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186 | def validate_config(config: dict) -> dict:
"""
Validate the yeast rank_response input configuration file.
Args:
config (dict): the configuration dictionary.
Returns:
dict: the validated configuration dictionary.
Raises:
KeyError: if the configuration is invalid due to either a missing
key or an invalid value.
TypeError: if the configuration is invalid due to an invalid type.
FileNotFoundError: if the configuration is invalid due to a missing
"""
# set default values if they are not in the config file
config.setdefault('rank_by_effect', False)
config.setdefault('rank_bin_size', 5)
config.setdefault('normalize', False)
config.setdefault('output_file', 'rank_response.csv')
config.setdefault('compress', False)
# this is used to check if a column is set to 'none' and replace it
# with None. currently set for the expression_{effect/pvalue}_{col/thres}
try:
if not os.path.exists(config['binding_data_path']):
raise FileNotFoundError(f"Binding data file "
f"{config['binding_data_path']} "
"does not exist")
except KeyError as exc:
raise KeyError("Missing key 'binding_data_path' in config") from exc
try:
config['binding_source'] = str(config['binding_source'])
except KeyError as exc:
raise KeyError("Missing key 'binding_source' in config") from exc
try:
if not isinstance(config['binding_identifier_col'], str):
raise TypeError("binding_identifier_col must be a string")
except KeyError as exc:
raise KeyError("Missing key 'binding_identifier_col' in config") \
from exc
try:
if not isinstance(config['binding_effect_col'], str):
raise TypeError("binding_effect_col must be a string")
except KeyError as exc:
raise KeyError("Missing key 'binding_effect_col' in config") \
from exc
try:
if not isinstance(config['binding_pvalue_col'], str):
raise TypeError("binding_pvalue_col must be a string")
except KeyError as exc:
raise KeyError("Missing key 'binding_pvalue_col' in config") \
from exc
try:
if not isinstance(config['rank_by_effect'], bool):
raise TypeError("rank_by_effect must be a boolean")
except KeyError as exc:
raise KeyError("Missing key 'rank_by_effect' in config") \
from exc
try:
if not os.path.exists(config['expression_data_path']):
raise FileNotFoundError(f"Expression data file "
f"{config['expression_data_path']} "
"does not exist")
except KeyError as exc:
raise KeyError("Missing key 'expression_data_path' in config") \
from exc
try:
config['expression_source'] = str(config['expression_source'])
except KeyError as exc:
raise KeyError("Missing key 'expression_source' in config") from exc
try:
if not isinstance(config['expression_identifier_col'], str):
raise TypeError("expression_identifier_col must be a string")
except KeyError as exc:
raise KeyError("Missing key 'expression_identifier_col' in config") \
from exc
try:
if not isinstance(config['expression_effect_col'],
(str, type(None))):
raise TypeError("expression_effect_col must be a string or None")
except KeyError as exc:
raise KeyError("Missing key 'expression_effect_col' in config") \
from exc
try:
if not isinstance(config['expression_effect_thres'],
(int, float, type(None))):
raise TypeError("expression_effect_thres must be numeric or None")
except KeyError as exc:
raise KeyError("Missing key 'expression_effect_thres' in config") \
from exc
for key in ['expression_effect_col', 'expression_effect_thres']:
config[key] = set_none_str_to_none(config[key])
if (config['expression_effect_col'] is None
and config['expression_effect_thres'] is not None)\
or (config['expression_effect_col'] is not None
and config['expression_effect_thres'] is None):
raise KeyError("expression_effect_thres must be None if "
"expression_effect_col is None")
try:
if not isinstance(config['expression_pvalue_col'], (str, type(None))):
raise TypeError("expression_pvalue_col must be a string or None")
except KeyError as exc:
raise KeyError("Missing key 'expression_pvalue_col' in config") \
from exc
try:
if not isinstance(config['expression_pvalue_thres'],
(int, float, type(None))):
raise TypeError("expression_pvalue_thres must be numeric or None")
except KeyError as exc:
raise KeyError("Missing key 'expression_pvalue_thres' in config") \
from exc
for key in ['expression_pvalue_col', 'expression_pvalue_thres']:
config[key] = set_none_str_to_none(config[key])
if (config['expression_pvalue_col'] is None
and config['expression_pvalue_thres'] is not None)\
or (config['expression_pvalue_col'] is not None
and config['expression_pvalue_thres'] is None):
raise KeyError("expression_pvalue_thres must be None if "
"expression_pvalue_col is None")
if config['expression_pvalue_col'] is None \
and config['expression_effect_col'] is None:
raise KeyError("expression_pvalue_col and expression_effect_col "
"cannot both be None")
try:
if not isinstance(config['rank_bin_size'], int):
raise TypeError("rank_bin_size must be an integer")
except KeyError as exc:
raise KeyError("Missing key 'rank_bin_size' in config") \
from exc
try:
if not isinstance(config['normalize'], bool):
raise TypeError("normalize must be a boolean")
except KeyError as exc:
raise KeyError("Missing key 'normalize' in config") \
from exc
try:
if not isinstance(config['output_file'], str):
raise TypeError("output_file must be a string")
if os.path.exists(config['output_file']):
warnings.warn("The output file already exists. "
"It will be overwritten.")
if not config['output_file'].endswith('.csv'):
warnings.warn("We suggest that the output file end with .csv")
except KeyError as exc:
raise KeyError("Missing key 'output_file' in config") \
from exc
try:
if not isinstance(config['compress'], bool):
raise TypeError("compress must be a boolean")
except KeyError as exc:
raise KeyError("Missing key 'compress' in config") \
from exc
return config
|