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annotate ebcsgen_pctl_model_checking.py @ 2:141b9c2bc816 draft

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planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 83232805a8721c48078c88367e3480a5553f0182
author sybila
date Fri, 14 Oct 2022 16:24:36 +0000
parents ea5108514910
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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1 import argparse
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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3 from eBCSgen.Analysis.PCTL import PCTL
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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4 from eBCSgen.Errors.FormulaParsingError import FormulaParsingError
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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5 from eBCSgen.Errors.InvalidInputError import InvalidInputError
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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6 from eBCSgen.Parsing.ParseBCSL import load_TS_from_json
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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7 from eBCSgen.Parsing.ParsePCTLformula import PCTLparser
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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10 args_parser = argparse.ArgumentParser(description='Model checking')
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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12 args_parser._action_groups.pop()
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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13 required = args_parser.add_argument_group('required arguments')
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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15 required.add_argument('--transition_file', required=True)
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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16 required.add_argument('--output', type=str, required=True)
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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17 required.add_argument('--formula', type=str, required=True)
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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19 args = args_parser.parse_args()
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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21 ts = load_TS_from_json(args.transition_file)
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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23 if len(ts.params) != 0:
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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24 raise InvalidInputError("Provided transition system is parametrised - model checking cannot be executed.")
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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26 formula = PCTLparser().parse(args.formula)
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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27 if formula.success:
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141b9c2bc816 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 83232805a8721c48078c88367e3480a5553f0182
sybila
parents: 0
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28 result = PCTL.model_checking(ts, formula)
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ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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29 f = open(args.output, "w")
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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30 f.write(result.decode("utf-8"))
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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31 f.close()
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
sybila
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32 else:
ea5108514910 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit d80d8e9710cba50aab3e6a1e10a527d26fc7e72b
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33 raise FormulaParsingError(formula.data, args.formula)