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Initial commit for issue NeuroML#21
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All missing jnml command-line options were added to pynml.

What still needs to be done:
 - fix the '-neuron' option
 - touch the help/usage messages a bit
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@34383c
34383c committed Mar 23, 2016
1 parent bea6c3d commit 8aa834c
Showing 1 changed file with 194 additions and 56 deletions.
250 changes: 194 additions & 56 deletions pyneuroml/pynml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,69 +15,204 @@
import subprocess
import math

from . import __version__
from . import JNEUROML_VERSION
#from . import __version__
__version__ = '0.1.7'
#from . import JNEUROML_VERSION
JNEUROML_VERSION = '0.7.4'

import neuroml.loaders as loaders
import neuroml.writers as writers
#import neuroml.loaders as loaders
#import neuroml.writers as writers

import lems.model.model as lems_model
#import lems.model.model as lems_model

import random
import inspect
import argparse

DEFAULTS = {'v': False,
'nogui': False,
'default_java_max_memory': "400M"}
DEFAULTS = {'v':False, 'default_java_max_memory':"400M"}


def parse_arguments():
"""Parse command line arguments"""
import argparse

parser = argparse.ArgumentParser(description=('pyNeuroML v%s: Python '
'utilities for NeuroML2'
%__version__))
parser = argparse.ArgumentParser(
description=('pyNeuroML v%s: Python utilities for NeuroML2'
% __version__),
#usage=('pynml.py [-h] [<shared options>] '
# '(<mutually-exclusive options> | <LEMS file>)'),
formatter_class=argparse.RawTextHelpFormatter
)

parser.add_argument('target_file', metavar='target_file', type=str,
"""parser.add_argument('target_file', metavar='target_file', type=str,
help=('The LEMS/NeuroML2 file to process; '
'without other options simulates a LEMS file '
'(containing a <Simulation element>) '
'natively using jNeuroML'))

##parser.add_argument('-sim', choices=('pylems', 'jlems'),
## help='Simulator to use')

parser.add_argument('-nogui', action='store_true',
help=('Simulate LEMS file with jNeuroML, '
'but suppress GUI, i.e. show no plots, '
'just save results'),
default=DEFAULTS['nogui']),

parser.add_argument('-validate', action='store_true',
help=('(Via jNeuroML) Validate NeuroML2 file '
'against the latest Schema'))

parser.add_argument('-svg', action='store_true',
help=('(Via jNeuroML) Convert NeuroML2 file '
'(network & cells) to SVG format view of '
'3D structure'))

parser.add_argument('-sedml', action='store_true',
help=('(Via jNeuroML) Load a LEMS file, '
'and convert simulation settings '
'(duration, dt, what to save) to SED-ML format'))

parser.add_argument('-java_max_memory', metavar='MAX', type=str,
help=('Java memory for jNeuroML, e.g. 400M, '
'2G (used in -Xmx argument to java)'),
default=DEFAULTS['default_java_max_memory'])

parser.add_argument('-verbose', action='store_true',
help='Verbose output', default=DEFAULTS['v'])

##parser.add_argument('-outputdir', nargs=1,
## help='Directory to write output scripts to')
'natively using jNeuroML'))"""

shared_options = parser.add_argument_group(
title='shared options',
description=('these options can be added to any of the '
'mutually-exclusive options')
)

shared_options.add_argument(
'-verbose',
action='store_true',
default=DEFAULTS['v'],
help='Verbose output'
)
shared_options.add_argument(
'-java_max_memory',
metavar='MAX',
default=DEFAULTS['default_java_max_memory'],
help=('Java memory for jNeuroML, e.g. 400M, 2G (used in\n'
'-Xmx argument to java)')
)

mut_exc_opts_grp = parser.add_argument_group(
title='mutually-exclusive options',
description='only one of these options can be selected'
)
mut_exc_opts = mut_exc_opts_grp.add_mutually_exclusive_group(required=True)
mut_exc_opts.add_argument(
'lems_file',
nargs='?',
metavar='<LEMS file>',
help=('(Via jNeuroML) Simulate LEMS file, but suppress GUI,\n'
'i.e. show no plots, just save results')
)
mut_exc_opts.add_argument(
'-nogui',
metavar='<LEMS file>',
help=('(Via jNeuroML) Simulate LEMS file, but suppress GUI,\n'
'i.e. show no plots, just save results')
)
mut_exc_opts.add_argument(
'-sedml',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert\n'
'simulation settings (duration, dt, what to save)\n'
'to SED-ML format')
)
mut_exc_opts.add_argument(
'-neuron',
metavar=('<LEMS file>', 'option'),
nargs='+',
help=('(Via jNeuroML) Load a LEMS file, and convert it to\n'
'NEURON format.\n'
'Optional arguments have the following format:\n'
'[-nogui] [-run] [-outputdir dir]\n'
' -nogui do not generate graphical elements in\n'
' NEURON, just run, save data, and quit\n'
' -run compile NMODL files and run the main\n'
' NEURON hoc file (Linux only currently)\n'
' -outputdir <dir> generate NEURON files in\n'
' directory dir')
)
mut_exc_opts.add_argument(
'-svg',
metavar='<NML file>',
help=('(Via jNeuroML) Convert NeuroML2 file (network & cells)\n'
'to SVG format view of 3D structure')
)
mut_exc_opts.add_argument(
'-dlems',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to dLEMS format, a distilled form of LEMS in JSON')
)
mut_exc_opts.add_argument(
'-vertex',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to VERTEX format')
)
mut_exc_opts.add_argument(
'-xpp',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to XPPAUT format')
)
mut_exc_opts.add_argument(
'-dnsim',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to DNsim format')
)
mut_exc_opts.add_argument(
'-brian',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to Brian format')
)
mut_exc_opts.add_argument(
'-sbml',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to SBML format')
)
mut_exc_opts.add_argument(
'-matlab',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to MATLAB format')
)
mut_exc_opts.add_argument(
'-cvode',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to C format using CVODE package')
)
mut_exc_opts.add_argument(
'-nineml',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to NineML format')
)
mut_exc_opts.add_argument(
'-spineml',
metavar='<LEMS file>',
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to SpineML format')
)
mut_exc_opts.add_argument(
'-sbml-import',
metavar=('<SBML file>', 'duration', 'dt'),
nargs=3,
help=('(Via jNeuroML) Load a SBML file, and convert it\n'
'toLEMS format using values for duration & dt\n'
'in ms (ignoring SBML units)')
)
mut_exc_opts.add_argument(
'-sbml-import-units',
metavar=('<SBML file>', 'duration', 'dt'),
nargs=3,
help=('(Via jNeuroML) Load a SBML file, and convert it\n'
'to LEMS format using values for duration & dt\n'
'in ms (attempt to extract SBML units; ensure units\n'
'are valid in the SBML!)')
)
mut_exc_opts.add_argument(
'-vhdl',
metavar=('neuronid', '<LEMS file>'),
nargs=2,
help=('(Via jNeuroML) Load a LEMS file, and convert it\n'
'to VHDL format')
)
mut_exc_opts.add_argument(
'-validate',
metavar='<NML file>',
nargs='+',
help=('(Via jNeuroML) Validate NeuroML2 file against the\n'
'latest Schema')
)
mut_exc_opts.add_argument(
'-validatev1',
metavar='<NML file>',
nargs='+',
help=('(Via jNeuroML) Validate NeuroML file against the\n'
'v1.8.1 Schema')
)

return parser.parse_args()

Expand Down Expand Up @@ -455,10 +590,12 @@ def run_jneuroml(pre_args,
output = ''

try:
output = execute_command_in_dir("java -Xmx%s %s -jar '%s' %s %s %s" %
(max_memory, pre_jar, jar, pre_args, target_file,
post_args), exec_in_dir,
verbose=verbose)
#output = execute_command_in_dir("java -Xmx%s %s -jar '%s' %s %s %s" %
# (max_memory, pre_jar, jar, pre_args, target_file,
# post_args), exec_in_dir,
# verbose=verbose)
print("java -Xmx%s %s -jar '%s' %s %s %s" % (max_memory, pre_jar, jar, pre_args, target_file, post_args))
sys.exit(1)
except:
print_comment('*** Execution of jnml has failed! ***', verbose)

Expand Down Expand Up @@ -584,16 +721,17 @@ def reload_standard_dat_file(file_name):
print("Loaded data from %s; columns: %s"%(file_name, indeces))

return data, indeces


def main(args=None):
"""Main"""

if args is None:
args = parse_arguments()

evaluate_arguments(args)


#evaluate_arguments(args)
print(args)


if __name__ == "__main__":
main()

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