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