def FuncFileFilter():
baseExeFolder = 'E:\design\\test\sourcesFunction\ConsoleApplication6.exe'
listDsmAndGmlFiles = os.listdir(baseExeFolder)
for fileDsmOrGml in listDsmAndGmlFiles:
#if fileDsmOrGml.split('.')[-1]=='gml':
# targetDirGml='G:\\design\\temp'+os.sep+fileDsmOrGml
# os.remove(targetDirGml)
if fileDsmOrGml.split('.')[-1] == 'dsm':
funcDsmFile = open(baseExeFolder + os.sep + fileDsmOrGml, "r")
countInstr = funcDsmFile.readline().count(";")
if countInstr <= 10:
funcDsmFile.close()
targetDsm = baseExeFolder + os.sep + fileDsmOrGml
targetGml = baseExeFolder + os.sep + fileDsmOrGml.split(
'.')[0] + '.gml'
os.remove(targetDsm)
os.remove(targetGml)
else:
funcDsmFile.close()
elif fileDsmOrGml.split('.')[-1] == 'gml':
funcGmlFile = open(baseExeFolder + os.sep + fileDsmOrGml, "r")
countTracelet = funcGmlFile.read().count('node')
if countTracelet < 3:
funcGmlFile.close()
targetGml = baseExeFolder + os.sep + fileDsmOrGml
targetDsm = baseExeFolder + os.sep + fileDsmOrGml.split(
'.')[0] + '.dsm'
os.remove(targetDsm)
os.remvoe(targetGml)
else:
funcGmlFile.close()
os.remove(baseExeFolder + os.sep + fileDsmOrGml)
return 0
def main():
parser = OptionParser()
parser.add_option('-r', dest='readsf', help='Fasta file of reads')
parser.add_option('-n',
dest='numreads',
type='int',
help='Number of reads to sample for MCMC')
parser.add_option('-k',
dest='clusters',
type='int',
help='Number of clusters')
parser.add_option('-m', dest='mers', type='int', help='Mers to count')
parser.add_option('-p',
dest='proc',
type='int',
help='Number of processes to run')
parser.add_option('--em',
dest='soft_assign',
action='store_true',
default=False,
help='Use a soft assignment of reads to clusters')
(options, args) = parser.parse_args()
if options.soft_assign:
em = '--em'
else:
em = ''
# randomly sample reads
total_reads = 0
for line in open(options.readsf):
if line[0] == '>':
total_reads += 1
if options.numreads and options.numreads < total_reads:
dna.fasta_rand_big(options.numreads, options.readsf, 'sample.fa')
else:
if os.path.isfile('sample.fa') or os.path.islink('sample.fa'):
os.remvoe('sample.fa')
os.symlink(options.readsf, 'sample.fa')
# CompostBin
p = subprocess.Popen(
'%s/compostbin.py -r sample.fa -c %d -k %d &> cb.log' %
(bin_dir, options.clusters, options.mers),
shell=True)
os.waitpid(p.pid, 0)
# initialize clusters
init_clusters(options.readsf, options.clusters, options.soft_assign)
# run seed_only
p = subprocess.Popen(
'%s/imm_cluster.py -k %d -r %s -p %d -s --seed_only %s >> cb.log' %
(bin_dir, options.clusters, options.readsf, options.proc, em),
shell=True)
os.waitpid(p.pid, 0)
def stop(self):
"""Stop the daemon"""
#chkpid
pid = self.chkpid()
if not pid:
message = "pidfile {0} does not exists. Daemon not running?\n".format(self.pidfile)
sys.stderr.write(message.format(self.pidfile))
sys.exit(1)
try:
while 1:
os.kill(pid, signal.SIGTERM)
time.sleep(0.1)
except OSError as err:
e = str(err.args)
if (e.find("No such process") > 0):
if os.path.exists(self.pidfile):
os.remvoe(self.pidfile)
else:
print(str(err.args))
sys.exit(1)
def main():
parser = OptionParser()
parser.add_option('-r', dest='readsf', help='Fasta file of reads')
parser.add_option('-n', dest='numreads', type='int', help='Number of reads to sample for MCMC')
parser.add_option('-k', dest='clusters', type='int', help='Number of clusters')
parser.add_option('-m', dest='mers', type='int', help='Mers to count')
parser.add_option('-p', dest='proc', type='int', help='Number of processes to run')
parser.add_option('--em', dest='soft_assign', action='store_true', default=False, help='Use a soft assignment of reads to clusters')
(options, args) = parser.parse_args()
if options.soft_assign:
em = '--em'
else:
em = ''
# randomly sample reads
total_reads = 0
for line in open(options.readsf):
if line[0] == '>':
total_reads += 1
if options.numreads and options.numreads < total_reads:
dna.fasta_rand_big(options.numreads, options.readsf, 'sample.fa')
else:
if os.path.isfile('sample.fa') or os.path.islink('sample.fa'):
os.remvoe('sample.fa')
os.symlink(options.readsf, 'sample.fa')
# CompostBin
p = subprocess.Popen('%s/compostbin.py -r sample.fa -c %d -k %d &> cb.log' % (bin_dir, options.clusters, options.mers), shell=True)
os.waitpid(p.pid, 0)
# initialize clusters
init_clusters(options.readsf, options.clusters, options.soft_assign)
# run seed_only
p = subprocess.Popen('%s/imm_cluster.py -k %d -r %s -p %d -s --seed_only %s >> cb.log' % (bin_dir, options.clusters, options.readsf, options.proc, em), shell=True)
os.waitpid(p.pid, 0)
def tearDown(self):
os.remvoe(self.template_file)
# make sure that other tests don't rely on these settings
settings.TEMPLATE_DIRS = self.default_template_dirs
def render(args):
x = args.coords[0]
y = args.coords[1]
z = args.coords[2]
coordstext = "x{}y{}z{}".format(x, y, z)
res = args.res.split("x")
mode = args.mode
spp = args.ssp
folder = lapse360folder + "/" + coordstext
files = glob.glob(folder + "/*.json")
files.insert(0, files.pop())
filesenum = enumerate(files)
numfiles = len(files)
for f in filesenum:
print(f)
start = time.time()
# load the json, change it, and dump it again
with open(f[1], "r") as scenefile:
config = json.load(scenefile)
config["sppTarget"] = spp
config["height"] = int(res[1])
config["width"] = int(res[0])
name = f[1].split("/")[-1].rsplit(".", 1)[0]
notexist = not os.path.exists(folder + "/" + name + ".octree")
if notexist:
snap = config["zfssnapshot"]
pool = snap.split('/')[0]
subprocess.call("sudo zfs destroy " + pool + "/" + coordstext, shell=True)
subprocess.call("sudo zfs clone -o readonly=on " + snap + " " + pool + "/" + coordstext, shell=True)
pngfilename = "{}/{}-{}".format(folder, name, str(spp))
if mode == "2d":
json.dump(config, open(f[1], "w"))
command = "{} -jar {} -scene-dir {}/ -render {}".format(java, chunky, folder, name)
subprocess.call(command, shell=True)
subprocess.call("convert " + pngfilename + ".png -gravity southeast -stroke '#000C' -strokewidth 2 -annotate 0 \"" + name + "\" -stroke none -fill white -annotate 0 \"" + name + "\" " + pngfilename + "-annotated.png", shell=True)
for each in glob.glob(folder + "/" + name + "*.dump"): os.remove(each)
try:
os.remove(pngfilename + ".png")
except:
pass
if mode == "3d":
config["camera"]["projectionMode"] = "ODS_LEFT"
json.dump(config, open(f[1], "w"))
command = "{} -jar {} -scene-dir {}/ -render {}".format(java, chunky, folder, name)
subprocess.call(command, shell=True)
subprocess.call("convert " + pngfilename + ".png -gravity southeast -stroke '#000C' -strokewidth 2 -annotate 0 \"" + name + "\" -stroke none -fill white -annotate 0 \"" + name + "\" " + pngfilename + "-ODS_LEFT-annotated.png", shell=True)
for each in glob.glob(folder + "/" + name + "*.dump"): os.remove(each)
try:
os.remove(pngfilename + ".png")
os.remvoe(pngfilename + "-ODS_LEFT-annotated.png")
except:
pass
config["camera"]["projectionMode"] = "ODS_RIGHT"
json.dump(config, open(f[1], "w"))
command = "{} -jar {} -scene-dir {}/ -render {}".format(java, chunky, folder, name)
subprocess.call(command, shell=True)
subprocess.call("convert " + pngfilename + ".png -gravity southeast -stroke '#000C' -strokewidth 2 -annotate 0 \"" + name + "\" -stroke none -fill white -annotate 0 \"" + name + "\" " + pngfilename + "-ODS_RIGHT-annotated.png", shell=True)
for each in glob.glob(folder + "/" + name + "*.dump"): os.remove(each)
try:
os.remove(pngfilename + ".png")
os.remvoe(pngfilename + "-ODS_RIGHT-annotated.png")
except:
pass
subprocess.call("convert " + pngfilename + "-ODS_LEFT-annotated.png " + pngfilename + "-ODS_RIGHT-annotated.png -append " + pngfilename + "-combined-annotated.png", shell=True)
if notexist:
snap = config["zfssnapshot"]
pool = snap.split('/')[0]
subprocess.call("sudo zfs clone -o readonly=on " + snap + " " + pool + "/" + coordstext, shell=True)
stop = time.time()
elapsed = stop - start
# tell me how much more coffee I have to dring until it's done
print("Just finished snapshot {} of {}, {} percent. {} hours left.".format( f[0] + 1, numfiles, 100.0 * (f[0] + 1) / numfiles, elapsed * (numfiles - f[0] + 1)/60/60))
def main(argv):
#all parameter we may need
keyFile = ''
cerFile = ''
keyPemFile = ''
cerPemFile = ''
pemFile = ''
token = ''
payload = '{"aps":{"alert":"default message","sound":"alert.aif"}}'
development = 1
generatePemFile = 0
#parsering the arguments
try:
opts, args = getopt.getopt(argv,"hk:c:p:m:t:d:",["help", "keyFile=", "cerFile=", "keyPemFile=", "cerPemFile=", "pemFile=", "token=", "payload=", "development=", "generatePemFile="])
except getopt.GetoptError:
print ('please use iosPushNotification.py -h or iosPushNotification.py --help for help')
sys.exit(2)
for opt, arg in opts:
if opt in ("-h", "--help"):
print ("""
#######################--help--#######################
-k --keyFile : for the p12 file.
-c --cerFile : for the cert file.
--keyPemFile : for pem file that generated from the p12 file.
--cerPemFile : for pem file that generated from the cert file.
--pemFile : the combined pem file, which is most widely used.
-t --token : the token of device to receive this notification.
-m --payload : the payload or the file path of payload to be sent.
-d --development : specified as 1 to send push notificaiont to staging server, 0 to send to produciton server, default as 1.
--generatePemFile : generate the pem file, name it as same as keyFile's name
#####################################################
""")
sys.exit()
elif opt in ("-k", "--keyFile"):
keyFile = arg
elif opt in ("-c", "--cerFile"):
cerFile = arg
elif opt == "--keyPemFile":
keyPemFile = arg
elif opt == "--cerPemFile":
cerPemFile = arg
elif opt in ("-p", "--pemFile"):
pemFile = arg
elif opt in ("-t", "--token"):
token = arg
elif opt in ("-m", "--payload"):
payload = arg
elif opt in ("-d", "--development"):
development = arg
elif opt in ("--generatePemFile"):
generatePemFile = arg
if (os.path.isfile(payload)):
payload = open(payload, "r").read()
payload = json.dumps(json.JSONDecoder().decode(payload))
print payload
# checking necessary paramenters
if not token:
print ('token is needed to send a push notification, pealse specified with ')
sys.exit(2)
hasPem = keyFile or (keyPemFile and cerPemFile) or pemFile
if not hasPem:
print ('key file and cert file is needed, you need to provided either original files or pem file')
sys.exit(2)
#sending push notification
if pemFile :
send_push_notification(token, payload, pemFile, dev = development == 1)
elif keyPemFile and cerPemFile :
pemFile = create_pem_file(keyPemFile, cerPemFile)
send_push_notification(token, payload, pemFile, dev = development == 1)
os.remvoe(pemFile)
elif keyFile :
pemFile = create_pem_file(keyFile, cerFile)
send_push_notification(token, payload, pemFile, dev = development == 1)
if (generatePemFile):
fileName = keyFile[:-4] + ".pem"
print (fileName)
os.rename(pemFile, fileName)
else :
os.remove(pemFile)
def tearDown(self):
os.remvoe(self.template_file)
# make sure that other tests don't rely on these settings
settings.TEMPLATE_DIRS = self.default_template_dirs