Config parser

InputDirConfig dataclass

Class for defining the fields within the input directory config.

Parameters:

Name	Type	Description	Default
tool	str	Name of the tool implementation (e.g. exomiser/phen2gene)	required
tool_version	str	Version of the tool implementation	required
variant_analysis	bool	Whether to extract prioritised variants from results.	required
gene_analysis	bool	Whether to extract prioritised genes from results.	required
disease_analysis	bool	Whether to extract prioritised diseases from results.	required
tool_specific_configuration_options	Any	Tool specific configurations	required

Source code in src/pheval/config_parser.py

@serde
@dataclass
class InputDirConfig:
    """
    Class for defining the fields within the input directory config.

    Args:
        tool (str): Name of the tool implementation (e.g. exomiser/phen2gene)
        tool_version (str): Version of the tool implementation
        variant_analysis (bool): Whether to extract prioritised variants from results.
        gene_analysis (bool): Whether to extract prioritised genes from results.
        disease_analysis (bool): Whether to extract prioritised diseases from results.
        tool_specific_configuration_options (Any): Tool specific configurations

    """

    tool: str
    tool_version: str
    variant_analysis: bool
    gene_analysis: bool
    disease_analysis: bool
    tool_specific_configuration_options: Any

parse_input_dir_config(input_dir)

Reads the config file.

Source code in src/pheval/config_parser.py

def parse_input_dir_config(input_dir: Path) -> InputDirConfig:
    """Reads the config file."""
    logger.info(f"Parsing config.yaml located in {input_dir}.")
    with open(Path(input_dir).joinpath("config.yaml")) as config_file:
        config = yaml.safe_load(config_file)
    config_file.close()
    _enforce_bool_fields(config)
    return from_yaml(InputDirConfig, yaml.dump(config))