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eds_scikit.biology.utils.config

create_config_from_stats 

create_config_from_stats(concepts_sets: List[ConceptsSet], config_name: str, stats_folder: str = 'Biology_summary')

Generate the configuration file from a statistical summary. It is needed here

PARAMETER DESCRIPTION
concepts_sets

List of concepts-sets to select

TYPE: List[ConceptsSet]

config_name

Name of the folder where the configuration will be saved.

TYPE: str

stats_folder

Name of the statistical summary folder

TYPE: str DEFAULT: 'Biology_summary'

Source code in eds_scikit/biology/utils/config.py 
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def create_config_from_stats(
    concepts_sets: List[ConceptsSet],
    config_name: str,
    stats_folder: str = "Biology_summary",
):
    """Generate the configuration file from a statistical summary. It is needed [here][eds_scikit.biology.cleaning.transform.transform_measurement]

    Parameters
    ----------
    concepts_sets : List[ConceptsSet]
        List of concepts-sets to select
    config_name : str
        Name of the folder where the configuration will be saved.
    stats_folder : str
        Name of the statistical summary folder
    """
    my_custom_config = pd.DataFrame()
    for concepts_set in concepts_sets:
        try:
            stats = pd.read_pickle(
                "{}/{}/measurement_stats.pkl".format(stats_folder, concepts_set.name)
            )
            stats["transformed_unit"] = (
                stats.groupby("unit_source_value")["count"]
                .sum("count")
                .sort_values(ascending=False)
                .index[0]
            )
            stats["concepts_set"] = concepts_set.name
            stats["Action"] = None
            stats["Coefficient"] = None

            my_custom_config = pd.concat([my_custom_config, stats])
        except OSError:
            logger.error(
                "{} has no statistical summary saved in {}",
                concepts_set.name,
                stats_folder,
            )
            pass

    if "care_site_short_name" in my_custom_config.columns:
        # Keep only the row computed from every care site
        my_custom_config = my_custom_config[
            my_custom_config.care_site_short_name == "ALL"
        ]

    os.makedirs(CONFIGS_PATH, exist_ok=True)

    my_custom_config.to_csv("{}/{}.csv".format(CONFIGS_PATH, config_name), index=False)

    register_configs()

list_all_configs 

list_all_configs() -> List[str]

Helper to get the names of all saved biology configurations

RETURNS DESCRIPTION
List[str]

The configurations names
Source code in eds_scikit/biology/utils/config.py 
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def list_all_configs() -> List[str]:
    """
    Helper to get the names of all saved biology configurations

    Returns
    -------
    List[str]
        The configurations names
    """
    registered = list(registry.data.get_all().keys())
    configs = [
        r.split(".")[-1] for r in registered if r.startswith("get_biology_config")
    ]
    return configs