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planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 4719a69f514aed27d90c7017f052463b0b43cbb0
author sybila
date Sat, 15 Oct 2022 09:23:30 +0000
parents cf609f659b21
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cf609f659b21 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit a7263af5f87e39dd0d3d29924e530c88d83a5ee6
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1 import argparse
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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 class FakeFile:
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11 def __init__(self, content):
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12 self.content = content.decode("utf-8")
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14 def read(self):
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15 return self.content
3bb6c1e9252e planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit 4719a69f514aed27d90c7017f052463b0b43cbb0
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18 args_parser = argparse.ArgumentParser(description='Parameter synthesis')
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20 args_parser._action_groups.pop()
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21 required = args_parser.add_argument_group('required arguments')
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22 optional = args_parser.add_argument_group('optional arguments')
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24 required.add_argument('--transition_file', required=True)
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25 required.add_argument('--output', type=str, required=True)
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26 required.add_argument('--formula', type=str, required=True)
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27 optional.add_argument('--region', type=str)
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29 args = args_parser.parse_args()
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31 if args.region:
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32 region = args.region.replace("=", "<=")
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33 else:
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34 region = None
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36 ts = load_TS_from_json(args.transition_file)
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38 if len(ts.params) == 0:
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39 raise InvalidInputError("Provided model is not parametrised - parameter synthesis cannot be executed.")
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41 if "?" not in args.formula:
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42 if not region:
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43 params = set()
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44 else:
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45 params = {param.split("<=")[1] for param in region.split(",")}
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47 undefined = set(ts.params) - params
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48 if undefined:
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49 raise InvalidInputError("Intervals undefined for parameters: {}.".format(", ".join(undefined)))
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51 formula = PCTLparser().parse(args.formula)
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52 if formula.success:
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53 result = PCTL.parameter_synthesis(ts, formula, region)
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54 if "?" not in args.formula:
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55 result = FakeFile(result)
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56 df = PCTL.process_output(result)
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57 df.to_csv(args.output, index=False)
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58 else:
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59 with open(args.output, "w") as f:
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60 f.write(result.decode("utf-8"))
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61 else:
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62 raise FormulaParsingError(formula.data, args.formula)