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Fix issue NeuroML#21
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Added the logic that evaluates the command-line options after they
have been parsed by argparse.

Removed all added debugging/testing code.

Improved help/usage messages.
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@34383c
34383c committed Mar 24, 2016
1 parent 8aa834c commit cc3506e
Showing 1 changed file with 108 additions and 59 deletions.
167 changes: 108 additions & 59 deletions pyneuroml/pynml.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,40 +15,33 @@
import subprocess
import math

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

#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, '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__),
#usage=('pynml.py [-h] [<shared options>] '
# '(<mutually-exclusive options> | <LEMS file>)'),
usage=('pynml.py [-h|--help] [<shared options>] '
'<one of the mutually-exclusive options>'),
formatter_class=argparse.RawTextHelpFormatter
)

"""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'))"""

shared_options = parser.add_argument_group(
title='shared options',
description=('these options can be added to any of the '
Expand Down Expand Up @@ -78,8 +71,7 @@ def parse_arguments():
'lems_file',
nargs='?',
metavar='<LEMS file>',
help=('(Via jNeuroML) Simulate LEMS file, but suppress GUI,\n'
'i.e. show no plots, just save results')
help='(Via jNeuroML) Load a LEMS file and simulate it'
)
mut_exc_opts.add_argument(
'-nogui',
Expand All @@ -96,18 +88,21 @@ def parse_arguments():
)
mut_exc_opts.add_argument(
'-neuron',
metavar=('<LEMS file>', 'option'),
nargs='+',
nargs=argparse.REMAINDER,
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')
'The full format of the \'-neuron\' option is:\n'
'-neuron [-nogui] [-run] [-outputdir dir] <LEMS file>\n'
' -nogui\n'
' do not generate gtaphical elements in NEURON,\n'
' just run, save data, and quit\n'
' -run\n'
' compile NMODL files and run the main NEURON\n'
' hoc file (Linux only currently)\n'
' -outputdir <dir>\n'
' generate NEURON files in directory <dir>\n'
' <LEMS file>\n'
' the LEMS file to use')
)
mut_exc_opts.add_argument(
'-svg',
Expand Down Expand Up @@ -203,14 +198,14 @@ def parse_arguments():
'-validate',
metavar='<NML file>',
nargs='+',
help=('(Via jNeuroML) Validate NeuroML2 file against the\n'
help=('(Via jNeuroML) Validate NeuroML2 file(s) against the\n'
'latest Schema')
)
mut_exc_opts.add_argument(
'-validatev1',
metavar='<NML file>',
nargs='+',
help=('(Via jNeuroML) Validate NeuroML file against the\n'
help=('(Via jNeuroML) Validate NeuroML file(s) against the\n'
'v1.8.1 Schema')
)

Expand Down Expand Up @@ -540,35 +535,92 @@ def get_next_hex_color():
return "#%06x" % random.randint(0,0xFFFFFF)

def evaluate_arguments(args):

global DEFAULTS
DEFAULTS['v'] = args.verbose

pre_args = ""
files = ""
post_args = ""

gui = " -nogui" if args.nogui==True else ""
post_args += gui

exit_on_fail = True

if args.validate:
pre_args += " -validate"
exit_on_fail = False

elif args.svg:
post_args += " -svg"


if args.lems_file:
files = args.lems_file
elif args.nogui:
files = args.nogui
post_args = "-nogui"
elif args.sedml:
post_args += " -sedml"

run_jneuroml(pre_args,
args.target_file,
post_args,
files = args.sedml
post_args = "-sedml"
elif args.neuron is not None:
num_neuron_args = len(args.neuron)
if num_neuron_args < 1 or num_neuron_args > 5:
print("ERROR: The \'-neuron\' option was given an invalid "
"number of arguments: %d given, 1-5 required"
% num_neuron_args)
sys.exit(-1)
files = args.neuron[-1]
post_args = "-neuron %s" % ' '.join(args.neuron[:-1])
elif args.svg:
files = args.svg
post_args = "-svg"
elif args.dlems:
files = args.dlems
post_args = "-dlems"
elif args.vertex:
files = args.vertex
post_args = "-vertex"
elif args.xpp:
files = args.xpp
post_args = "-xpp"
elif args.dnsim:
files = args.dnsim
post_args = "-dnsim"
elif args.brian:
files = args.brian
post_args = "-brian"
elif args.sbml:
files = args.sbml
post_args = "-sbml"
elif args.matlab:
files = args.matlab
post_args = "-matlab"
elif args.cvode:
files = args.cvode
post_args = "-cvode"
elif args.nineml:
files = args.nineml
post_args = "-nineml"
elif args.spineml:
files = args.spineml
post_args = "-spineml"
elif args.sbml_import:
pre_args = "-sbml-import"
files = args.sbml_import[0]
post_args = ' '.join(args.sbml_import[1:])
elif args.sbml_import_units:
pre_args = "-smbl-import-units"
files = args.sbml_import_units[0]
post_args = ' '.join(args.sbml_import_units[1:])
elif args.vhdl:
files = args.vhdl[1]
post_args = "-vhdl %s" % args.vhdl[0]
elif args.validate:
pre_args = "-validate"
files = ' '.join(args.validate)
exit_on_fail = False
elif args.validatev1:
pre_args = "-validatev1"
files = ' '.join(args.validatev1)
exit_on_fail = False

run_jneuroml(pre_args,
files,
post_args,
max_memory = args.java_max_memory,
exit_on_fail = exit_on_fail)


def run_jneuroml(pre_args,
target_file,
post_args,
Expand All @@ -590,12 +642,10 @@ 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)
print("java -Xmx%s %s -jar '%s' %s %s %s" % (max_memory, pre_jar, jar, pre_args, target_file, post_args))
sys.exit(1)
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)
except:
print_comment('*** Execution of jnml has failed! ***', verbose)

Expand Down Expand Up @@ -729,8 +779,7 @@ def main(args=None):
if args is None:
args = parse_arguments()

#evaluate_arguments(args)
print(args)
evaluate_arguments(args)


if __name__ == "__main__":
Expand Down

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