tomo: workflow/__main_

annotate workflow/main.py @ 75:d5e1d4ea2b7e draft default tip

planemo upload for repository https://github.com/rolfverberg/galaxytools commit 6afde341a94586fe3972bdbbfbf5dabd5e8dec69

author	rv43
date	Thu, 23 Mar 2023 13:39:14 +0000
parents	1cf15b61cd83
children

rev	line source
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	1 #!/usr/bin/env python3
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	2
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	3 import logging
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	4 logging.getLogger(__name__)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	5
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	6 import argparse
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	7 import pathlib
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	8 import sys
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	9
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	10 from .models import TomoWorkflow as Workflow
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	11 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	12 from deepdiff import DeepDiff
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	13 except:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	14 pass
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	15
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	16 parser = argparse.ArgumentParser(description='''Operate on representations of
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	17 Tomo data workflows saved to files.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	18 parser.add_argument('-l', '--log',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	19 # type=argparse.FileType('w'),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	20 default=sys.stdout,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	21 help='Logging stream or filename')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	22 parser.add_argument('--log_level',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	23 choices=logging._nameToLevel.keys(),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	24 default='INFO',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	25 help='''Specify a preferred logging level.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	26 subparsers = parser.add_subparsers(title='subcommands', required=True)#, dest='command')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	27
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	28
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	29 # CONSTRUCT
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	30 def construct(args:list) -> None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	31 if args.template_file is not None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	32 wf = Workflow.construct_from_file(args.template_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	33 wf.cli()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	34 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	35 wf = Workflow.construct_from_cli()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	36 wf.write_to_file(args.output_file, force_overwrite=args.force_overwrite)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	37
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	38 construct_parser = subparsers.add_parser('construct', help='''Construct a valid Tomo
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	39 workflow representation on the command line and save it to a file. Optionally use
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	40 an existing file as a template and/or preform the reconstruction or transfer to Galaxy.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	41 construct_parser.set_defaults(func=construct)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	42 construct_parser.add_argument('-t', '--template_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	43 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	44 required=False,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	45 help='''Full or relative template file path for the constructed workflow.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	46 construct_parser.add_argument('-f', '--force_overwrite',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	47 action='store_true',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	48 help='''Use this flag to overwrite the output file if it already exists.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	49 construct_parser.add_argument('-o', '--output_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	50 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	51 help='''Full or relative file path to which the constructed workflow will be written.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	52
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	53
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	54 # VALIDATE
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	55 def validate(args:list) -> bool:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	56 try:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	57 wf = Workflow.construct_from_file(args.input_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	58 logger.info(f'Success: {args.input_file} represents a valid Tomo workflow configuration.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	59 return(True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	60 except BaseException as e:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	61 logger.error(f'{e.__class__.__name__}: {str(e)}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	62 logger.info(f'''Failure: {args.input_file} does not represent a valid Tomo workflow
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	63 configuration.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	64 return(False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	65
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	66 validate_parser = subparsers.add_parser('validate',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	67 help='''Validate a file as a representation of a Tomo workflow (this is most useful
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	68 after a .yaml file has been manually edited).''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	69 validate_parser.set_defaults(func=validate)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	70 validate_parser.add_argument('input_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	71 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	72 help='''Full or relative file path to validate as a Tomo workflow.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	73
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	74
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	75 # CONVERT
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	76 def convert(args:list) -> None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	77 wf = Workflow.construct_from_file(args.input_file)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	78 wf.write_to_file(args.output_file, force_overwrite=args.force_overwrite)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	79
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	80 convert_parser = subparsers.add_parser('convert', help='''Convert one Tomo workflow
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	81 representation to another. File format of both input and output files will be
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	82 automatically determined from the files' extensions.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	83 convert_parser.set_defaults(func=convert)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	84 convert_parser.add_argument('-f', '--force_overwrite',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	85 action='store_true',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	86 help='''Use this flag to overwrite the output file if it already exists.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	87 convert_parser.add_argument('-i', '--input_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	88 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	89 required=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	90 help='''Full or relative input file path to be converted.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	91 convert_parser.add_argument('-o', '--output_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	92 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	93 required=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	94 help='''Full or relative file path to which the converted input will be written.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	95
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	96
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	97 # DIFF / COMPARE
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	98 def diff(args:list) -> bool:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	99 raise ValueError('diff not tested')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	100 # wf1 = Workflow.construct_from_file(args.file1).dict_for_yaml()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	101 # wf2 = Workflow.construct_from_file(args.file2).dict_for_yaml()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	102 # diff = DeepDiff(wf1,wf2,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	103 # ignore_order_func=lambda level:'independent_dimensions' not in level.path(),
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	104 # report_repetition=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	105 # ignore_string_type_changes=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	106 # ignore_numeric_type_changes=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	107 diff_report = diff.pretty()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	108 if len(diff_report) > 0:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	109 logger.info(f'The configurations in {args.file1} and {args.file2} are not identical.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	110 print(diff_report)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	111 return(True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	112 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	113 logger.info(f'The configurations in {args.file1} and {args.file2} are identical.')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	114 return(False)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	115
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	116 diff_parser = subparsers.add_parser('diff', aliases=['compare'], help='''Print a comparison of
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	117 two Tomo workflow representations stored in files. The files may have different formats.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	118 diff_parser.set_defaults(func=diff)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	119 diff_parser.add_argument('file1',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	120 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	121 help='''Full or relative path to the first file for comparison.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	122 diff_parser.add_argument('file2',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	123 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	124 help='''Full or relative path to the second file for comparison.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	125
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	126
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	127 # LINK TO GALAXY
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	128 def link_to_galaxy(args:list) -> None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	129 from .link_to_galaxy import link_to_galaxy
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	130 link_to_galaxy(args.input_file, galaxy=args.galaxy, user=args.user,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	131 password=args.password, api_key=args.api_key)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	132
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	133 link_parser = subparsers.add_parser('link_to_galaxy', help='''Construct a Galaxy history and link
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	134 to an existing Tomo workflow representations in a NeXus file.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	135 link_parser.set_defaults(func=link_to_galaxy)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	136 link_parser.add_argument('-i', '--input_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	137 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	138 required=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	139 help='''Full or relative input file path to the existing Tomo workflow representations as
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	140 a NeXus file.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	141 link_parser.add_argument('-g', '--galaxy',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	142 required=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	143 help='Target Galaxy instance URL/IP address')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	144 link_parser.add_argument('-u', '--user',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	145 default=None,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	146 help='Galaxy user email address')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	147 link_parser.add_argument('-p', '--password',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	148 default=None,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	149 help='Password for the Galaxy user')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	150 link_parser.add_argument('-a', '--api_key',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	151 default=None,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	152 help='Galaxy admin user API key (required if not defined in the tools list file)')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	153
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	154
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	155 # RUN THE RECONSTRUCTION
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	156 def run_tomo(args:list) -> None:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	157 from .run_tomo import run_tomo
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	158 run_tomo(args.input_file, args.output_file, args.modes, center_file=args.center_file,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	159 num_core=args.num_core, output_folder=args.output_folder, save_figs=args.save_figs)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	160
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	161 tomo_parser = subparsers.add_parser('run_tomo', help='''Construct and add reconstructed tomography
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	162 data to an existing Tomo workflow representations in a NeXus file.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	163 tomo_parser.set_defaults(func=run_tomo)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	164 tomo_parser.add_argument('-i', '--input_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	165 required=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	166 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	167 help='''Full or relative input file path containing raw and/or reduced data.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	168 tomo_parser.add_argument('-o', '--output_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	169 required=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	170 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	171 help='''Full or relative input file path containing raw and/or reduced data.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	172 tomo_parser.add_argument('-c', '--center_file',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	173 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	174 help='''Full or relative input file path containing the rotation axis centers info.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	175 #tomo_parser.add_argument('-f', '--force_overwrite',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	176 # action='store_true',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	177 # help='''Use this flag to overwrite any existing reduced data.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	178 tomo_parser.add_argument('-n', '--num_core',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	179 type=int,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	180 default=-1,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	181 help='''Specify the number of processors to use.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	182 tomo_parser.add_argument('--output_folder',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	183 type=pathlib.Path,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	184 default='.',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	185 help='Full or relative path to an output folder')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	186 tomo_parser.add_argument('-s', '--save_figs',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	187 choices=['yes', 'no', 'only'],
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	188 default='no',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	189 help='''Specify weather to display ('yes' or 'no'), save ('yes'), or only save ('only').''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	190 tomo_parser.add_argument('--reduce_data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	191 dest='modes',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	192 const='reduce_data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	193 action='append_const',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	194 help='''Use this flag to create and add reduced data to the input file.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	195 tomo_parser.add_argument('--find_center',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	196 dest='modes',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	197 const='find_center',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	198 action='append_const',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	199 help='''Use this flag to find and add the calibrated center axis info to the input file.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	200 tomo_parser.add_argument('--reconstruct_data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	201 dest='modes',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	202 const='reconstruct_data',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	203 action='append_const',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	204 help='''Use this flag to create and add reconstructed data data to the input file.''')
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	205 tomo_parser.add_argument('--combine_data',
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	206 dest='modes',
71 1cf15b61cd83 planemo upload for repository https://github.com/rolfverberg/galaxytools commit 366e516aef0735af2998c6ff3af037181c8d5213 rv43 parents: 69 diff changeset	207 const='combine_data',
69 fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	208 action='append_const',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	209 help='''Use this flag to combine reconstructed data data and add to the input file.''')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	210
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	211
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	212 if __name__ == '__main__':
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	213 args = parser.parse_args(sys.argv[1:])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	214
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	215 # Set log configuration
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	216 # When logging to file, the stdout log level defaults to WARNING
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	217 logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	218 level = logging.getLevelName(args.log_level)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	219 if args.log is sys.stdout:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	220 logging.basicConfig(format=logging_format, level=level, force=True,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	221 handlers=[logging.StreamHandler()])
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	222 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	223 if isinstance(args.log, str):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	224 logging.basicConfig(filename=f'{args.log}', filemode='w',
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	225 format=logging_format, level=level, force=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	226 elif isinstance(args.log, io.TextIOWrapper):
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	227 logging.basicConfig(filemode='w', format=logging_format, level=level,
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	228 stream=args.log, force=True)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	229 else:
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	230 raise ValueError(f'Invalid argument --log: {args.log}')
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	231 stream_handler = logging.StreamHandler()
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	232 logging.getLogger().addHandler(stream_handler)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	233 stream_handler.setLevel(logging.WARNING)
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	234 stream_handler.setFormatter(logging.Formatter(logging_format))
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	235
fba792d5f83b planemo upload for repository https://github.com/rolfverberg/galaxytools commit ab9f412c362a4ab986d00e21d5185cfcf82485c1 rv43 parents: diff changeset	236 args.func(args)

Mercurial > repos > rv43 > tomo

annotate workflow/__main__.py @ 75:d5e1d4ea2b7e draft default tip

annotate workflow/main.py @ 75:d5e1d4ea2b7e draft default tip