comparison ebcsgen_static_analysis.py @ 0:35cc9bb0b4e9 draft

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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children
comparison
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-1:000000000000 0:35cc9bb0b4e9
1 import argparse
2
3 from eBCSgen.Errors.ComplexParsingError import ComplexParsingError
4 from eBCSgen.Errors.ModelParsingError import ModelParsingError
5 from eBCSgen.Errors.UnspecifiedParsingError import UnspecifiedParsingError
6 from eBCSgen.Parsing.ParseBCSL import Parser
7
8
9 def save_model(model, filename):
10 f = open(filename, "w")
11 f.write(repr(model))
12 f.close()
13
14
15 args_parser = argparse.ArgumentParser(description='Static analysis')
16
17 args_parser._action_groups.pop()
18 required = args_parser.add_argument_group('required arguments')
19 optional = args_parser.add_argument_group('optional arguments')
20
21 required.add_argument('--model', type=str, required=True)
22 required.add_argument('--output', type=str, required=True)
23 required.add_argument('--method', type=str, required=True)
24 optional.add_argument('--complex')
25
26 args = args_parser.parse_args()
27
28 model_parser = Parser("model")
29 model_str = open(args.model, "r").read()
30 model = model_parser.parse(model_str)
31
32 if model.success:
33 if args.method == "reduce":
34 model.data.reduce_context()
35 save_model(model.data, args.output)
36 elif args.method == "eliminate":
37 model.data.eliminate_redundant()
38 save_model(model.data, args.output)
39 else:
40 complex_parser = Parser("rate_complex")
41 complex = complex_parser.parse(args.complex)
42 if complex.success:
43 result = model.data.static_non_reachability(complex.data.children[0])
44 f = open(args.output, "w")
45 s = "can possibly" if result else "cannot"
46 message = "The given agent\n\t{}\n{} be reached in the model.".format(complex.data.children[0], s)
47 f.write(message)
48 f.close()
49 else:
50 raise ComplexParsingError(complex.data, args.complex)
51 else:
52 if "error" in model.data:
53 raise UnspecifiedParsingError(model.data["error"])
54 raise ModelParsingError(model.data, model_str)