def __init__(self, opalService, jobID):
""" A JobStatus can be constructed passing a OpalService object and string
containing a valid jobID """
self.opalService = opalService
self.jobID = jobID
self.jobStatus = \
self.opalService.appServicePort.queryStatus(queryStatusRequest(jobID))
def pollStatus(jobID,outputDirectory):
""" Determines current status of run and executes fetching of results if the run is completed. """
global service_url
appServicePort = AppServiceLocator().getAppServicePort(service_url)
status = appServicePort.queryStatus(queryStatusRequest(jobID))
if status._code == 4:
stderr.write("Error! The calculation failed!\n")
stderr.write("Message: %s\n" % status._message)
sys.exit(13)
elif status._code != 8:
stderr.write("Sorry, the calculation hasn't been completed yet. Please wait a short while and attempt to fetch the files again.\n")
sys.exit(13)
else:
resp = appServicePort.getOutputs(getOutputsRequest(jobID))
fetchResults(jobID, outputDirectory, resp._outputFile, status._code==4)
def queryStatus(self):
#import sys
#print >> sys.__stderr__, "calling from queryStatus", self.busy
if self.busy:
return
if self.status is None:
raise RuntimeError("No job has been launched yet")
import chimera
from AppService_client import queryStatusRequest
import socket
req = queryStatusRequest(self.jobID)
if chimera.nogui:
try:
status = self.appServicePort.queryStatus(req)
except socket.error, e:
from chimera import NonChimeraError
raise NonChimeraError(str(e))
self._saveStatus(status)
def queryStatus(self):
#import sys
#print >> sys.__stderr__, "calling from queryStatus", self.busy
if self.busy:
return
if self.status is None:
raise RuntimeError("No job has been launched yet")
import chimera
from AppService_client import queryStatusRequest
import socket
req = queryStatusRequest(self.jobID)
if chimera.nogui:
try:
status = self.appServicePort.queryStatus(req)
except socket.error, e:
from chimera import NonChimeraError
raise NonChimeraError(str(e))
self._saveStatus(status)
def checkprogress(jobid=None, appServicePort=None, calctype=None):
"""
Finds out if the job has been completed
"""
if have_opal:
# construct soap request
try:
status = appServicePort.queryStatus(queryStatusRequest(jobid))
except Exception, e:
return ["error"]
if status._code == 4:
return ["error"]
if status._code == 8:
return ["complete", status]
else:
return ["running", status]
def checkprogress(jobid=None, appServicePort=None, calctype=None):
"""
Finds out if the job has been completed
"""
if have_opal:
# construct soap request
try:
status = appServicePort.queryStatus(queryStatusRequest(jobid))
except Exception, e:
return ["error"]
if status._code == 4:
return ["error"]
if status._code == 8:
return ["complete", status]
else:
return ["running", status]
def pollStatus(jobID, outputDirectory):
""" Determines current status of run and executes fetching of results if the run is completed. """
global service_url
appServicePort = AppServiceLocator().getAppServicePort(service_url)
status = appServicePort.queryStatus(queryStatusRequest(jobID))
if status._code == 4:
stderr.write("Error! The calculation failed!\n")
stderr.write("Message: %s\n" % status._message)
sys.exit(13)
elif status._code != 8:
stderr.write(
"Sorry, the calculation hasn't been completed yet. Please wait a short while and attempt to fetch the files again.\n"
)
sys.exit(13)
else:
resp = appServicePort.getOutputs(getOutputsRequest(jobID))
fetchResults(jobID, outputDirectory, resp._outputFile,
status._code == 4)
print "Polling job status"
while 1:
# print current status
print "Status:"
print "\tCode:", status._code
print "\tMessage:", status._message
print "\tOutput Base URL:", status._baseURL
if (status._code == 8) or (status._code == 4): # STATUS_DONE || STATUS_FAILED
break
print "Waiting 30 seconds"
sleep(30)
# Query job status
status = appServicePort.queryStatus(queryStatusRequest(jobID))
# If execution is successful retrieve job outputs.
if status._code == 8: # 8 = GramJob.STATUS_DONE
# Create local directory to hold output files
output_dir = 'meme_out'
mkdir(output_dir);
# Instantiate a collection of outputs
outputs = appServicePort.getOutputs(getOutputsRequest(jobID))
# Instantiate a request object for retrieving output files
fileRequest = getOutputAsBase64ByNameRequest()
# Retreive each output file and save to local directory.
print "Polling job status"
while 1:
# print current status
print "Status:"
print "\tCode:", status._code
print "\tMessage:", status._message
print "\tOutput Base URL:", status._baseURL
if (status._code == 8) or (status._code == 4): # STATUS_DONE || STATUS_FAILED
break
print "Waiting 30 seconds"
sleep(30)
# Query job status
status = appServicePort.queryStatus(queryStatusRequest(jobID))
# If execution is successful retrieve job outputs.
if status._code == 8: # 8 = GramJob.STATUS_DONE
# Create local directory to hold output files
output_dir = "meme_out"
mkdir(output_dir)
# Instantiate a collection of outputs
outputs = appServicePort.getOutputs(getOutputsRequest(jobID))
# Instantiate a request object for retrieving output files
fileRequest = getOutputAsBase64ByNameRequest()
# Retreive each output file and save to local directory.
def updateStatus(self):
""" this function retrives a updated version of the jobStatus
from the Opal server """
#import pdb; pdb.set_trace()
self.jobStatus = \
self.opalService.appServicePort.queryStatus(queryStatusRequest(self.jobID))
def __init__(self, opalService, jobID):
""" """
self.opalService = opalService
self.jobID = jobID
self.jobStatus = \
self.opalService.appServicePort.queryStatus(queryStatusRequest(jobID))
def ws_compute(self):
if self._port_list[0][3]['url'] != None:
url = self._port_list[0][3]['url']
adv = self._port_list[0][3]['adv']
else:
url = ""
print "ERROR: There are no input arguments provided for this web service"
cmdline = ""
numProcs = None
tagged = []
untagged = []
flags = []
files = []
for i in self._port_list:
pn = i[0]
meta = i[3]
if ((self.hasInputFromPort(pn) and self.getInputFromPort(pn) != "") or meta['default'] != None) and adv == True:
# print "META"
# print meta
if meta['type'] == 'FLAG':
if self.hasInputFromPort(pn):
if self.getInputFromPort(pn) == True:
flags.append(meta['arg'])
elif meta['default'] == 'True':
flags.append(meta['arg'])
elif meta['type'] == 'TAGGED':
if self.hasInputFromPort(pn):
val = self.getInputFromPort(pn)
elif meta['default'] != None:
val = meta['default']
if meta['file'] == True:
file_an = core.modules.basic_modules.File.translate_to_string(val)
file_bn = os.path.basename(file_an)
tagged.append(meta['arg'] + file_bn)
files.append(file_an)
else:
tagged.append(meta['arg'] + val)
elif meta['type'] == 'UNTAGGED':
if self.hasInputFromPort(pn):
val = self.getInputFromPort(pn)
elif meta['default'] != None:
val = meta['default']
if meta['file'] == True:
file_an = core.modules.basic_modules.File.translate_to_string(val)
file_bn = os.path.basename(file_an)
untagged.append(file_bn)
files.append(file_an)
else:
untagged.append(val)
cmdline = ""
for i in flags:
cmdline += i + " "
for i in tagged:
cmdline += i + " "
for i in untagged:
cmdline += i + " "
inputFiles = []
for i in files:
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = os.path.basename(i)
inputFile._attachment = open(i, "r")
inputFiles.append(inputFile)
if cmdline == "":
if self.hasInputFromPort('commandLine'):
cmdline = self.getInputFromPort('commandLine')
if self.hasInputFromPort('numProcs'):
numProcs = self.getInputFromPort('numProcs')
if self.hasInputFromPort("inFiles"):
inFilesPath = self.getInputFromPort("inFiles")
if inFilesPath != None:
for i in inFilesPath:
inputFile = ns0.InputFileType_Def('inputFile')
inputFile._name = os.path.basename(i)
inputFile._attachment = open(i, "r")
inputFiles.append(inputFile)
print os.path.basename(url) + " from " + os.path.dirname(url) + " is going to run with arguments:\n " + cmdline
appLocator = AppServiceLocator()
appServicePort = appLocator.getAppServicePort(url)
req = launchJobRequest()
req._argList = cmdline
req._inputFile = inputFiles
if numProcs != None:
req._numProcs = numProcs
resp = appServicePort.launchJob(req)
self.jobID = resp._jobID
print "Job outputs URL: " + resp._status._baseURL # urlparse.urljoin(url, '/' + self.jobID)
status = resp._status._code
while (status != 4 and status != 8):
status = appServicePort.queryStatus(queryStatusRequest(self.jobID))._code
time.sleep(5)
if (status == 8):
resp = appServicePort.getOutputs(getOutputsRequest(self.jobID))
outurls = [str(resp._stdOut), str(resp._stdErr)]
if (resp._outputFile != None):
for i in resp._outputFile:
outurls.append(str(i._url))
print "Opal job completed successfully"
else:
print "ERROR: Opal job failed"
resp = appServicePort.getOutputs(getOutputsRequest(self.jobID))
outurls = [str(resp._stdOut), str(resp._stdErr)]
self.setResult("outurls", tuple(outurls))
