LocalCSVCodelistFactory

LocalCSVCodelistFactory allows for the creation of multiple codelists from a single CSV file. Use this class when you have a single CSV file that contains multiple codelists.

To use, create an instance of the class and then call the create_codelist method with the name of the codelist you want to create; this codelist name must be an entry in the name_code_type_column.

Source code in phenex/codelists/codelists.py

class LocalCSVCodelistFactory:
    """
    LocalCSVCodelistFactory allows for the creation of multiple codelists from a single CSV file. Use this class when you have a single CSV file that contains multiple codelists.

    To use, create an instance of the class and then call the `create_codelist` method with the name of the codelist you want to create; this codelist name must be an entry in the name_code_type_column.
    """

    def __init__(
        self,
        path: str,
        name_code_column: str = "code",
        name_codelist_column: str = "codelist",
        name_code_type_column: str = "code_type",
    ) -> None:
        """
        Parameters:
            path: Path to the CSV file.
            name_code_column: The name of the column containing the codes.
            name_codelist_column: The name of the column containing the codelist names.
            name_code_type_column: The name of the column containing the code types.
        """
        self.path = path
        self.name_code_column = name_code_column
        self.name_codelist_column = name_codelist_column
        self.name_code_type_column = name_code_type_column
        try:
            self.df = pd.read_csv(path)
        except:
            raise ValueError("Could not read the file at the given path.")

    def get_codelist(self, name: str) -> Codelist:
        try:
            df_codelist = self.df[self.df[self.name_codelist_column] == name]
            code_dict = (
                df_codelist.groupby(self.name_code_type_column)[self.name_code_column]
                .apply(list)
                .to_dict()
            )
            return Codelist(name=name, codelist=code_dict)
        except:
            raise ValueError("Could not find the codelist with the given name.")

__init__(path, name_code_column='code', name_codelist_column='codelist', name_code_type_column='code_type')

Parameters:

Name	Type	Description	Default
path	str	Path to the CSV file.	required
name_code_column	str	The name of the column containing the codes.	'code'
name_codelist_column	str	The name of the column containing the codelist names.	'codelist'
name_code_type_column	str	The name of the column containing the code types.	'code_type'

Source code in phenex/codelists/codelists.py

def __init__(
    self,
    path: str,
    name_code_column: str = "code",
    name_codelist_column: str = "codelist",
    name_code_type_column: str = "code_type",
) -> None:
    """
    Parameters:
        path: Path to the CSV file.
        name_code_column: The name of the column containing the codes.
        name_codelist_column: The name of the column containing the codelist names.
        name_code_type_column: The name of the column containing the code types.
    """
    self.path = path
    self.name_code_column = name_code_column
    self.name_codelist_column = name_codelist_column
    self.name_code_type_column = name_code_type_column
    try:
        self.df = pd.read_csv(path)
    except:
        raise ValueError("Could not read the file at the given path.")