def SendSms2Server(self,message,phoneNumber):
sendMessage=message.decode('GBK').encode('UTF-8')
fp=open(r'D:\Projects\boc\logs\sms.log','a+')
b=NPBinding(url='http://xxx:xxx:xxx:xxx:8080/axis/services/SendSms?wsdl',tracefile=fp)
b.SetAuth(AUTH.httpbasic,'sendsms','')
b.sendSms(phoneNumber=phoneNumber,message=sendMessage)
fp.close()
def insertJobOut(username, wkey, jobnum, outdir, edir):
file=str(outdir)+"/tmp/sge/"+str(jobnum)
command="python " + edir + "/readout.py -f "+file
child = os.popen(command)
jobout = child.read().rstrip()
err = child.close()
if err:
raise RuntimeError, 'ERROR: %s failed w/ exit code %d' % (command, err)
jobout=plaintext2html(re.sub('\'', "\"", jobout))
kw = {'url':url}
b = NPBinding(**kw)
mesg=b.insertJobOut(a=username , c=wkey , b=jobnum, f=jobout)
def checkAllJobsFinished(username, wkey, service_name):
kw = {'url':url}
b = NPBinding(**kw)
mesg=b.checkAllJobsFinished(a=username , c=wkey , b=service_name)
data=json.dumps(mesg)
wkey=json.loads(data)
ret=str(wkey['return'])
#print "JOBs checked:"+ret+"\n"
if (ret.startswith("ERROR")):
print service_name + ":" + ret + "\n"
print "Check the service:"+service_name+"\n"
sys.exit(2);
def updateJob( username, wkey, jobname, service_name, field, jobnum, result):
#print "username="******", wkey="+str(wkey)+", jobname="+str(jobname)+", ser="+str(service_name)+", field="+str(field)+", jobnum="+str(jobnum)+", res="+str(result)
kw = {'url':url}
b = NPBinding(**kw)
mesg=b.updateJob(a=username , c=wkey , b=jobname, e=service_name , d=field, g=jobnum, f=result)
data=json.dumps(mesg)
wkey=json.loads(data)
ret=str(wkey['return'])
#print "JOB updated:"+ret+"\n"
if (ret.startswith("ERROR")):
print jobname + ":" + ret + "\n"
print "Check the job#:"+jobnum+"\n"
sys.exit(2);
def run(): from ZSI.client import Binding, NamedParamBinding from stopeight.server.zsiTools import ABCPoint,ABCLine,ABCSymbol from stopeight.server import zsiTools from numpy import ndarray import sys import traceback from ZSI import TC from stopeight.server import server_include url=server_include.server_url+str(server_include.server_port) fp = open(__file__+'.log', 'a') b = NamedParamBinding(typesmodule=zsiTools,url=url, tracefile=fp) try: input = ABCSymbol() #line = ABCLine.from_numpy_array([[0,50],[25,25],[50,0],[70,70]]) line = ABCLine.from_numpy_array([[0,55],[25,25],[55,0]]) # for identifying echo in result line.id=0 input.add_line(line) # for identifying echo in result input.id=0 for i in input.lines: print 'Input line: ' for p in i: print p.x,p.y pass print 'sending SOAP method: saveLine...' # parameter name doesn't seem to matter result = b.saveLine(sdklffjkdsla=input) for i in result['ABCSymbol']: print 'Saved line id: %d'%(i.id) for p in i: print p.x,p.y pass except: exceptionType, exceptionValue, exceptionTraceback = sys.exc_info() print "*** print_tb:" traceback.print_tb(exceptionTraceback, limit=1, file=sys.stdout) print "*** print_exception:" traceback.print_exception(exceptionType, exceptionValue, exceptionTraceback, limit=10, file=sys.stdout) fp.close()
def insertJob( username, wkey, com, jobname, service_name, jobnum, result):
#print "username="******", wkey="+wkey+", com="+com+", jobname="+jobname+", ser="+service_name+", jobnum="+jobnum+", res="+result
#kw = {'url':url, 'tracefile':sys.stdout}
kw = {'url':url}
b = NPBinding(**kw)
mesg=b.insertJob(a=username , c=wkey , b=com , e=jobname, d=service_name , f=jobnum, h=result)
data=json.dumps(mesg)
wkey=json.loads(data)
ret=str(wkey['return'])
#print "JOB inserted:"+ret+"\n"
if (ret.startswith("ERROR")):
print jobname + ":" + ret + "\n"
print "Check the job#:"+jobnum+"\n"
sys.exit(2);
def run():
from ZSI.client import Binding, NamedParamBinding
from stopeight.server.zsiTools import ABCPoint, ABCLine, ABCSymbol
from stopeight.server import zsiTools
# from numpy import *
import sys
import traceback
from ZSI import TC
from stopeight.server import server_include
url = server_include.server_url + str(server_include.server_port)
fp = open(__file__ + ".log", "a")
b = NamedParamBinding(typesmodule=zsiTools, url=url, tracefile=fp)
try:
input = ABCSymbol()
line = ABCLine()
# This line id is going to be deleted
line.id = 1
input.add_line(line)
# for identifying echo in result
input.id = 0
for i in input.lines:
print "Input line id: %d" % (i.id)
print "sending SOAP method: deleteLine..."
# parameter name doesn't seem to matter
result = b.deleteLine(sdklffjkdsla=input)
for i in result["ABCSymbol"]:
print "Deleted line id: %d" % (i.id)
for p in i:
print p.x, p.y
pass
except:
exceptionType, exceptionValue, exceptionTraceback = sys.exc_info()
print "*** print_tb:"
traceback.print_tb(exceptionTraceback, limit=1, file=sys.stdout)
print "*** print_exception:"
traceback.print_exception(exceptionType, exceptionValue, exceptionTraceback, limit=10, file=sys.stdout)
fp.close()
def run(): from ZSI.client import Binding, NamedParamBinding from stopeight.server.zsiTools import ABCPoint,ABCLine,ABCSymbol from stopeight.server import zsiTools #from numpy import * import sys import traceback from ZSI import TC from stopeight.server import server_include url=server_include.server_url+str(server_include.server_port) fp = open(__file__+'.log', 'a') b = NamedParamBinding(typesmodule=zsiTools,url=url, tracefile=fp) try: input = ABCSymbol() line = ABCLine() # the id of the line has to be known in advance line.id=1 input.add_line(line) # for identifying echo in result input.id=0 for i in input.lines: print 'Input line id: %d'%(i.id) print 'sending SOAP method: getLine...' # parameter name doesn't seem to matter result = b.getLine(sdklffjkdsla=input) for i in result['ABCSymbol']: print 'Received line id: %d'%(i.id) for p in i: print p.x,p.y pass except: exceptionType, exceptionValue, exceptionTraceback = sys.exc_info() print "*** print_tb:" traceback.print_tb(exceptionTraceback, limit=1, file=sys.stdout) print "*** print_exception:" traceback.print_exception(exceptionType, exceptionValue, exceptionTraceback, limit=10, file=sys.stdout) fp.close()
def main():
try:
parser = OptionParser()
parser.add_option('-i',
'--inputparam',
help='input parameters for the workflow',
dest='inputparam')
parser.add_option(
'-p',
'--defaultparam',
help='defined parameter file that will be run on cluster',
dest='defaultparam')
parser.add_option('-u',
'--username',
help='defined user in the cluster',
dest='username')
parser.add_option('-k',
'--wkey',
help='defined key for the workflow',
dest='wkey')
parser.add_option('-w',
'--workflowfile',
help='workflow filename',
dest='workflowfile')
parser.add_option('-d', '--dbhost', help='dbhost name', dest='dbhost')
parser.add_option('-o',
'--outdir',
help='output directory in the cluster',
dest='outdir')
(options, args) = parser.parse_args()
except:
print "OptionParser Error:for help use --help"
sys.exit(2)
INPUTPARAM = options.inputparam
DEFAULTPARAM = options.defaultparam
USERNAME = options.username
WKEY = options.wkey
WORKFLOWFILE = options.workflowfile
DBHOST = options.dbhost
OUTDIR = options.outdir
if (DBHOST == None):
DBHOST = "galaxyweb"
if (USERNAME == None):
USERNAME = getpass.getuser()
if (WKEY == None):
WKEY = "start"
if (OUTDIR == None):
OUTDIR = "~/out"
if (INPUTPARAM != None):
if path.isfile(INPUTPARAM) and access(INPUTPARAM, R_OK):
INPUTPARAM = import_param(INPUTPARAM)
else:
INPUTPARAM = re.sub(" ", "", INPUTPARAM)
#print INPUTPARAM
#sys.exit()
services = import_workflow(WORKFLOWFILE)
url = "http://" + str(DBHOST) + ".umassmed.edu/pipeline/service.php"
#kw = {'url':url, 'tracefile':sys.stdout}
kw = {'url': url}
b = NPBinding(**kw)
wfname = os.path.splitext(basename(WORKFLOWFILE))[0]
mesg = b.startWorkflow(a=INPUTPARAM,
c=DEFAULTPARAM,
b=USERNAME,
e=wfname,
d=WKEY,
f=OUTDIR)
data = json.dumps(mesg)
wkey = json.loads(data)
ret = str(wkey['return'])
print "WORKFLOW STARTED:" + ret + "\n"
if (ret.startswith("ERROR")):
print wfname + ":" + ret + "\n"
print "Check the parameter files:\n"
sys.exit(2)
for service in services:
br = 1
while (br == 1):
print service.servicename + ":" + wkey[
'return'] + ":" + service.command
res = json.loads(
json.dumps(
b.startService(a=service.servicename,
c=wkey['return'],
b=service.command)))
ret = str(res['return'])
print ret + "\n"
if (ret.startswith("RUNNING") and float(service.waittime) > 0):
print service.waittime + "\n"
time.sleep(float(service.waittime))
elif (ret.startswith("ERROR")):
print service.servicename + ":" + ret + "\n"
print "Check the command:\n"
print service.command + "\n"
sys.exit(2)
else:
br = 0
br = 1
while (br == 1):
res = json.loads(json.dumps(b.endWorkflow(a=wkey['return'])))
ret = str(res['return'])
print ret + "\n"
if (ret.startswith("WRUNNING")):
time.sleep(5)
else:
br = 0
from ZSI.client import NamedParamBinding as NPBinding
import sys
from ZSI.client import AUTH
b = NPBinding(url='http://:8080/axis/services/SendSms?wsdl',
tracefile=sys.stdout)
b.SetAuth(AUTH.httpbasic, 'sendsms', '')
message = 'kkkkkkkkk'
a = message.decode('GBK').encode('UTF-8')
b.sendSms(phoneNumber='1111111111', message=a)
def main():
try:
parser = OptionParser()
parser.add_option('-i', '--inputparam', help='input parameters for the workflow', dest='inputparam')
parser.add_option('-p', '--defaultparam', help='defined parameter file that will be run on cluster', dest='defaultparam')
parser.add_option('-u', '--username', help='defined user in the cluster', dest='username')
parser.add_option('-k', '--wkey', help='defined key for the workflow', dest='wkey')
parser.add_option('-w', '--workflowfile', help='workflow filename', dest='workflowfile')
parser.add_option('-d', '--dbhost', help='dbhost name', dest='dbhost')
parser.add_option('-o', '--outdir', help='output directory in the cluster', dest='outdir')
(options, args) = parser.parse_args()
except:
print "OptionParser Error:for help use --help"
sys.exit(2)
INPUTPARAM = options.inputparam
DEFAULTPARAM = options.defaultparam
USERNAME = options.username
WKEY = options.wkey
WORKFLOWFILE = options.workflowfile
DBHOST = options.dbhost
OUTDIR = options.outdir
if (DBHOST==None):
DBHOST="galaxyweb"
if (USERNAME==None):
USERNAME=getpass.getuser()
if (WKEY==None):
WKEY="start"
if (OUTDIR==None):
OUTDIR="~/out"
if (INPUTPARAM!=None):
if path.isfile(INPUTPARAM) and access(INPUTPARAM, R_OK):
INPUTPARAM = import_param(INPUTPARAM)
else:
INPUTPARAM = re.sub(" ", "", INPUTPARAM)
#print INPUTPARAM
#sys.exit()
services=import_workflow(WORKFLOWFILE)
url="http://"+str(DBHOST)+".umassmed.edu/pipeline/service.php"
#kw = {'url':url, 'tracefile':sys.stdout}
kw = {'url':url}
b = NPBinding(**kw)
wfname = os.path.splitext(basename(WORKFLOWFILE))[0]
mesg=b.startWorkflow(a=INPUTPARAM , c=DEFAULTPARAM , b=USERNAME , e=wfname, d=WKEY , f=OUTDIR)
data=json.dumps(mesg)
wkey=json.loads(data)
ret=str(wkey['return'])
print "WORKFLOW STARTED:"+ret+"\n"
if (ret.startswith("ERROR")):
print wfname + ":" + ret + "\n"
print "Check the parameter files:\n"
sys.exit(2);
for service in services:
br=1
while ( br==1):
print service.servicename + ":" + wkey['return'] + ":" + service.command
res=json.loads(json.dumps(b.startService(a=service.servicename, c=wkey['return'], b=service.command)))
ret=str(res['return'])
print ret + "\n"
if (ret.startswith("RUNNING") and float(service.waittime)>0):
print service.waittime+"\n"
time.sleep(float(service.waittime))
elif (ret.startswith("ERROR")):
print service.servicename + ":" + ret + "\n"
print "Check the command:\n"
print service.command + "\n"
sys.exit(2);
else:
br=0
br=1
while ( br==1):
res=json.loads(json.dumps(b.endWorkflow(a=wkey['return'])))
ret=str(res['return'])
print ret + "\n"
if (ret.startswith("WRUNNING")):
time.sleep(5)
else:
br=0
def main():
try:
parser = OptionParser()
parser.add_option('-i', '--inputparam', help='input parameters for the workflow', dest='inputparam')
parser.add_option('-p', '--defaultparam', help='defined parameter file that will be run on cluster', dest='defaultparam')
parser.add_option('-u', '--username', help='defined user in the cluster', dest='username')
parser.add_option('-k', '--wkey', help='defined key for the workflow', dest='wkey')
parser.add_option('-w', '--workflowfile', help='workflow filename', dest='workflowfile')
parser.add_option('-d', '--dbhost', help='dbhost name', dest='dbhost')
parser.add_option('-o', '--outdir', help='output directory in the cluster', dest='outdir')
(options, args) = parser.parse_args()
except:
print "OptionParser Error:for help use --help"
sys.exit(2)
INPUTPARAM = options.inputparam
DEFAULTPARAM = options.defaultparam
USERNAME = options.username
WKEY = options.wkey
WORKFLOWFILE = options.workflowfile
DBHOST = options.dbhost
OUTDIR = options.outdir
if (USERNAME==None):
USERNAME=getpass.getuser()
if (len(USERNAME)<3):
print "Error:Username doesn't exist"
sys.exit(2)
url="http://galaxyweb.umassmed.edu/dolphin_amazon/service.php"
com="wget -qO- http://instance-data/latest/meta-data/public-ipv4"
amazon_instance=str(os.popen(com).readline().rstrip())
if (WKEY==None):
WKEY="start"
if (OUTDIR==None):
OUTDIR="~/out"
if (OUTDIR.find("/")==-1):
OUTDIR="~/"+OUTDIR
if (INPUTPARAM!=None):
if path.isfile(INPUTPARAM) and access(INPUTPARAM, R_OK):
INPUTPARAM = import_param(INPUTPARAM)
else:
INPUTPARAM = re.sub(" ", "", INPUTPARAM)
services=import_workflow(WORKFLOWFILE)
slen=str(len(services))
#kw = {'url':url, 'tracefile':sys.stdout}
kw = {'url':url}
b = NPBinding(**kw)
wfname = os.path.splitext(basename(WORKFLOWFILE))[0]
mesg=b.startWorkflow(a=INPUTPARAM , c=DEFAULTPARAM , b=USERNAME , e=wfname, d=WKEY , f=OUTDIR, i=slen, h=amazon_instance)
data=json.dumps(mesg)
wkey=json.loads(data)
ret=str(wkey['return'])
print "WORKFLOW STARTED:"+ret+"\n"
if (ret.startswith("ERROR")):
print wfname + ":" + ret + "\n"
print "Check the parameter files:\n"
sys.exit(2);
for service in services:
br=1
while ( br==1):
print service.servicename #+ ":" + wkey['return'] + ":" + service.command
res=json.loads(json.dumps(b.startService(a=service.servicename, c=wkey['return'], b=service.command)))
ret=str(res['return'])
print ret + "\n"
if (ret.startswith("RUNNING") and float(service.waittime)>0):
#print service.waittime+"\n"
time.sleep(float(service.waittime))
elif (ret.startswith("ERROR")):
#print service.servicename + ":" + ret + "\n"
print "Check the command:\n"
print service.command + "\n"
sys.exit(2);
else:
br=0
br=1
print "All the services Ended"
while ( br==1):
res=json.loads(json.dumps(b.endWorkflow(a=wkey['return'])))
ret=str(res['return'])
#print ret + "\n"
if (ret.startswith("WRUNNING")):
time.sleep(5)
else:
br=0