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annotate ebcsgen_static_analysis.py @ 0:35cc9bb0b4e9 draft

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planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
author sybila
date Sat, 08 Oct 2022 14:07:25 +0000
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35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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diff changeset
1 import argparse
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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3 from eBCSgen.Errors.ComplexParsingError import ComplexParsingError
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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4 from eBCSgen.Errors.ModelParsingError import ModelParsingError
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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5 from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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6 from eBCSgen.Parsing.ParseBCSL import Parser
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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9 def save_model(model, filename):
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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10 f = open(filename, "w")
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11 f.write(repr(model))
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12 f.close()
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35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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15 args_parser = argparse.ArgumentParser(description='Static analysis')
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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17 args_parser._action_groups.pop()
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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18 required = args_parser.add_argument_group('required arguments')
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19 optional = args_parser.add_argument_group('optional arguments')
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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21 required.add_argument('--model', type=str, required=True)
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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22 required.add_argument('--output', type=str, required=True)
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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23 required.add_argument('--method', type=str, required=True)
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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24 optional.add_argument('--complex')
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35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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26 args = args_parser.parse_args()
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35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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28 model_parser = Parser("model")
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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29 model_str = open(args.model, "r").read()
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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30 model = model_parser.parse(model_str)
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32 if model.success:
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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33 if args.method == "reduce":
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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34 model.data.reduce_context()
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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35 save_model(model.data, args.output)
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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36 elif args.method == "eliminate":
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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37 model.data.eliminate_redundant()
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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38 save_model(model.data, args.output)
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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39 else:
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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40 complex_parser = Parser("rate_complex")
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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41 complex = complex_parser.parse(args.complex)
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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42 if complex.success:
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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43 result = model.data.static_non_reachability(complex.data.children[0])
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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44 f = open(args.output, "w")
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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45 s = "can possibly" if result else "cannot"
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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46 message = "The given agent\n\t{}\n{} be reached in the model.".format(complex.data.children[0], s)
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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47 f.write(message)
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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48 f.close()
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49 else:
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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50 raise ComplexParsingError(complex.data, args.complex)
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51 else:
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52 if "error" in model.data:
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53 raise UnspecifiedParsingError(model.data["error"])
35cc9bb0b4e9 planemo upload for repository https://github.com/sybila/galaxytools/tree/master/tools/ebcsgen commit f39ef50b0964744be7816de065024eeb1fb69364
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54 raise ModelParsingError(model.data, model_str)