def test_stoch_simul_copasi_lsf(self):
"""model simulation using LSF if found"""
try:
subprocess.call(["qstat"])
self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--simulate", "lsf_ir_model_stoch_simul.conf"]), 0)
except OSError as e:
print("Skipping test as no LSF (Load Sharing Facility) was found.")
def test_param_estim_copasi_lsf(self):
"""model parameter estimation using LSF if found"""
try:
subprocess.call(["bjobs"])
self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--param-estim", "lsf_ir_model_param_estim.conf"]), 0)
except OSError as e:
print("Skipping test as no LSF (Load Sharing Facility) was found.")
def test_stoch_simul_copasi_sge(self):
"""model simulation using SGE if found"""
try:
subprocess.call(["qstat"])
self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--simulate", "sge_ir_model_stoch_simul.conf"]), 0)
except OSError as e:
print("Skipping test as no SGE (Sun Grid Engine) was found.")
def test_param_estim_copasi_sge(self):
"""model parameter estimation using SGE if found"""
try:
subprocess.call(["qstat"])
self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--param-estim", "sge_ir_model_param_estim.conf"]), 0)
except OSError as e:
print("Skipping test as no SGE (Sun Grid Engine) was found.")
def test_non_identif_param_estim_copasi(self): """model parameter estimation with identifiability issues """ self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--param-estim", "ir_model_non_identif_param_estim.conf"]), 0)
def test_param_estim_copasi(self): """model parameter estimation""" self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--param-estim", "ir_model_param_estim.conf"]), 0)
def test_stoch_simulation(self): """model stochastic simulation""" self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--simulate", "ir_model_stoch_simul.conf"]), 0)
def test_det_simulation(self): """model deterministic simulation""" self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--simulate", "ir_model_det_simul.conf"]), 0)
def test_double_param_scan_inhib_only(self):
"""model double param scan - inhibition only"""
self.assertEqual(
run_sb_pipe.main(["run_sb_pipe", "--double-param-scan", "ir_model_insulin_ir_beta_dbl_inhib.conf"]), 0
)
def test_single_param_scan_inhib_overexp(self):
"""model single param scan - inhibition/overexpression"""
self.assertEqual(
run_sb_pipe.main(["run_sb_pipe", "--single-param-scan", "ir_model_ir_beta_inhib_overexp.conf"]), 0
)
def test_single_param_scan_ci(self):
"""model single param scan - confidence interval"""
self.assertEqual(run_sb_pipe.main(["run_sb_pipe", "--single-param-scan", "ir_model_k1_scan.conf"]), 0)
