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annotate ebcsgen_pctl_parameter_synthesis.py @ 0:f1b47d8bcbf9 draft

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planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
author sybila
date Fri, 07 Oct 2022 12:35:23 +0000
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children 5668805ac1c2
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f1b47d8bcbf9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
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1 import argparse
f1b47d8bcbf9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
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3 from eBCSgen.Analysis.PCTL import PCTL
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4 from eBCSgen.Errors.FormulaParsingError import FormulaParsingError
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5 from eBCSgen.Errors.InvalidInputError import InvalidInputError
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6 from eBCSgen.Parsing.ParseBCSL import load_TS_from_json
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7 from eBCSgen.Parsing.ParsePCTLformula import PCTLparser
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10 args_parser = argparse.ArgumentParser(description='Parameter synthesis')
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12 args_parser._action_groups.pop()
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13 required = args_parser.add_argument_group('required arguments')
f1b47d8bcbf9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
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14 optional = args_parser.add_argument_group('optional arguments')
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16 required.add_argument('--transition_file', required=True)
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17 required.add_argument('--output', type=str, required=True)
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18 required.add_argument('--formula', type=str, required=True)
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19 optional.add_argument('--region', type=str)
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21 args = args_parser.parse_args()
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23 if args.region:
f1b47d8bcbf9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
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24 region = args.region.replace("=", "<=")
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25 else:
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26 region = None
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28 ts = load_TS_from_json(args.transition_file)
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30 if len(ts.params) == 0:
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31 raise InvalidInputError("Provided model is not parametrised - parameter synthesis cannot be executed.")
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33 if "?" not in args.formula:
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34 if not region:
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35 params = set()
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36 else:
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37 params = {param.split("<=")[1] for param in region.split(",")}
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38
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39 undefined = set(ts.params) - params
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40 if undefined:
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41 raise InvalidInputError("Intervals undefined for parameters: {}.".format(", ".join(undefined)))
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43 formula = PCTLparser().parse(args.formula)
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44 if formula.success:
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45 result = PCTL.parameter_synthesis(ts, formula, region)
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46 f = open(args.output, "w")
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47 f.write(result.decode("utf-8"))
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48 f.close()
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49 else:
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50 raise FormulaParsingError(formula.data, args.formula)