Mercurial > repos > sybila > ebcsgen_pctl_parameter_synthesis
view ebcsgen_pctl_parameter_synthesis.py @ 2:3bb6c1e9252e draft default tip
planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 4719a69f514aed27d90c7017f052463b0b43cbb0
author | sybila |
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date | Sat, 15 Oct 2022 09:23:30 +0000 |
parents | cf609f659b21 |
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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 class FakeFile: def __init__(self, content): self.content = content.decode("utf-8") def read(self): return self.content 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) if "?" not in args.formula: result = FakeFile(result) df = PCTL.process_output(result) df.to_csv(args.output, index=False) else: with open(args.output, "w") as f: f.write(result.decode("utf-8")) else: raise FormulaParsingError(formula.data, args.formula)