When the configuration is missing Mikado generates an unrelated error

[ljyanesm]

For example, when running:

mikado pick --source Mikado_permissive_ms --mode=permissive --procs=2 --start-method=spawn --json-conf mikado_config.yaml -od Daijin/5-mikado/pick/permissive_ms -l Daijin/5-mikado/pick/permissive_ms/mikado-permissive_ms.pick.log --loci-out mikado-permissive_ms.loci.gff3 -lv INFO -db Daijin/5-mikado/mikado.db Daijin/5-mikado/mikado_prepared.gtf

Having a missing scoring file in the mikado configuration i.e: /redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml

Mikado generates the following error:

2021-03-26 12:08:38,252 - pick - configurator.py:188 - CRITICAL - load_and_validate_config - MainProcess - The configuration file is invalid. Validation errors:
['No scoring configuration file found. Options: '
 '/redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/sample_data/plant.yaml']
{'name': ['Missing data for required field.'],
 'out_dir': ['Missing data for required field.']}


2021-03-26 12:08:38,252 - pick - configurator.py:191 - CRITICAL - load_and_validate_config - MainProcess - {'name': ['Missing data for required field.'], 'out_dir': ['Missing data for required field.']}
2021-03-26 12:08:38,252 - pick - configurator.py:204 - ERROR - load_and_validate_config - MainProcess - Loading the configuration file failed with error:
{'name': ['Missing data for required field.'], 'out_dir': ['Missing data for required field.']}


Traceback (most recent call last):
  File "/redacted/mikado/Mikado/configuration/configurator.py", line 183, in load_and_validate_config
    config = MikadoConfiguration.Schema().load(config, partial=external)
  File "/python/site-packages/marshmallow_dataclass/__init__.py", line 582, in load
    return clazz(**all_loaded)
  File "<string>", line 14, in __init__
  File "/redacted/mikado/Mikado/configuration/configuration.py", line 76, in __post_init__
    self.check()
  File "/redacted/mikado/Mikado/configuration/configuration.py", line 86, in check
    self.load_scoring(logger=logger)
  File "/redacted/mikado/Mikado/configuration/configuration.py", line 164, in load_scoring
    raise InvalidConfiguration("No scoring configuration file found. Options: {}".format(",".join(options)))
Mikado.exceptions.InvalidConfiguration: 'No scoring configuration file found. Options: /redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/sample_data/plant.yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/redacted/mikado/Mikado/configuration/configurator.py", line 186, in load_and_validate_config
    config = DaijinConfiguration.Schema().load(config, partial=external)
  File "/python/site-packages/marshmallow_dataclass/__init__.py", line 577, in load
    all_loaded = super().load(data, many=many, **kwargs)
  File "/python/site-packages/marshmallow/schema.py", line 727, in load
    return self._do_load(
  File "/python/site-packages/marshmallow/schema.py", line 909, in _do_load
    raise exc
marshmallow.exceptions.ValidationError: {'name': ['Missing data for required field.'], 'out_dir': ['Missing data for required field.']}
Mikado crashed, cause:
'The configuration file passed is invalid. Please double check.'
Traceback (most recent call last):
  File "/redacted/mikado/Mikado/configuration/configurator.py", line 183, in load_and_validate_config
    config = MikadoConfiguration.Schema().load(config, partial=external)
  File "/python/site-packages/marshmallow_dataclass/__init__.py", line 582, in load
    return clazz(**all_loaded)
  File "<string>", line 14, in __init__
  File "/redacted/mikado/Mikado/configuration/configuration.py", line 76, in __post_init__
    self.check()
  File "/redacted/mikado/Mikado/configuration/configuration.py", line 86, in check
    self.load_scoring(logger=logger)
  File "/redacted/mikado/Mikado/configuration/configuration.py", line 164, in load_scoring
    raise InvalidConfiguration("No scoring configuration file found. Options: {}".format(",".join(options)))
Mikado.exceptions.InvalidConfiguration: 'No scoring configuration file found. Options: /redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/Mikado/configuration/scoring_files_not_here/plant.yaml,/redacted/mikado/sample_data/plant.yaml'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/redacted/mikado/Mikado/configuration/configurator.py", line 186, in load_and_validate_config
    config = DaijinConfiguration.Schema().load(config, partial=external)
  File "/python/site-packages/marshmallow_dataclass/__init__.py", line 577, in load
    all_loaded = super().load(data, many=many, **kwargs)
  File "/python/site-packages/marshmallow/schema.py", line 727, in load
    return self._do_load(
  File "/python/site-packages/marshmallow/schema.py", line 909, in _do_load
    raise exc
marshmallow.exceptions.ValidationError: {'name': ['Missing data for required field.'], 'out_dir': ['Missing data for required field.']}

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/redacted/mikado/Mikado/__main__.py", line 68, in main
    args.func(args)
  File "/redacted/mikado/Mikado/subprograms/pick.py", line 248, in pick
    mikado_configuration = load_and_validate_config(args.configuration, logger=logger)
  File "/redacted/mikado/Mikado/configuration/configurator.py", line 205, in load_and_validate_config
    raise InvalidConfiguration("The configuration file passed is invalid. Please double check.")
Mikado.exceptions.InvalidConfiguration: 'The configuration file passed is invalid. Please double check.'

Of which only the first exception relate to the issue at hand, but the final exception listed is unrelated.