def runStochKitLocal(self, params):
""" Submit a local StochKit job """
modelDb = StochKitModelWrapper.get_by_id(params["id"])
if not modelDb:
return {'status':False,
'msg':'Failed to retrive the model to simulate.'}
model = modelDb.createStochKitModel()
# Execute as concentration or population?
execType = params['execType'].lower()
if execType not in ["deterministic", "stochastic", "sensitivity"]:
raise Exception('exec_type must be deterministic, sensitivity, or stochastic. Found "{0}"'.format(execType))
if model.units.lower() == 'concentration' and execType.lower() == 'stochastic':
raise Exception('Concentration models cannot be executed stochastically')
# Assemble the argument list
args = ''
args += ' -t {0} '.format(params['time'])
num_output_points = int(float(params['time'])/float(params['increment']))
args += ' -i {0} '.format(num_output_points)
path = os.path.abspath(os.path.dirname(__file__))
# Algorithm, SSA or Tau-leaping?
if params['execType'] != 'deterministic':
executable = "{0}/../../StochKit/{1}".format(path, params['algorithm'])
args += ' --realizations {0} '.format(params['realizations'])
args += ' --keep-trajectories '
if int(params['seed']) < 0:
random.seed()
params['seed'] = random.randint(0, 2147483647)
args += '--seed {0} '.format(params['seed'])
else:
executable = "{0}/../../ode/stochkit_ode.py".format(path)
# Columns need to be labeled for visulatization page to work.
args += ' --label'
cmd = executable + ' ' + args
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
# Wow, what a hack
if params['execType'] == 'deterministic' and model.units.lower() == 'population':
document = model.serialize()
model = StochMLDocument.fromString(document).toModel(model.name)
for reactionN in model.getAllReactions():
reaction = model.getAllReactions()[reactionN]
if reaction.massaction:
if len(reaction.reactants) == 1 and reaction.reactants.values()[0] == 2:
reaction.marate.setExpression(reaction.marate.expression + ' / 2')
modelFileName = '{0}/{1}.xml'.format(dataDir, model.name)
fmodelHandle = open(modelFileName, 'w')
fmodelHandle.write(model.serialize())
fmodelHandle.close()
cmd += ' -m {0} --out-dir {1}/result'.format(modelFileName, dataDir)
logging.info("cmd =\n{}".format(cmd))
logging.debug('simulation.runLocal(): cmd={0}'.format(cmd))
logging.debug('*'*80)
logging.debug('*'*80)
#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, cmd)
logging.debug('simulation.runLocal(): exstring={0}'.format(exstring))
logging.debug('*'*80)
logging.debug('*'*80)
handle = subprocess.Popen(exstring.split(), preexec_fn=os.setsid)
# Create a wrapper to store the Job description in the datastore
job = StochKitJobWrapper()
job.resource = 'Local'
# stochkit_job.uuid = res['uuid']
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = params['jobName']
job.modelName = model.name
job.pid = handle.pid
# Create a StochKitJob instance
job.indata = json.dumps( { "type" : 'StochKit2 Ensemble',
"final_time" : params['time'],
"realizations" : params['realizations'],
"increment" : params['increment'],
"seed" : params['seed'],
"exec_type" : params['execType'],
"units" : model.units.lower(),
"epsilon" : params['epsilon'],
"threshold" : params['threshold'] } )
job.outData = dataDir
job.stdout = '{0}/stdout'.format(dataDir)
job.stderr = '{0}/stderr'.format(dataDir)
job.status = 'Running'
job.put()
return job
def runMolns(self, params):
""" Submit a remote molns StochKit job """
modelDb = StochKitModelWrapper.get_by_id(params["id"])
sys.stderr.write("*" * 80 + "\n")
sys.stderr.write("*" * 80 + "\n")
sys.stderr.write("runMolns\n")
logging.info('runMolns')
sys.stderr.write("*" * 80 + "\n")
sys.stderr.write("*" * 80 + "\n")
if not modelDb:
return {
'status': False,
'msg': 'Failed to retrive the model to simulate.'
}
model = modelDb.createStochKitModel()
# Execute as concentration or population?
execType = params['execType'].lower()
if execType not in ["deterministic", "stochastic", "sensitivity"]:
raise Exception(
'exec_type must be deterministic, sensitivity, or stochastic. Found "{0}"'
.format(execType))
if model.units.lower() == 'concentration' and execType.lower(
) == 'stochastic':
raise Exception(
'Concentration models cannot be executed stochastically')
# Assemble the argument list
args = ''
args += ' -t {0} '.format(params['time'])
num_output_points = int(
float(params['time']) / float(params['increment']))
args += ' -i {0} '.format(num_output_points)
path = os.path.abspath(os.path.dirname(__file__))
# Algorithm, SSA or Tau-leaping?
if params['execType'] != 'deterministic':
executable = "/usr/local/StochKit/{0}".format(params['algorithm'])
args += ' --realizations {0} '.format(params['realizations'])
args += ' --keep-trajectories '
if int(params['seed']) < 0:
random.seed()
params['seed'] = random.randint(0, 2147483647)
args += '--seed {0} '.format(params['seed'])
else:
executable = "/usr/local/ode-1.0.2/stochkit_ode.py"
# Columns need to be labeled for visulatization page to work.
args += ' --label'
cmd = executable + ' ' + args
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir=basedir + 'output')
# Wow, what a hack
if params['execType'] == 'deterministic' and model.units.lower(
) == 'population':
document = model.serialize()
model = StochMLDocument.fromString(document).toModel(model.name)
for reactionN in model.getAllReactions():
reaction = model.getAllReactions()[reactionN]
if reaction.massaction:
if len(reaction.reactants
) == 1 and reaction.reactants.values()[0] == 2:
reaction.marate.setExpression(
reaction.marate.expression + ' / 2')
modelFileName = '{0}/{1}.xml'.format(dataDir, model.name)
with open(modelFileName, 'w') as fmodelHandle:
fmodelHandle.write(model.serialize())
cmd += ' -m {0} --out-dir ./result'.format(
os.path.basename(modelFileName))
sys.stderr.write('*' * 80 + "\n")
logging.error("cmd =\n{}".format(cmd))
sys.stderr.write('simulation.runMolns(): cmd={0}\n'.format(cmd))
with tempfile.NamedTemporaryFile() as exec_file:
exec_file.write(cmd + "\n")
exec_file.write("tar -czf result.tar.gz result")
exec_file.flush()
controllerName = 'EC2_controller' #TODO: look this up
exec_str = "bash {0} {1}".format(exec_file.name, modelFileName)
sys.stderr.write(
"result = molns.MOLNSExec.start_job(['{0}', '{1}])".format(
controllerName, exec_str))
sys.stderr.write('*' * 80 + "\n")
molnsConfigDb = db.GqlQuery(
"SELECT * FROM MolnsConfigWrapper WHERE user_id = :1",
self.user.user_id()).get()
if not molnsConfigDb:
raise Exception("Molns not initialized")
config = molns.MOLNSConfig(config_dir=molnsConfigDb.folder)
result = molns.MOLNSExec.start_job([controllerName, exec_str],
config)
sys.stderr.write('result = {0}'.format(result))
sys.stderr.write('*' * 80 + "\n")
# Create a wrapper to store the Job description in the datastore
# Create a StochKitJob instance
job = StochKitJobWrapper()
job.resource = 'Molns'
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = params['jobName']
job.modelName = model.name
#job.pid = None
job.pid = result['id']
job.indata = json.dumps({
"type": 'StochKit2 Ensemble',
"final_time": params['time'],
"realizations": params['realizations'],
"increment": params['increment'],
"seed": params['seed'],
"exec_type": params['execType'],
"units": model.units.lower(),
"epsilon": params['epsilon'],
"threshold": params['threshold']
})
job.outData = dataDir
job.status = 'Running'
job.put()
return job
def runStochKitLocal(self, params):
""" Submit a local StochKit job """
modelDb = StochKitModelWrapper.get_by_id(params["id"])
if not modelDb:
return {
'status': False,
'msg': 'Failed to retrive the model to simulate.'
}
model = modelDb.createStochKitModel()
# Execute as concentration or population?
execType = params['execType'].lower()
if execType not in ["deterministic", "stochastic", "sensitivity"]:
raise Exception(
'exec_type must be deterministic, sensitivity, or stochastic. Found "{0}"'
.format(execType))
if model.units.lower() == 'concentration' and execType.lower(
) == 'stochastic':
raise Exception(
'Concentration models cannot be executed stochastically')
# Assemble the argument list
args = ''
args += ' -t {0} '.format(params['time'])
num_output_points = int(
float(params['time']) / float(params['increment']))
args += ' -i {0} '.format(num_output_points)
path = os.path.abspath(os.path.dirname(__file__))
# Algorithm, SSA or Tau-leaping?
if params['execType'] != 'deterministic':
executable = "{0}/../../StochKit/{1}".format(
path, params['algorithm'])
args += ' --realizations {0} '.format(params['realizations'])
args += ' --keep-trajectories '
if int(params['seed']) < 0:
random.seed()
params['seed'] = random.randint(0, 2147483647)
args += '--seed {0} '.format(params['seed'])
else:
executable = "{0}/../../ode/stochkit_ode.py".format(path)
# Columns need to be labeled for visulatization page to work.
args += ' --label'
cmd = executable + ' ' + args
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir=basedir + 'output')
# Wow, what a hack
if params['execType'] == 'deterministic' and model.units.lower(
) == 'population':
document = model.serialize()
model = StochMLDocument.fromString(document).toModel(model.name)
for reactionN in model.getAllReactions():
reaction = model.getAllReactions()[reactionN]
if reaction.massaction:
if len(reaction.reactants
) == 1 and reaction.reactants.values()[0] == 2:
reaction.marate.setExpression(
reaction.marate.expression + ' / 2')
modelFileName = '{0}/{1}.xml'.format(dataDir, model.name)
fmodelHandle = open(modelFileName, 'w')
fmodelHandle.write(model.serialize())
fmodelHandle.close()
cmd += ' -m {0} --out-dir {1}/result'.format(modelFileName, dataDir)
if params['execType'] == 'deterministic':
cmd += ' -r {0} -a {1} --mxsteps {2}'.format(
params['rTol'], params['aTol'], params['mxSteps'])
logging.info("cmd =\n{}".format(cmd))
logging.debug('simulation.runLocal(): cmd={0}'.format(cmd))
logging.debug('*' * 80)
logging.debug('*' * 80)
#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, cmd)
logging.debug('simulation.runLocal(): exstring={0}'.format(exstring))
logging.debug('*' * 80)
logging.debug('*' * 80)
handle = subprocess.Popen(exstring.split(), preexec_fn=os.setsid)
# Create a wrapper to store the Job description in the datastore
job = StochKitJobWrapper()
job.resource = 'local'
# stochkit_job.uuid = res['uuid']
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = params['jobName']
job.modelName = model.name
job.pid = handle.pid
# Create a StochKitJob instance
job.indata = json.dumps({
"type": 'StochKit2 Ensemble',
"final_time": params['time'],
"realizations": params['realizations'],
"increment": params['increment'],
"seed": params['seed'],
"exec_type": params['execType'],
"units": model.units.lower(),
"epsilon": params['epsilon'],
"rTol": params['rTol'],
"aTol": params['aTol'],
"mxSteps": params['mxSteps'],
"threshold": params['threshold']
})
job.outData = dataDir
job.stdout = '{0}/stdout'.format(dataDir)
job.stderr = '{0}/stderr'.format(dataDir)
job.status = 'Running'
job.put()
return job
def runMolns(self, params):
""" Submit a remote molns StochKit job """
modelDb = StochKitModelWrapper.get_by_id(params["id"])
sys.stderr.write("*"*80 + "\n")
sys.stderr.write("*"*80 + "\n")
sys.stderr.write("runMolns\n")
logging.info('runMolns')
sys.stderr.write("*"*80 + "\n")
sys.stderr.write("*"*80 + "\n")
if not modelDb:
return {'status':False,
'msg':'Failed to retrive the model to simulate.'}
model = modelDb.createStochKitModel()
# Execute as concentration or population?
execType = params['execType'].lower()
if execType not in ["deterministic", "stochastic", "sensitivity"]:
raise Exception('exec_type must be deterministic, sensitivity, or stochastic. Found "{0}"'.format(execType))
if model.units.lower() == 'concentration' and execType.lower() == 'stochastic':
raise Exception('Concentration models cannot be executed stochastically')
# Assemble the argument list
args = ''
args += ' -t {0} '.format(params['time'])
num_output_points = int(float(params['time'])/float(params['increment']))
args += ' -i {0} '.format(num_output_points)
path = os.path.abspath(os.path.dirname(__file__))
# Algorithm, SSA or Tau-leaping?
if params['execType'] != 'deterministic':
executable = "/usr/local/StochKit/{0}".format(params['algorithm'])
args += ' --realizations {0} '.format(params['realizations'])
args += ' --keep-trajectories '
if int(params['seed']) < 0:
random.seed()
params['seed'] = random.randint(0, 2147483647)
args += '--seed {0} '.format(params['seed'])
else:
executable = "/usr/local/ode-1.0.2/stochkit_ode.py"
# Columns need to be labeled for visulatization page to work.
args += ' --label'
cmd = executable + ' ' + args
basedir = path + '/../'
dataDir = tempfile.mkdtemp(dir = basedir + 'output')
# Wow, what a hack
if params['execType'] == 'deterministic' and model.units.lower() == 'population':
document = model.serialize()
model = StochMLDocument.fromString(document).toModel(model.name)
for reactionN in model.getAllReactions():
reaction = model.getAllReactions()[reactionN]
if reaction.massaction:
if len(reaction.reactants) == 1 and reaction.reactants.values()[0] == 2:
reaction.marate.setExpression(reaction.marate.expression + ' / 2')
modelFileName = '{0}/{1}.xml'.format(dataDir, model.name)
with open(modelFileName, 'w') as fmodelHandle:
fmodelHandle.write(model.serialize())
cmd += ' -m {0} --out-dir ./result'.format(os.path.basename(modelFileName))
sys.stderr.write('*'*80+"\n")
logging.error("cmd =\n{}".format(cmd))
sys.stderr.write('simulation.runMolns(): cmd={0}\n'.format(cmd))
with tempfile.NamedTemporaryFile() as exec_file:
exec_file.write(cmd+"\n")
exec_file.write("tar -czf result.tar.gz result")
exec_file.flush()
controllerName = 'EC2_controller' #TODO: look this up
exec_str = "bash {0} {1}".format(exec_file.name, modelFileName)
sys.stderr.write("result = molns.MOLNSExec.start_job(['{0}', '{1}])".format(controllerName, exec_str))
sys.stderr.write('*'*80+"\n")
molnsConfigDb = db.GqlQuery("SELECT * FROM MolnsConfigWrapper WHERE user_id = :1", self.user.user_id()).get()
if not molnsConfigDb:
raise Exception("Molns not initialized")
config = molns.MOLNSConfig(config_dir=molnsConfigDb.folder)
result = molns.MOLNSExec.start_job([controllerName, exec_str], config)
sys.stderr.write('result = {0}'.format(result))
sys.stderr.write('*'*80+"\n")
# Create a wrapper to store the Job description in the datastore
# Create a StochKitJob instance
job = StochKitJobWrapper()
job.resource = 'Molns'
job.user_id = self.user.user_id()
job.startTime = time.strftime("%Y-%m-%d-%H-%M-%S")
job.name = params['jobName']
job.modelName = model.name
#job.pid = None
job.pid = result['id']
job.indata = json.dumps( { "type" : 'StochKit2 Ensemble',
"final_time" : params['time'],
"realizations" : params['realizations'],
"increment" : params['increment'],
"seed" : params['seed'],
"exec_type" : params['execType'],
"units" : model.units.lower(),
"epsilon" : params['epsilon'],
"threshold" : params['threshold'] } )
job.outData = dataDir
job.status = 'Running'
job.put()
return job
