def wait_readwrite(fileno, timeout=-1, timeout_exc=_socket.timeout('timed out')):
evt = core.readwrite_event(fileno, _wait_helper, timeout, (getcurrent(), timeout_exc))
try:
switch_result = get_hub().switch()
assert evt is switch_result, 'Invalid switch into wait_readwrite(): %r' % (switch_result, )
finally:
evt.cancel()
def wait_write(fileno, timeout=-1, timeout_exc=_socket.timeout('timed out')):
evt = core.write_event(fileno, _wait_helper, timeout,
(getcurrent(), timeout_exc))
try:
switch_result = get_hub().switch()
assert evt is switch_result, 'Invalid switch into wait_write(): %r' % (
switch_result, )
finally:
evt.cancel()
def _sendfile_use_sendfile(self, file, offset=0, count=None):
self._check_sendfile_params(file, offset, count)
sockno = self.fileno()
try:
fileno = file.fileno()
except (AttributeError, io.UnsupportedOperation) as err:
raise _GiveupOnSendfile(err)
try:
fsize = os.fstat(fileno).st_size
except OSError as err:
raise _GiveupOnSendfile(err)
if not fsize:
return 0
blocksize = fsize if not count else count
timeout = self.gettimeout()
if timeout == 0:
raise ValueError('non-blocking sockets are not supported')
if hasattr(selectors, 'PollSelector'):
selector = selectors.PollSelector()
else:
selector = selectors.SelectSelector()
selector.register(sockno, selectors.EVENT_WRITE)
total_sent = 0
selector_select = selector.select
os_sendfile = os.sendfile
try:
while True:
if timeout and not selector_select(timeout):
raise _socket.timeout('timed out')
if count:
blocksize = count - total_sent
if blocksize <= 0:
break
try:
sent = os_sendfile(sockno, fileno, offset, blocksize)
except BlockingIOError:
if not timeout:
selector_select()
continue
except OSError as err:
if total_sent == 0:
raise _GiveupOnSendfile(err)
raise err from None
else:
if sent == 0:
break
offset += sent
total_sent += sent
return total_sent
finally:
if total_sent > 0 and hasattr(file, 'seek'):
file.seek(offset)
def ssh_client(hostname, username, password):
"""
SSH client with a workaround for using IPv4 addresses
"""
ssh = paramiko.SSHClient()
ssh.set_missing_host_key_policy(paramiko.AutoAddPolicy())
ssh.connect(hostname, username=username, password=password, timeout=60)
return ssh
if ssh.get_transport() is None:
# An SSH Transport attaches to a stream (usually a socket), negotiates an encrypted session,
# authenticates, and then creates stream tunnels, called channels, across the session.
# If connection is not established, returns None.
raise timeout("No pingable IP found")
def _sendfile_use_sendfile(self, file, offset=0, count=None):
self._check_sendfile_params(file, offset, count)
sockno = self.fileno()
try:
fileno = file.fileno()
except (AttributeError, io.UnsupportedOperation) as err:
raise _GiveupOnSendfile(err) # not a regular file
try:
fsize = os.fstat(fileno).st_size
except OSError as err:
raise _GiveupOnSendfile(err) # not a regular file
if not fsize:
return 0 # empty file
# Truncate to 1GiB to avoid OverflowError, see bpo-38319.
blocksize = min(count or fsize, 2 ** 30)
timeout = self.gettimeout()
if timeout == 0:
raise ValueError("non-blocking sockets are not supported")
# poll/select have the advantage of not requiring any
# extra file descriptor, contrarily to epoll/kqueue
# (also, they require a single syscall).
if hasattr(selectors, 'PollSelector'):
selector = selectors.PollSelector()
else:
selector = selectors.SelectSelector()
selector.register(sockno, selectors.EVENT_WRITE)
total_sent = 0
# localize variable access to minimize overhead
selector_select = selector.select
os_sendfile = os.sendfile
try:
while True:
if timeout and not selector_select(timeout):
raise _socket.timeout('timed out')
if count:
blocksize = count - total_sent
if blocksize <= 0:
break
try:
sent = os_sendfile(sockno, fileno, offset, blocksize)
except BlockingIOError:
if not timeout:
# Block until the socket is ready to send some
# data; avoids hogging CPU resources.
selector_select()
continue
except OSError as err:
if total_sent == 0:
# We can get here for different reasons, the main
# one being 'file' is not a regular mmap(2)-like
# file, in which case we'll fall back on using
# plain send().
raise _GiveupOnSendfile(err)
raise err from None
else:
if sent == 0:
break # EOF
offset += sent
total_sent += sent
return total_sent
finally:
if total_sent > 0 and hasattr(file, 'seek'):
file.seek(offset)
def _sendfile_use_sendfile(self, file, offset=0, count=None):
self._check_sendfile_params(file, offset, count)
sockno = self.fileno()
try:
fileno = file.fileno()
except (AttributeError, io.UnsupportedOperation) as err:
raise _GiveupOnSendfile(err) # not a regular file
try:
fsize = os.fstat(fileno).st_size
except OSError as err:
raise _GiveupOnSendfile(err) # not a regular file
if not fsize:
return 0 # empty file
blocksize = fsize if not count else count
timeout = self.gettimeout()
if timeout == 0:
raise ValueError("non-blocking sockets are not supported")
# poll/select have the advantage of not requiring any
# extra file descriptor, contrarily to epoll/kqueue
# (also, they require a single syscall).
if hasattr(selectors, 'PollSelector'):
selector = selectors.PollSelector()
else:
selector = selectors.SelectSelector()
selector.register(sockno, selectors.EVENT_WRITE)
total_sent = 0
# localize variable access to minimize overhead
selector_select = selector.select
os_sendfile = os.sendfile
try:
while True:
if timeout and not selector_select(timeout):
raise _socket.timeout('timed out')
if count:
blocksize = count - total_sent
if blocksize <= 0:
break
try:
sent = os_sendfile(sockno, fileno, offset, blocksize)
except BlockingIOError:
if not timeout:
# Block until the socket is ready to send some
# data; avoids hogging CPU resources.
selector_select()
continue
except OSError as err:
if total_sent == 0:
# We can get here for different reasons, the main
# one being 'file' is not a regular mmap(2)-like
# file, in which case we'll fall back on using
# plain send().
raise _GiveupOnSendfile(err)
raise err from None
else:
if sent == 0:
break # EOF
offset += sent
total_sent += sent
return total_sent
finally:
if total_sent > 0 and hasattr(file, 'seek'):
file.seek(offset)
if sbginp: #If we are in the user-interactive mode, ask for a valid option for the subgroup output to continue.
while testsbg:
sbgopt=raw_input("\nDo you want to generate a multifasta file with the sequences analyzed?\nWrite 'Y' to make it or 'N' to continue): ")
if sbgopt.lower() in yesopt:
print '\nDONE:'
subgroupseq(filename,int(minlen),int(maxlen),currTime,wrng)
print '- '*29+'-'
testsbg=0
elif sbgopt.lower() in noopt:
testsbg=0
else:
print "Bad option, try again."
else: #If we are in the command-line mode and the parameter for the subgroup output is given, do the analysis.
subgroupseq(filename,int(minlen),int(maxlen),currTime,wrng)
print '- '*34+'-'
timeout(1)
#=========================================================================#
if testps:
if psinp: #If we are in the user-interactive mode, ask for a valid option for the pseudosequence output to continue.
while testps:
psopt=raw_input("\nDo you want to generate a pseudosequence?\nWrite 'Y' to build it or 'N' to continue): ")
if psopt.lower() in yesopt:
pschk=1
while pschk:
nrep=raw_input("Please, give the NUMBER of repeats of the ambiguous\nresidue to concatenate the sequences: ")
try:
if int(nrep)>=0:
print '\nDONE:'
pseudoseq(filename,int(nrep),int(minlen),int(maxlen),currTime,wrng) #Correct number of repetitions, continue.
print '- '*29+'-'
pschk=0
