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comparison workflow/__main__.py @ 69:fba792d5f83b draft

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planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1
author rv43
date Fri, 10 Mar 2023 16:02:04 +0000
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children 1cf15b61cd83
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68:ba5866d0251d 69:fba792d5f83b
1 #!/usr/bin/env python3
2
3 import logging
4 logging.getLogger(__name__)
5
6 import argparse
7 import pathlib
8 import sys
9
10 from .models import TomoWorkflow as Workflow
11 try:
12 from deepdiff import DeepDiff
13 except:
14 pass
15
16 parser = argparse.ArgumentParser(description='''Operate on representations of
17 Tomo data workflows saved to files.''')
18 parser.add_argument('-l', '--log',
19 # type=argparse.FileType('w'),
20 default=sys.stdout,
21 help='Logging stream or filename')
22 parser.add_argument('--log_level',
23 choices=logging._nameToLevel.keys(),
24 default='INFO',
25 help='''Specify a preferred logging level.''')
26 subparsers = parser.add_subparsers(title='subcommands', required=True)#, dest='command')
27
28
29 # CONSTRUCT
30 def construct(args:list) -> None:
31 if args.template_file is not None:
32 wf = Workflow.construct_from_file(args.template_file)
33 wf.cli()
34 else:
35 wf = Workflow.construct_from_cli()
36 wf.write_to_file(args.output_file, force_overwrite=args.force_overwrite)
37
38 construct_parser = subparsers.add_parser('construct', help='''Construct a valid Tomo
39 workflow representation on the command line and save it to a file. Optionally use
40 an existing file as a template and/or preform the reconstruction or transfer to Galaxy.''')
41 construct_parser.set_defaults(func=construct)
42 construct_parser.add_argument('-t', '--template_file',
43 type=pathlib.Path,
44 required=False,
45 help='''Full or relative template file path for the constructed workflow.''')
46 construct_parser.add_argument('-f', '--force_overwrite',
47 action='store_true',
48 help='''Use this flag to overwrite the output file if it already exists.''')
49 construct_parser.add_argument('-o', '--output_file',
50 type=pathlib.Path,
51 help='''Full or relative file path to which the constructed workflow will be written.''')
52
53
54 # VALIDATE
55 def validate(args:list) -> bool:
56 try:
57 wf = Workflow.construct_from_file(args.input_file)
58 logger.info(f'Success: {args.input_file} represents a valid Tomo workflow configuration.')
59 return(True)
60 except BaseException as e:
61 logger.error(f'{e.__class__.__name__}: {str(e)}')
62 logger.info(f'''Failure: {args.input_file} does not represent a valid Tomo workflow
63 configuration.''')
64 return(False)
65
66 validate_parser = subparsers.add_parser('validate',
67 help='''Validate a file as a representation of a Tomo workflow (this is most useful
68 after a .yaml file has been manually edited).''')
69 validate_parser.set_defaults(func=validate)
70 validate_parser.add_argument('input_file',
71 type=pathlib.Path,
72 help='''Full or relative file path to validate as a Tomo workflow.''')
73
74
75 # CONVERT
76 def convert(args:list) -> None:
77 wf = Workflow.construct_from_file(args.input_file)
78 wf.write_to_file(args.output_file, force_overwrite=args.force_overwrite)
79
80 convert_parser = subparsers.add_parser('convert', help='''Convert one Tomo workflow
81 representation to another. File format of both input and output files will be
82 automatically determined from the files' extensions.''')
83 convert_parser.set_defaults(func=convert)
84 convert_parser.add_argument('-f', '--force_overwrite',
85 action='store_true',
86 help='''Use this flag to overwrite the output file if it already exists.''')
87 convert_parser.add_argument('-i', '--input_file',
88 type=pathlib.Path,
89 required=True,
90 help='''Full or relative input file path to be converted.''')
91 convert_parser.add_argument('-o', '--output_file',
92 type=pathlib.Path,
93 required=True,
94 help='''Full or relative file path to which the converted input will be written.''')
95
96
97 # DIFF / COMPARE
98 def diff(args:list) -> bool:
99 raise ValueError('diff not tested')
100 # wf1 = Workflow.construct_from_file(args.file1).dict_for_yaml()
101 # wf2 = Workflow.construct_from_file(args.file2).dict_for_yaml()
102 # diff = DeepDiff(wf1,wf2,
103 # ignore_order_func=lambda level:'independent_dimensions' not in level.path(),
104 # report_repetition=True,
105 # ignore_string_type_changes=True,
106 # ignore_numeric_type_changes=True)
107 diff_report = diff.pretty()
108 if len(diff_report) > 0:
109 logger.info(f'The configurations in {args.file1} and {args.file2} are not identical.')
110 print(diff_report)
111 return(True)
112 else:
113 logger.info(f'The configurations in {args.file1} and {args.file2} are identical.')
114 return(False)
115
116 diff_parser = subparsers.add_parser('diff', aliases=['compare'], help='''Print a comparison of
117 two Tomo workflow representations stored in files. The files may have different formats.''')
118 diff_parser.set_defaults(func=diff)
119 diff_parser.add_argument('file1',
120 type=pathlib.Path,
121 help='''Full or relative path to the first file for comparison.''')
122 diff_parser.add_argument('file2',
123 type=pathlib.Path,
124 help='''Full or relative path to the second file for comparison.''')
125
126
127 # LINK TO GALAXY
128 def link_to_galaxy(args:list) -> None:
129 from .link_to_galaxy import link_to_galaxy
130 link_to_galaxy(args.input_file, galaxy=args.galaxy, user=args.user,
131 password=args.password, api_key=args.api_key)
132
133 link_parser = subparsers.add_parser('link_to_galaxy', help='''Construct a Galaxy history and link
134 to an existing Tomo workflow representations in a NeXus file.''')
135 link_parser.set_defaults(func=link_to_galaxy)
136 link_parser.add_argument('-i', '--input_file',
137 type=pathlib.Path,
138 required=True,
139 help='''Full or relative input file path to the existing Tomo workflow representations as
140 a NeXus file.''')
141 link_parser.add_argument('-g', '--galaxy',
142 required=True,
143 help='Target Galaxy instance URL/IP address')
144 link_parser.add_argument('-u', '--user',
145 default=None,
146 help='Galaxy user email address')
147 link_parser.add_argument('-p', '--password',
148 default=None,
149 help='Password for the Galaxy user')
150 link_parser.add_argument('-a', '--api_key',
151 default=None,
152 help='Galaxy admin user API key (required if not defined in the tools list file)')
153
154
155 # RUN THE RECONSTRUCTION
156 def run_tomo(args:list) -> None:
157 from .run_tomo import run_tomo
158 run_tomo(args.input_file, args.output_file, args.modes, center_file=args.center_file,
159 num_core=args.num_core, output_folder=args.output_folder, save_figs=args.save_figs)
160
161 tomo_parser = subparsers.add_parser('run_tomo', help='''Construct and add reconstructed tomography
162 data to an existing Tomo workflow representations in a NeXus file.''')
163 tomo_parser.set_defaults(func=run_tomo)
164 tomo_parser.add_argument('-i', '--input_file',
165 required=True,
166 type=pathlib.Path,
167 help='''Full or relative input file path containing raw and/or reduced data.''')
168 tomo_parser.add_argument('-o', '--output_file',
169 required=True,
170 type=pathlib.Path,
171 help='''Full or relative input file path containing raw and/or reduced data.''')
172 tomo_parser.add_argument('-c', '--center_file',
173 type=pathlib.Path,
174 help='''Full or relative input file path containing the rotation axis centers info.''')
175 #tomo_parser.add_argument('-f', '--force_overwrite',
176 # action='store_true',
177 # help='''Use this flag to overwrite any existing reduced data.''')
178 tomo_parser.add_argument('-n', '--num_core',
179 type=int,
180 default=-1,
181 help='''Specify the number of processors to use.''')
182 tomo_parser.add_argument('--output_folder',
183 type=pathlib.Path,
184 default='.',
185 help='Full or relative path to an output folder')
186 tomo_parser.add_argument('-s', '--save_figs',
187 choices=['yes', 'no', 'only'],
188 default='no',
189 help='''Specify weather to display ('yes' or 'no'), save ('yes'), or only save ('only').''')
190 tomo_parser.add_argument('--reduce_data',
191 dest='modes',
192 const='reduce_data',
193 action='append_const',
194 help='''Use this flag to create and add reduced data to the input file.''')
195 tomo_parser.add_argument('--find_center',
196 dest='modes',
197 const='find_center',
198 action='append_const',
199 help='''Use this flag to find and add the calibrated center axis info to the input file.''')
200 tomo_parser.add_argument('--reconstruct_data',
201 dest='modes',
202 const='reconstruct_data',
203 action='append_const',
204 help='''Use this flag to create and add reconstructed data data to the input file.''')
205 tomo_parser.add_argument('--combine_datas',
206 dest='modes',
207 const='combine_datas',
208 action='append_const',
209 help='''Use this flag to combine reconstructed data data and add to the input file.''')
210
211
212 if __name__ == '__main__':
213 args = parser.parse_args(sys.argv[1:])
214
215 # Set log configuration
216 # When logging to file, the stdout log level defaults to WARNING
217 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
218 level = logging.getLevelName(args.log_level)
219 if args.log is sys.stdout:
220 logging.basicConfig(format=logging_format, level=level, force=True,
221 handlers=[logging.StreamHandler()])
222 else:
223 if isinstance(args.log, str):
224 logging.basicConfig(filename=f'{args.log}', filemode='w',
225 format=logging_format, level=level, force=True)
226 elif isinstance(args.log, io.TextIOWrapper):
227 logging.basicConfig(filemode='w', format=logging_format, level=level,
228 stream=args.log, force=True)
229 else:
230 raise ValueError(f'Invalid argument --log: {args.log}')
231 stream_handler = logging.StreamHandler()
232 logging.getLogger().addHandler(stream_handler)
233 stream_handler.setLevel(logging.WARNING)
234 stream_handler.setFormatter(logging.Formatter(logging_format))
235
236 args.func(args)