def run(self):
np = 2
try:
inform("Running file %s with %s" %
(trim_path(self.modelpath), JNeuroMLNetPyNEEngine.name),
indent=1)
from omv.engines.jneuroml import JNeuroMLEngine
jnml = JNeuroMLEngine.get_executable()
self.stdout = check_output([
jnml, self.modelpath, '-netpyne', '-nogui', '-run', '-np',
'%s' % np
],
cwd=os.path.dirname(self.modelpath),
env=JNeuroMLEngine.get_environment())
inform("Success with running ",
JNeuroMLNetPyNEEngine.name,
indent=1)
self.returncode = 0
except sp.CalledProcessError as err:
inform("Error with ", JNeuroMLNetPyNEEngine.name, indent=1)
self.returncode = err.returncode
self.stdout = err.output
raise EngineExecutionError
def run(self):
try:
path_s = resolve_paths(self.modelpath)
from omv.engines.jneuroml import JNeuroMLEngine
jnml = JNeuroMLEngine.get_executable()
cmds = [jnml, '-validatev1']
for p in path_s:
cmds.append(p)
inform("Running with %s, using %s..." %
(JNeuroMLValidateV1Engine.name, cmds),
indent=1)
self.stdout = sp.check_output(cmds,
cwd=os.path.dirname(self.modelpath),
env=JNeuroMLEngine.get_environment())
inform("Success with running ",
JNeuroMLValidateV1Engine.name,
indent=1,
verbosity=1)
self.returncode = 0
except sp.CalledProcessError as err:
self.returncode = err.returncode
self.stdout = err.output
raise EngineExecutionError
def get_jnmlnrnenv():
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLNRNEngine.path = JNeuroMLEngine.path + \
":" + path_nrn
JNeuroMLNRNEngine.environment_vars = {}
JNeuroMLNRNEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLNRNEngine.environment_vars.update(environment_vars_nrn)
JNeuroMLNRNEngine.environment_vars.update(
JNeuroMLEngine.get_environment())
inform("PATH: " + JNeuroMLNRNEngine.path)
inform("Env vars: %s" % JNeuroMLNRNEngine.environment_vars)
del JNeuroMLNRNEngine.environment_vars['PYTHONPATH']
return JNeuroMLNRNEngine.environment_vars
def run(self):
try:
inform("Running file %s with %s" %
(trim_path(self.modelpath), JNeuroMLBrian2Engine.name),
indent=1)
from omv.engines.jneuroml import JNeuroMLEngine
jnml = JNeuroMLEngine.get_executable()
self.stdout = check_output([jnml, self.modelpath, '-brian2'],
cwd=os.path.dirname(self.modelpath),
env=JNeuroMLEngine.get_environment())
self.stdout += check_output([
'python',
self.modelpath.replace('.xml', '_brian2.py'), '-nogui'
],
cwd=os.path.dirname(self.modelpath))
inform("Success with running ",
JNeuroMLBrian2Engine.name,
indent=1)
self.returncode = 0
except sp.CalledProcessError as err:
inform("Error with ", JNeuroMLBrian2Engine.name, indent=1)
self.returncode = err.returncode
self.stdout = err.output
raise EngineExecutionError