)
transport = TSocket.TServerSocket(port=LinksHandler.DEFAULT_PORT)
tfactory = TTransport.TBufferedTransportFactory()
pfactory = TBinaryProtocol.TBinaryProtocolFactory()
server = TServer.TThreadedServer(processor, transport, tfactory, pfactory)
def Lock():
from multiprocessing.synchronize import Lock
return Lock()
class PollsterBot(Daemon):
def __init__(self, pid):
Daemon.__init__(self, pid)
# Reddit https://praw.readthedocs.io/en/stable/pages/comment_parsing.html
self.reddit = {}
self.default_subs = 'pollster_bot'
self.bot_name = 'pollster_bot'
self.version = '1.0'
self.touched_comment_ids = []
# create logger
self.logger = logging.getLogger('Pollster_Bot')
self.logger.setLevel(logging.INFO)
# File handler set to DEBUG
fh = logging.FileHandler(filename=os.path.join(
os.path.dirname(__file__), 'PollsterBotLog.txt'))
fh.setLevel(logging.DEBUG)
# create console handler and set level to debug
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
# create formatter
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
# add formatter to ch
ch.setFormatter(formatter)
fh.setFormatter(formatter)
# add ch, fh to logger
self.logger.addHandler(ch)
self.logger.addHandler(fh)
self.lock = Lock()
self.logger.info('Starting Pollster Bot ver. ' + self.version)
# Huffington post http://elections.huffingtonpost.com/pollster/api
self.uri = 'http://elections.huffingtonpost.com/pollster/api/charts.json'
# Set states
self.states = {}
self.states = self.load_json_file('data/states.json')
# phrases
phrases = self.load_json_file('data/phrases.json')
self.greetings = phrases['greeting']
self.winning = phrases['winning']
self.losing = phrases['losing']
# keywords to call the pollster bot
self.keywords = self.load_json_file('data/keywords.json')['keywords']
# subs
subs = self.load_json_file('data/subs.json')['subs']
for sub in subs:
self.default_subs += '+' + sub
self.log_in_credentials = self.load_json_file(
'data/login_credentials.json')
def login(self):
self.logger.info('Login started Pollster Bot ver. ' + self.version)
login_name = self.log_in_credentials['user']
login_password = self.log_in_credentials['password']
self.reddit = praw.Reddit(user_agent='Pollster')
self.reddit.login(login_name, login_password, disable_warning=False)
self.logger.info('Login Completed Pollster Bot ver. ' + self.version)
# Returns a dictionary of states.
def load_json_file(self, filename):
self.logger.info('Read {} Pollster Bot ver. {}'.format(
filename, self.version))
fn = os.path.join(os.path.dirname(__file__), filename)
with open(fn) as data_file:
return json.load(data_file)
def get_greeting(self):
return random.choice(self.greetings)
def get_winning(self, winner, points):
return random.choice(self.winning).format(winner, points)
def get_losing(self, loser, points):
return random.choice(self.losing).format(loser, points)
# Gets all submissions in the subreddit as a generator.
def get_submissions(self, subreddit, submission_limit=25):
donald_submissions = self.reddit.get_subreddit(subreddit).get_hot(
limit=submission_limit)
return donald_submissions
@staticmethod
def get_comments(submission, comment_limit=25):
submission.replace_more_comments(limit=comment_limit, threshold=0)
return submission.comments
def get_flat_comments(self, submission, comment_limit=25):
try:
submission.replace_more_comments(limit=comment_limit, threshold=0)
except requests.exceptions.ConnectionError:
self.logger.error('Error fetching comments!')
return None
return praw.helpers.flatten_tree(submission.comments)
def get_recent_comments(self, subreddit):
comments = self.reddit.get_comments(subreddit)
return praw.helpers.flatten_tree(comments)
def get_comments_with_helper(self, subreddit):
comments = praw.helpers.comment_stream(self.reddit, subreddit)
return praw.helpers.flatten_tree(comments)
# Gets polls from state, defaults to 2016-president race
def get_poll_huffington(self, state, page=1, topic='2016-president'):
poll_params = {'page': page, 'state': state, 'topic': topic}
my_response = requests.get(self.uri, params=poll_params)
if my_response.ok:
polling_data = []
entry_data = {}
json_response = my_response.json()
for entry in json_response:
entry_data['title'] = entry['title']
entry_data['state'] = entry['state']
entry_data['url'] = entry['url']
entry_data['last_updated'] = entry['last_updated']
entry_data['estimates'] = []
for estimate in entry['estimates']:
estimate_data = {}
estimate_data['choice'] = estimate['choice']
estimate_data['value'] = estimate['value']
estimate_data['party'] = estimate['party']
entry_data['estimates'].append(estimate_data)
polling_data.append(entry_data)
return polling_data
# Returns a list of states abbreviations.
@staticmethod
def check_comment_for_dictionary_keys_and_values(comment, dictionary):
comment_string = comment.body
matches = []
abbrevs = []
# Check full names
for x in dictionary.keys():
if x in comment_string and x not in matches:
matches.append(x)
for x in dictionary.values():
if x in comment_string and x not in matches:
matches.append(x)
# Return Abbrevs
for match in matches:
if match in dictionary.values():
abbrevs.append(match)
else:
for key in dictionary.keys():
if key is match:
abbrevs.append(dictionary[key])
return abbrevs
@staticmethod
def check_word_in_list_in_string(list, string):
"""
Returns not None if a word in the list is contained in the string
:param list:
:param string:
:return: None if list has no elements contained in string
"""
stuff = [string for word in list if (word in string)]
return stuff
def header_huffington(self):
"""
Builds a header for the huffington post output
:return:
"""
head = '\n ^^Polls ^^fetched ^^from ^^[http://elections.huffingtonpost.com/](http://elections.huffingtonpost.com/).\n\n'
head += '***{}***\n\n'.format(self.get_greeting())
head += '.\n\n'
head += '.\n\n'
return head
def footer(self):
"""
Builds bot header
:return:
"""
foot = '\n\nSummon pollster bot by typing in Pollster_Bot and then any state or states.\n\nEx. Pollster Bot CA Texas Maine RI visit [/r/Pollster_Bot](https://www.reddit.com/r/Pollster_Bot/) for more info'
foot += "\n\n***If you have any feedback on this bot please [Click Here](http://i.imgur.com/YFIri5g.jpg).***"
foot += '^^Pollster ^^bot ^^ver. ^^{}'.format(self.version)
return foot
@staticmethod
def format_estimates(estimates):
reply = ''
reply += '\nChoice | Percentage | Party\n'
reply += '------|----------|-----\n'
for estimate in estimates:
if not estimate['party']:
estimate['party'] = ''
reply += '{} | {} | {} \n'.format(estimate['choice'],
str(estimate['value']),
estimate['party'])
return reply + '\n\n'
def format_poll(self, poll):
state = ''
for name, abb in self.states.items():
if poll['state'] == abb:
state = name
reply = ''
reply += '\n\n***' + state + ' Poll:' + '***\n\n'
reply += self.format_estimates(poll['estimates'])
datetime_string = poll['last_updated']
dt = parser.parse(datetime_string)
datetime_string = dt.strftime('%b %d %Y %I:%M%p')
reply += 'Date of poll: {} ^^GMT\n\n'.format(datetime_string)
reply += r'^^Link ^^to ^^poll ^^' + str(poll['url'] + '\n\n')
return reply
def check_condition(self, comment):
"""
Checks if we have a keyword in the comment, then if we have a list of states also.
:param comment:
:return: if we should act on the comment or not
"""
if comment.id in self.touched_comment_ids:
return False, None
# First check for keywords in comment, for now we don't care about formatting after the keyword
has_keyword = self.check_word_in_list_in_string(
self.keywords, comment.body)
if not has_keyword:
return False, None
# Next we check if we have states or abbreviations
abbrevs = self.check_comment_for_dictionary_keys_and_values(
comment, self.states)
if len(abbrevs) < 1:
return False, None
if str(comment.author) == self.bot_name:
return False, None
for reply in comment.replies:
if str(reply.author) == self.bot_name:
return False, None
return True, abbrevs
def bot_action(self, comment, abbrevs):
self.lock.acquire()
response = self.header_huffington()
done_reqs = []
for abbrev in abbrevs:
if abbrev not in done_reqs:
done_reqs.append(abbrev)
polls = self.get_poll_huffington(abbrev)
for poll in polls:
response += self.format_poll(poll)
response += self.footer()
try:
comment.reply(response)
self.touched_comment_ids.append(comment.id)
# log
log_out = ''
log_out += 'Time: {} \nAuthor: {} \nBody: {}\n States: {} \nResponse: {} \n'.format(
(datetime.timedelta(milliseconds=(time.time()))),
comment.author, comment.body, abbrevs, response)
self.logger.info(log_out)
except praw.errors.RateLimitExceeded:
self.logger.warn("RateLimitExceeded!!! Response not posted!!!")
finally:
self.lock.release()
def slow_loop(self):
submissions = self.get_submissions(self.default_subs,
submission_limit=100)
for submission in submissions:
self.logger.info(u'Crawling Submission ' + submission.title)
time_start = time.time()
comments = self.get_recent_comments(submission)
for comment in comments:
check, abbrevs = self.check_condition(comment)
if check:
self.bot_action(comment, abbrevs)
time_end = time.time()
crawl_time = int(time_end) - int(time_start)
crawl_string = 'Crawl time: ' + str(crawl_time) + ' seconds'
self.logger.info(crawl_string)
def main_loop(self):
for comment in self.get_recent_comments(self.default_subs):
check, abbrevs = self.check_condition(comment)
if check:
self.bot_action(comment, abbrevs)
time.sleep(2)
def run_forever(self):
self.logger.info('Forever Loop started Pollster Bot ver. ' +
self.version)
self.login()
while 1 < 2:
self.main_loop()
def run(self):
self.logger.info('Running Pollster Bot ver. ' + self.version)
self.run_forever()