--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/workflow/__main__.py	Fri Mar 10 16:02:04 2023 +0000
@@ -0,0 +1,236 @@
+#!/usr/bin/env python3
+
+import logging
+logging.getLogger(__name__)
+
+import argparse
+import pathlib
+import sys
+
+from .models import TomoWorkflow as Workflow
+try:
+    from deepdiff import DeepDiff
+except:
+    pass
+
+parser = argparse.ArgumentParser(description='''Operate on representations of
+        Tomo data workflows saved to files.''')
+parser.add_argument('-l', '--log',
+#        type=argparse.FileType('w'),
+        default=sys.stdout,
+        help='Logging stream or filename')
+parser.add_argument('--log_level',
+        choices=logging._nameToLevel.keys(),
+        default='INFO',
+        help='''Specify a preferred logging level.''')
+subparsers = parser.add_subparsers(title='subcommands', required=True)#, dest='command')
+
+
+# CONSTRUCT
+def construct(args:list) -> None:
+    if args.template_file is not None:
+        wf = Workflow.construct_from_file(args.template_file)
+        wf.cli()
+    else:
+        wf = Workflow.construct_from_cli()
+    wf.write_to_file(args.output_file, force_overwrite=args.force_overwrite)
+
+construct_parser = subparsers.add_parser('construct', help='''Construct a valid Tomo
+        workflow representation on the command line and save it to a file. Optionally use
+        an existing file as a template and/or preform the reconstruction or transfer to Galaxy.''')
+construct_parser.set_defaults(func=construct)
+construct_parser.add_argument('-t', '--template_file',
+        type=pathlib.Path,
+        required=False,
+        help='''Full or relative template file path for the constructed workflow.''')
+construct_parser.add_argument('-f', '--force_overwrite',
+        action='store_true',
+        help='''Use this flag to overwrite the output file if it already exists.''')
+construct_parser.add_argument('-o', '--output_file',
+        type=pathlib.Path,
+        help='''Full or relative file path to which the constructed workflow will be written.''')
+
+
+# VALIDATE
+def validate(args:list) -> bool:
+    try:
+        wf = Workflow.construct_from_file(args.input_file)
+        logger.info(f'Success: {args.input_file} represents a valid Tomo workflow configuration.')
+        return(True)
+    except BaseException as e:
+        logger.error(f'{e.__class__.__name__}: {str(e)}')
+        logger.info(f'''Failure: {args.input_file} does not represent a valid Tomo workflow
+                configuration.''')
+        return(False)
+
+validate_parser = subparsers.add_parser('validate',
+        help='''Validate a file as a representation of a Tomo workflow (this is most useful
+                after a .yaml file has been manually edited).''')
+validate_parser.set_defaults(func=validate)
+validate_parser.add_argument('input_file',
+        type=pathlib.Path,
+        help='''Full or relative file path to validate as a Tomo workflow.''')
+
+
+# CONVERT
+def convert(args:list) -> None:
+    wf = Workflow.construct_from_file(args.input_file)
+    wf.write_to_file(args.output_file, force_overwrite=args.force_overwrite)
+
+convert_parser = subparsers.add_parser('convert', help='''Convert one Tomo workflow
+        representation to another. File format of both input and output files will be
+        automatically determined from the files' extensions.''')
+convert_parser.set_defaults(func=convert)
+convert_parser.add_argument('-f', '--force_overwrite',
+        action='store_true',
+        help='''Use this flag to overwrite the output file if it already exists.''')
+convert_parser.add_argument('-i', '--input_file',
+        type=pathlib.Path,
+        required=True,
+        help='''Full or relative input file path to be converted.''')
+convert_parser.add_argument('-o', '--output_file',
+        type=pathlib.Path,
+        required=True,
+        help='''Full or relative file path to which the converted input will be written.''')
+
+
+# DIFF / COMPARE
+def diff(args:list) -> bool:
+    raise ValueError('diff not tested')
+#    wf1 = Workflow.construct_from_file(args.file1).dict_for_yaml()
+#    wf2 = Workflow.construct_from_file(args.file2).dict_for_yaml()
+#    diff = DeepDiff(wf1,wf2,
+#                    ignore_order_func=lambda level:'independent_dimensions' not in level.path(),
+#                    report_repetition=True,
+#                    ignore_string_type_changes=True,
+#                    ignore_numeric_type_changes=True)
+    diff_report = diff.pretty()
+    if len(diff_report) > 0:
+        logger.info(f'The configurations in {args.file1} and {args.file2} are not identical.')
+        print(diff_report)
+        return(True)
+    else:
+        logger.info(f'The configurations in {args.file1} and {args.file2} are identical.')
+        return(False)
+
+diff_parser = subparsers.add_parser('diff', aliases=['compare'], help='''Print a comparison of 
+        two Tomo workflow representations stored in files. The files may have different formats.''')
+diff_parser.set_defaults(func=diff)
+diff_parser.add_argument('file1',
+        type=pathlib.Path,
+        help='''Full or relative path to the first file for comparison.''')
+diff_parser.add_argument('file2',
+        type=pathlib.Path,
+        help='''Full or relative path to the second file for comparison.''')
+
+
+# LINK TO GALAXY
+def link_to_galaxy(args:list) -> None:
+    from .link_to_galaxy import link_to_galaxy
+    link_to_galaxy(args.input_file, galaxy=args.galaxy, user=args.user,
+            password=args.password, api_key=args.api_key)
+
+link_parser = subparsers.add_parser('link_to_galaxy', help='''Construct a Galaxy history and link
+        to an existing Tomo workflow representations in a NeXus file.''')
+link_parser.set_defaults(func=link_to_galaxy)
+link_parser.add_argument('-i', '--input_file',
+        type=pathlib.Path,
+        required=True,
+        help='''Full or relative input file path to the existing Tomo workflow representations as 
+                a NeXus file.''')
+link_parser.add_argument('-g', '--galaxy',
+        required=True,
+        help='Target Galaxy instance URL/IP address')
+link_parser.add_argument('-u', '--user',
+        default=None,
+        help='Galaxy user email address')
+link_parser.add_argument('-p', '--password',
+        default=None,
+        help='Password for the Galaxy user')
+link_parser.add_argument('-a', '--api_key',
+        default=None,
+        help='Galaxy admin user API key (required if not defined in the tools list file)')
+
+
+# RUN THE RECONSTRUCTION
+def run_tomo(args:list) -> None:
+    from .run_tomo import run_tomo
+    run_tomo(args.input_file, args.output_file, args.modes, center_file=args.center_file,
+            num_core=args.num_core, output_folder=args.output_folder, save_figs=args.save_figs)
+
+tomo_parser = subparsers.add_parser('run_tomo', help='''Construct and add reconstructed tomography
+        data to an existing Tomo workflow representations in a NeXus file.''')
+tomo_parser.set_defaults(func=run_tomo)
+tomo_parser.add_argument('-i', '--input_file',
+        required=True,
+        type=pathlib.Path,
+        help='''Full or relative input file path containing raw and/or reduced data.''')
+tomo_parser.add_argument('-o', '--output_file',
+        required=True,
+        type=pathlib.Path,
+        help='''Full or relative input file path containing raw and/or reduced data.''')
+tomo_parser.add_argument('-c', '--center_file',
+        type=pathlib.Path,
+        help='''Full or relative input file path containing the rotation axis centers info.''')
+#tomo_parser.add_argument('-f', '--force_overwrite',
+#        action='store_true',
+#        help='''Use this flag to overwrite any existing reduced data.''')
+tomo_parser.add_argument('-n', '--num_core',
+        type=int,
+        default=-1,
+        help='''Specify the number of processors to use.''')
+tomo_parser.add_argument('--output_folder',
+        type=pathlib.Path,
+        default='.',
+        help='Full or relative path to an output folder')
+tomo_parser.add_argument('-s', '--save_figs',
+        choices=['yes', 'no', 'only'],
+        default='no',
+        help='''Specify weather to display ('yes' or 'no'), save ('yes'), or only save ('only').''')
+tomo_parser.add_argument('--reduce_data',
+        dest='modes',
+        const='reduce_data',
+        action='append_const',
+        help='''Use this flag to create and add reduced data to the input file.''')
+tomo_parser.add_argument('--find_center',
+        dest='modes',
+        const='find_center',
+        action='append_const',
+        help='''Use this flag to find and add the calibrated center axis info to the input file.''')
+tomo_parser.add_argument('--reconstruct_data',
+        dest='modes',
+        const='reconstruct_data',
+        action='append_const',
+        help='''Use this flag to create and add reconstructed data data to the input file.''')
+tomo_parser.add_argument('--combine_datas',
+        dest='modes',
+        const='combine_datas',
+        action='append_const',
+        help='''Use this flag to combine reconstructed data data and add to the input file.''')
+
+
+if __name__ == '__main__':
+    args = parser.parse_args(sys.argv[1:])
+
+    # Set log configuration
+    # When logging to file, the stdout log level defaults to WARNING
+    logging_format = '%(asctime)s : %(levelname)s - %(module)s : %(funcName)s - %(message)s'
+    level = logging.getLevelName(args.log_level)
+    if args.log is sys.stdout:
+        logging.basicConfig(format=logging_format, level=level, force=True,
+                handlers=[logging.StreamHandler()])
+    else:
+        if isinstance(args.log, str):
+            logging.basicConfig(filename=f'{args.log}', filemode='w',
+                    format=logging_format, level=level, force=True)
+        elif isinstance(args.log, io.TextIOWrapper):
+            logging.basicConfig(filemode='w', format=logging_format, level=level,
+                    stream=args.log, force=True)
+        else:
+            raise ValueError(f'Invalid argument --log: {args.log}')
+        stream_handler = logging.StreamHandler()
+        logging.getLogger().addHandler(stream_handler)
+        stream_handler.setLevel(logging.WARNING)
+        stream_handler.setFormatter(logging.Formatter(logging_format))
+
+    args.func(args)