def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
inform("%s installed JNeuroML..." % JNeuroMLNetPyNEEngine.name,
indent=2,
verbosity=1)
if not NetPyNEEngine.is_installed(None):
NetPyNEEngine.install(None)
inform("%s installed NetPyNE (& NEURON)..." %
JNeuroMLNetPyNEEngine.name,
indent=2,
verbosity=1)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLNetPyNEEngine.path = JNeuroMLEngine.path + ":" + path_nrn
JNeuroMLNetPyNEEngine.environment_vars = {}
JNeuroMLNetPyNEEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLNetPyNEEngine.environment_vars.update(
NetPyNEEngine.environment_vars)
JNeuroMLNetPyNEEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + JNeuroMLNetPyNEEngine.path)
inform("Env vars: %s" % JNeuroMLNetPyNEEngine.environment_vars)
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 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 install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
JNeuroMLNRNEngine.get_jnmlnrnenv()
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
JNeuroMLValidateEngine.path = JNeuroMLEngine.path
JNeuroMLValidateEngine.environment_vars = {}
JNeuroMLValidateEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
JNeuroMLValidateEngine.path = JNeuroMLEngine.path
JNeuroMLValidateEngine.environment_vars = {}
JNeuroMLValidateEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed..." %
JNeuroMLPyNNNRNEngine.name,
indent=1)
return JNeuroMLEngine.is_installed(
None) and PyNNNRNEngine.is_installed(None)
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not Brian1Engine.is_installed(None):
Brian1Engine.install(None)
JNeuroMLBrianEngine.path = JNeuroMLEngine.path + \
":" + Brian1Engine.path
JNeuroMLBrianEngine.environment_vars = {}
JNeuroMLBrianEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLBrianEngine.environment_vars.update(
Brian1Engine.environment_vars)
inform("PATH: " + JNeuroMLBrianEngine.path)
inform("Env vars: %s" % JNeuroMLBrianEngine.environment_vars)
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not MooseEngine.is_installed(None):
MooseEngine.install(None)
JNeuroMLMooseEngine.path = JNeuroMLEngine.path + \
":" + JNeuroMLMooseEngine.path
JNeuroMLMooseEngine.environment_vars = {}
JNeuroMLMooseEngine.environment_vars.update(
JNeuroMLEngine.environment_vars)
JNeuroMLMooseEngine.environment_vars.update(
MooseEngine.environment_vars)
inform("PATH: " + JNeuroMLMooseEngine.path)
inform("Env vars: %s" % JNeuroMLMooseEngine.environment_vars)
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
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)
inform("PATH: " + JNeuroMLNRNEngine.path)
inform("Env vars: %s" % JNeuroMLNRNEngine.environment_vars)
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
inform("%s installed JNeuroML..." % JNeuroMLNetPyNEEngine.name, indent=2, verbosity =1)
if not NetPyNEEngine.is_installed(None):
NetPyNEEngine.install(None)
inform("%s installed NetPyNE (& NEURON)..." % JNeuroMLNetPyNEEngine.name, indent=2, verbosity =1)
environment_vars_nrn, path_nrn = NeuronEngine.get_nrn_environment()
JNeuroMLNetPyNEEngine.path = JNeuroMLEngine.path+":"+path_nrn
JNeuroMLNetPyNEEngine.environment_vars = {}
JNeuroMLNetPyNEEngine.environment_vars.update(JNeuroMLEngine.environment_vars)
JNeuroMLNetPyNEEngine.environment_vars.update(NetPyNEEngine.environment_vars)
JNeuroMLNetPyNEEngine.environment_vars.update(environment_vars_nrn)
inform("PATH: " + JNeuroMLNetPyNEEngine.path)
inform("Env vars: %s" % JNeuroMLNetPyNEEngine.environment_vars)
def install(version):
if not JNeuroMLEngine.is_installed(None):
JNeuroMLEngine.install(None)
if not NeuronEngine.is_installed(None):
NeuronEngine.install(None)
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)
inform("PATH: " + JNeuroMLNRNEngine.path)
inform("Env vars: %s" % 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
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_using_jnmlnrn_env(engine, modelpath, args):
try:
env = JNeuroMLNRNEngine.get_jnmlnrnenv()
inform("Running file %s with %s, env: %s" %
(trim_path(modelpath), engine, env),
indent=1)
from omv.engines.jneuroml import JNeuroMLEngine
jnml = JNeuroMLEngine.get_executable()
cmds = [jnml, modelpath]
cmds.extend(args)
stdout = check_output(cmds,
cwd=os.path.dirname(modelpath),
env=env)
inform("Success with running ", engine, indent=1)
returncode = 0
return stdout, returncode
except sp.CalledProcessError as err:
inform("Error with ", engine, indent=1)
returncode = err.returncode
stdout = err.output
return stdout, returncode
def is_installed(version):
if is_verbose():
inform("Checking whether %s is installed..." %
JNeuroMLMooseEngine.name, indent=1)
return JNeuroMLEngine.is_installed(None) and MooseEngine.is_installed(None)
def is_installed(version):
return JNeuroMLEngine.is_installed(None)
def is_installed(version):
return JNeuroMLEngine.is_installed(None)
