def test_stoch_sim_copasi(self):
if self._output == 'OK':
self.assertEqual(
sbpipe(simulate="ir_model_stoch_simul.yaml", quiet=True), 0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_ps1_ci(self):
if self._output == 'OK':
self.assertEqual(
sbpipe(parameter_scan1="ir_model_k1_scan.yaml", quiet=True), 0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_sim_python_ir(self):
if self._output == 'OK':
self.assertEqual(
sbpipe(simulate="insulin_receptor.yaml", quiet=True), 0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_stoch_ps1_inhib_only(self):
if self._output == 'OK':
self.assertEqual(
sbpipe(parameter_scan1="ir_model_ir_beta_inhib_stoch.yaml",
quiet=True), 0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_pe_copasi1(self):
if self._output == 'OK':
self.assertEqual(
sbpipe(parameter_estimation="ir_model_param_estim.yaml",
quiet=True), 0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_octave_model_simulation(self):
if self._output == 'OK':
self.assertEqual(
sbpipe(simulate="nonlinear_octave_model_sim.yaml", quiet=True),
0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_pe_r(self):
if self._output == 'OK':
self.assertEqual(
sbpipe(parameter_estimation="pe_simple_reacts.yaml",
quiet=True), 0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_ps2_inhib_only(self):
if self._output == 'OK':
self.assertEqual(
sbpipe(
parameter_scan2="ir_model_insulin_ir_beta_dbl_inhib.yaml",
quiet=True), 0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_sim_r(self):
if not is_r_package_installed("reshape2"):
sys.stdout.write("R reshape2 not found: SKIP ... ")
sys.stdout.flush()
elif not is_r_package_installed("deSolve"):
sys.stdout.write("R deSolve not found: SKIP ... ")
sys.stdout.flush()
elif not is_r_package_installed("minpack.lm"):
sys.stdout.write("R minpack.lm not found: SKIP ... ")
sys.stdout.flush()
else:
self.assertEqual(sbpipe(simulate="sim_simple_reacts.yaml", quiet=True), 0)
def test_stoch_sim_copasi_sge(self):
if self._output == 'OK':
try:
subprocess.Popen(['qstat'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()[0]
self.assertEqual(
sbpipe(simulate="sge_ir_model_stoch_simul.yaml",
quiet=True), 0)
except OSError as e:
print("Skipping test as no SGE (Sun Grid Engine) was found.")
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_stoch_sim_copasi_lsf(self):
if self._output == 'OK':
try:
subprocess.Popen(['bjobs'],
stdout=subprocess.PIPE,
stderr=subprocess.PIPE).communicate()[0]
self.assertEqual(
sbpipe(simulate="lsf_ir_model_stoch_simul.yaml",
quiet=True), 0)
except OSError as e:
print(
"Skipping test as no LSF (Load Sharing Facility) was found."
)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_sim4(self):
if self._output == 'OK':
self.assertEqual(sbpipe(simulate="ir_model_det_simul4.yaml", quiet=True), 1)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_sim_r_pde_lotka_volterra(self):
if not is_r_package_installed("deSolve"):
sys.stdout.write("R deSolve not found: SKIP ... ")
sys.stdout.flush()
else:
self.assertEqual(sbpipe(simulate="2Dpde_lotka_volterra.yaml", quiet=True), 0)
def test_stoch_sim_r_periodic_drift(self):
if not is_r_package_installed("sde"):
sys.stdout.write("R sde not found: SKIP ... ")
sys.stdout.flush()
else:
self.assertEqual(sbpipe(simulate="sde_periodic_drift.yaml", quiet=True), 0)
def test_java_simqueue_simulation(self):
if self._output == 'OK':
self.assertEqual(sbpipe(simulate="simqueue.yaml", quiet=True), 0)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_pe_copasi4(self):
if self._output == 'OK':
self.assertEqual(sbpipe(parameter_estimation="interrupted_param_estim4.yaml", quiet=True), 1)
else:
sys.stdout.write(self._output)
sys.stdout.flush()
def test_stoch_sim_r_cox_ingersoll_ross_process(self):
if not is_r_package_installed("sde"):
sys.stdout.write("R sde not found: SKIP ... ")
sys.stdout.flush()
else:
self.assertEqual(sbpipe(simulate="sde_cox_ingersoll_ross_process.yaml", quiet=True), 0)