Mercurial > repos > galaxyp > openms_simplesearchengine
comparison fill_ctd_clargs.py @ 14:a1724438d580 draft default tip
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 5c080b1e2b99f1c88f4557e9fec8c45c9d23b906
author | galaxyp |
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date | Fri, 14 Jun 2024 21:35:59 +0000 |
parents | da78f97a6dda |
children |
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13:da78f97a6dda | 14:a1724438d580 |
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1 #!/usr/bin/env python3 | |
2 | |
3 import operator | |
4 from argparse import ArgumentParser | |
5 from functools import reduce # forward compatibility for Python 3 | |
6 from io import StringIO | |
7 | |
8 from CTDopts.CTDopts import ( | |
9 _Null, | |
10 CTDModel, | |
11 ModelTypeError, | |
12 Parameters | |
13 ) | |
14 | |
15 | |
16 def getFromDict(dataDict, mapList): | |
17 return reduce(operator.getitem, mapList, dataDict) | |
18 | |
19 | |
20 def setInDict(dataDict, mapList, value): | |
21 getFromDict(dataDict, mapList[:-1])[mapList[-1]] = value | |
22 | |
23 | |
24 if __name__ == "__main__": | |
25 # note add_help=False since otherwise arguments starting with -h will | |
26 # trigger an error (despite allow_abbreviate) | |
27 parser = ArgumentParser(prog="fill_ctd_clargs", | |
28 description="fill command line arguments" | |
29 "into a CTD file and write the CTD file to stdout", | |
30 add_help=False, allow_abbrev=False) | |
31 parser.add_argument("--ini_file", dest="ini_file", help="input ini file", | |
32 metavar='INI', default=None, required=True) | |
33 parser.add_argument("--ctd_file", dest="ctd_file", help="input ctd file" | |
34 "if given then optional parameters from the ini file" | |
35 "will be filled with the defaults from this CTD file", | |
36 metavar='CTD', default=None, required=False) | |
37 args, cliargs = parser.parse_known_args() | |
38 | |
39 # load CTDModel | |
40 ini_model = None | |
41 try: | |
42 ini_model = CTDModel(from_file=args.ini_file) | |
43 except ModelTypeError: | |
44 pass | |
45 try: | |
46 ini_model = Parameters(from_file=args.ini_file) | |
47 except ModelTypeError: | |
48 pass | |
49 assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) | |
50 | |
51 # get a dictionary of the ctd arguments where the values of the parameters | |
52 # given on the command line are overwritten | |
53 ini_values = ini_model.parse_cl_args(cl_args=cliargs, ignore_required=True) | |
54 | |
55 if args.ctd_file: | |
56 ctd_model = CTDModel(from_file=args.ctd_file) | |
57 ctd_values = ctd_model.get_defaults() | |
58 for param in ini_model.get_parameters(): | |
59 if not param.required and (param.default is None or type(param.default) is _Null): | |
60 lineage = param.get_lineage(name_only=True) | |
61 try: | |
62 default = getFromDict(ctd_values, lineage) | |
63 except KeyError: | |
64 continue | |
65 setInDict(ini_values, lineage, default) | |
66 | |
67 # write the ctd with the values taken from the dictionary | |
68 out = StringIO() | |
69 ctd_tree = ini_model.write_ctd(out, ini_values) | |
70 print(out.getvalue()) |