def runCloud(self, data):
self.user_data.set_selected(1)
job = SensitivityJobWrapper()
service = backendservices(self.user_data)
if not service.isOneOrMoreComputeNodesRunning():
raise Exception('No cloud computing resources found. (Have they been started?)')
job.user_id = self.user.user_id()
model = modeleditor.StochKitModelWrapper.get_by_id(data["id"])
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.status = "Pending"
job.modelName = model.name
runtime = float(data["time"])
dt = float(data["increment"])
job.indata = json.dumps(data)
parameters = []
for parameter in data['selections']["pc"]:
if data['selections']["pc"][parameter]:
parameters.append(parameter)
stochkitmodel = model.createStochKitModel()
# Wow, what a hack
if stochkitmodel.units.lower() == 'population':
document = stochkitmodel.serialize()
stochkitmodel = StochMLDocument.fromString(document).toModel(model.name)
for reactionN in stochkitmodel.getAllReactions():
reaction = stochkitmodel.getAllReactions()[reactionN]
if reaction.massaction:
if len(reaction.reactants) == 1 and reaction.reactants.values()[0] == 2:
reaction.marate.setExpression(reaction.marate.expression + ' / 2')
params = {
"job_type": "sensitivity",
"document": str( stochkitmodel.serialize() ),
"paramstring": "stochkit_ode.py --sensi --parameters {0} -t {1} -i {2}".format(
" ".join(parameters), runtime, int(runtime / dt)
),
"bucketname": self.user_data.getBucketName()
}
# Send the task to the backend
cloud_result = service.submit_cloud_task(params)
# if not cloud_result["success"]:
if not cloud_result["success"]:
return None, cloud_result
job.cloudDatabaseID = cloud_result["db_id"]
job.celeryPID = cloud_result["celery_pid"]
job.resource = cloud_result['resource']
job.outData = None
job.zipFileName = None
job.output_stored = 'True'
job.put()
return job
def runCloud(self, data):
self.user_data.set_selected(1)
job = SensitivityJobWrapper()
service = backendservices(self.user_data)
if not service.isOneOrMoreComputeNodesRunning():
raise Exception(
'No cloud computing resources found. (Have they been started?)'
)
job.user_id = self.user.user_id()
model = modeleditor.StochKitModelWrapper.get_by_id(data["id"])
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.status = "Pending"
job.modelName = model.name
runtime = float(data["time"])
dt = float(data["increment"])
job.indata = json.dumps(data)
parameters = []
for parameter in data['selections']["pc"]:
if data['selections']["pc"][parameter]:
parameters.append(parameter)
stochkitmodel = model.createStochKitModel()
# Wow, what a hack
if stochkitmodel.units.lower() == 'population':
document = stochkitmodel.serialize()
stochkitmodel = StochMLDocument.fromString(document).toModel(
model.name)
for reactionN in stochkitmodel.getAllReactions():
reaction = stochkitmodel.getAllReactions()[reactionN]
if reaction.massaction:
if len(reaction.reactants
) == 1 and reaction.reactants.values()[0] == 2:
reaction.marate.setExpression(
reaction.marate.expression + ' / 2')
params = {
"job_type":
"sensitivity",
"document":
str(stochkitmodel.serialize()),
"paramstring":
"stochkit_ode.py --sensi --parameters {0} -t {1} -i {2}".format(
" ".join(parameters), runtime, int(runtime / dt)),
"bucketname":
self.user_data.getBucketName()
}
# Send the task to the backend
cloud_result = service.submit_cloud_task(params)
# if not cloud_result["success"]:
if not cloud_result["success"]:
return None, cloud_result
job.cloudDatabaseID = cloud_result["db_id"]
job.celeryPID = cloud_result["celery_pid"]
job.resource = cloud_result['resource']
job.outData = None
job.zipFileName = None
job.output_stored = 'True'
job.put()
return job
def runLocal(self, data):
'''
'''
self.user_data.set_selected(0)
job = SensitivityJobWrapper()
job.resource = "local"
job.user_id = self.user.user_id()
model = modeleditor.StochKitModelWrapper.get_by_id(data["id"])
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.modelName = model.name
runtime = float(data["time"])
dt = float(data["increment"])
job.indata = json.dumps(data)
path = os.path.abspath(os.path.dirname(__file__))
parameters = []
for parameter in data['selections']["pc"]:
if data['selections']["pc"][parameter]:
parameters.append(parameter)
if len(parameters) == 0:
raise Exception("At least one parameter must be selected");
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
job.outData = dataDir
modelFileName = '{0}/{1}.xml'.format(job.outData, model.name)
fmodelHandle = open(modelFileName, 'w')
stochkitmodel = model.createStochKitModel()
# Wow, what a hack
if stochkitmodel.units.lower() == 'population':
document = stochkitmodel.serialize()
stochkitmodel = StochMLDocument.fromString(document).toModel(model.name)
for reactionN in stochkitmodel.getAllReactions():
reaction = stochkitmodel.getAllReactions()[reactionN]
if reaction.massaction:
if len(reaction.reactants) == 1 and reaction.reactants.values()[0] == 2:
reaction.marate.setExpression(reaction.marate.expression + ' / 2')
fmodelHandle.write(stochkitmodel.serialize())
fmodelHandle.close()
job.status = "Pending"
args = "--sensi -m {0} --parameters {1} -t {2} --out-dir {3} -i {4}".format(modelFileName, " ".join(parameters), runtime, dataDir + '/result', int(runtime / dt))
ode = "{0}/../../ode/stochkit_ode.py {1}".format(path, args)
exstring = '{0}/backend/wrapper.py {1}/stdout {1}/stderr {1}/return_code {2}'.format(basedir, dataDir, ode)
handle = subprocess.Popen(exstring.split(), preexec_fn=os.setsid)
job.pid = handle.pid
job.put()
return job
def runLocal(self, data):
'''
'''
self.user_data.set_selected(0)
job = SensitivityJobWrapper()
job.resource = "local"
job.user_id = self.user.user_id()
model = modeleditor.StochKitModelWrapper.get_by_id(data["id"])
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = data["jobName"]
job.modelName = model.name
runtime = float(data["time"])
dt = float(data["increment"])
job.indata = json.dumps(data)
path = os.path.abspath(os.path.dirname(__file__))
parameters = []
for parameter in data['selections']["pc"]:
if data['selections']["pc"][parameter]:
parameters.append(parameter)
if len(parameters) == 0:
raise Exception("At least one parameter must be selected")
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir=basedir + 'output')
job.outData = dataDir
modelFileName = '{0}/{1}.xml'.format(job.outData, model.name)
fmodelHandle = open(modelFileName, 'w')
stochkitmodel = model.createStochKitModel()
# Wow, what a hack
if stochkitmodel.units.lower() == 'population':
document = stochkitmodel.serialize()
stochkitmodel = StochMLDocument.fromString(document).toModel(
model.name)
for reactionN in stochkitmodel.getAllReactions():
reaction = stochkitmodel.getAllReactions()[reactionN]
if reaction.massaction:
if len(reaction.reactants
) == 1 and reaction.reactants.values()[0] == 2:
reaction.marate.setExpression(
reaction.marate.expression + ' / 2')
fmodelHandle.write(stochkitmodel.serialize())
fmodelHandle.close()
job.status = "Pending"
args = "--sensi -m {0} --parameters {1} -t {2} --out-dir {3} -i {4}".format(
modelFileName, " ".join(parameters), runtime, dataDir + '/result',
int(runtime / dt))
ode = "{0}/../../ode/stochkit_ode.py {1}".format(path, args)
exstring = '{0}/backend/wrapper.py {1}/stdout {1}/stderr {1}/return_code {2}'.format(
basedir, dataDir, ode)
handle = subprocess.Popen(exstring.split(), preexec_fn=os.setsid)
job.pid = handle.pid
job.put()
return job
