Mercurial > repos > galaxyp > openms_digestor
comparison fill_ctd_clargs.py @ 14:13399dc8f687 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 3d1e5f37fd16524a415f707772eeb7ead848c5e3
author | galaxyp |
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date | Thu, 01 Dec 2022 19:09:26 +0000 |
parents | 7af5860ae563 |
children |
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13:28bc63599d10 | 14:13399dc8f687 |
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1 #!/usr/bin/env python3 | 1 #!/usr/bin/env python3 |
2 | |
3 import operator | |
2 from argparse import ArgumentParser | 4 from argparse import ArgumentParser |
5 from functools import reduce # forward compatibility for Python 3 | |
3 from io import StringIO | 6 from io import StringIO |
4 | 7 |
5 from CTDopts.CTDopts import ( | 8 from CTDopts.CTDopts import ( |
9 _Null, | |
6 CTDModel, | 10 CTDModel, |
7 ModelTypeError, | 11 ModelTypeError, |
8 Parameters | 12 Parameters |
9 ) | 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 | |
10 | 23 |
11 if __name__ == "__main__": | 24 if __name__ == "__main__": |
12 # note add_help=False since otherwise arguments starting with -h will | 25 # note add_help=False since otherwise arguments starting with -h will |
13 # trigger an error (despite allow_abbreviate) | 26 # trigger an error (despite allow_abbreviate) |
14 parser = ArgumentParser(prog="fill_ctd_clargs", | 27 parser = ArgumentParser(prog="fill_ctd_clargs", |
15 description="fill command line arguments" | 28 description="fill command line arguments" |
16 "into a CTD file and write the CTD file to", | 29 "into a CTD file and write the CTD file to stdout", |
17 add_help=False, allow_abbrev=False) | 30 add_help=False, allow_abbrev=False) |
18 parser.add_argument("--ctd", dest="ctd", help="input ctd file", | 31 parser.add_argument("--ini_file", dest="ini_file", help="input ini file", |
19 metavar='CTD', default=None, required=True) | 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) | |
20 args, cliargs = parser.parse_known_args() | 37 args, cliargs = parser.parse_known_args() |
38 | |
21 # load CTDModel | 39 # load CTDModel |
22 model = None | 40 ini_model = None |
23 try: | 41 try: |
24 model = CTDModel(from_file=args.ctd) | 42 ini_model = CTDModel(from_file=args.ini_file) |
25 except ModelTypeError: | 43 except ModelTypeError: |
26 pass | 44 pass |
27 try: | 45 try: |
28 model = Parameters(from_file=args.ctd) | 46 ini_model = Parameters(from_file=args.ini_file) |
29 except ModelTypeError: | 47 except ModelTypeError: |
30 pass | 48 pass |
31 assert model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ctd) | 49 assert ini_model is not None, "Could not parse %s, seems to be no CTD/PARAMS" % (args.ini_file) |
32 | 50 |
33 # get a dictionary of the ctd arguments where the values of the parameters | 51 # get a dictionary of the ctd arguments where the values of the parameters |
34 # given on the command line are overwritten | 52 # given on the command line are overwritten |
35 margs = model.parse_cl_args(cl_args=cliargs, ignore_required=True) | 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) | |
36 | 66 |
37 # write the ctd with the values taken from the dictionary | 67 # write the ctd with the values taken from the dictionary |
38 out = StringIO() | 68 out = StringIO() |
39 ctd_tree = model.write_ctd(out, margs) | 69 ctd_tree = ini_model.write_ctd(out, ini_values) |
40 print(out.getvalue()) | 70 print(out.getvalue()) |