annotate ebcsgen_pctl_parameter_synthesis.py @ 0:cf609f659b21 draft

planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6

import argparse

from eBCSgen.Analysis.PCTL import PCTL
from eBCSgen.Errors.FormulaParsingError import FormulaParsingError
from eBCSgen.Errors.InvalidInputError import InvalidInputError
from eBCSgen.Parsing.ParseBCSL import load_TS_from_json
from eBCSgen.Parsing.ParsePCTLformula import PCTLparser


args_parser = argparse.ArgumentParser(description='Parameter synthesis')

args_parser._action_groups.pop()
required = args_parser.add_argument_group('required arguments')
optional = args_parser.add_argument_group('optional arguments')

required.add_argument('--transition_file', required=True)
required.add_argument('--output', type=str, required=True)
required.add_argument('--formula', type=str, required=True)
optional.add_argument('--region', type=str)

args = args_parser.parse_args()

if args.region:
    region = args.region.replace("=", "<=")
else:
    region = None

ts = load_TS_from_json(args.transition_file)

if len(ts.params) == 0:
    raise InvalidInputError("Provided model is not parametrised - parameter synthesis cannot be executed.")

if "?" not in args.formula:
    if not region:
        params = set()
    else:
        params = {param.split("<=")[1] for param in region.split(",")}

    undefined = set(ts.params) - params
    if undefined:
        raise InvalidInputError("Intervals undefined for parameters: {}.".format(", ".join(undefined)))

formula = PCTLparser().parse(args.formula)
if formula.success:
    result = PCTL.parameter_synthesis(ts, formula, region)
    f = open(args.output, "w")
    f.write(result.decode("utf-8"))
    f.close()
else:
    raise FormulaParsingError(formula.data, args.formula)