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SexColumnMapper

Mapper for a column that indicates the sex of the individual

Parameters:

Name Type Description Default
male_symbol str

the synbol for males, e.g. "M", "male", "MALE"

 required
female_symbol str

the synbol for females, e.g. "F", "female", "FEMALE"

 required
column_name str

name of the sex column in the original table

 required
other_symbol str

symbol for other sex

 None
unknown_symbol str

symbol for unknown sex

 None
not_provided str

symbol for cases where the sex is not indicated in the original table

 False
Source code in pyphetools/creation/sex_column_mapper.py 
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class SexColumnMapper:
    """
    Mapper for a column that indicates the sex of the individual

    :param male_symbol: the synbol for males, e.g. "M", "male", "MALE"
    :type male_symbol: str
    :param female_symbol: the synbol for females, e.g. "F", "female", "FEMALE"
    :type female_symbol: str
    :param column_name: name of the sex column in the original table
    :type column_name: str
    :param other_symbol: symbol for other sex
    :type other_symbol: str
    :param unknown_symbol: symbol for unknown sex
    :type unknown_symbol: str
    :param not_provided: symbol for cases where the sex is not indicated in the original table
    :type not_provided: str
    """


    def __init__(self, male_symbol, female_symbol, column_name, other_symbol=None, unknown_symbol=None, not_provided=False) -> None:
        """
        Constructor
        """
        self._male_symbol = male_symbol
        self._female_symbol = female_symbol
        self._other_symbol = other_symbol
        self._unknown_symbol = unknown_symbol
        if column_name is None:
            raise ValueError("Must provide non-null column_name argument")
        self._column_name = column_name
        self._not_provided = not_provided
        self._erroneous_input_counter = defaultdict(int)


    def map_cell(self, cell_contents) -> str:
        if self._not_provided:
            return Constants.UNKNOWN_SEX_SYMBOL
        contents = cell_contents.strip()
        if contents == self._female_symbol:
            return Constants.FEMALE_SYMBOL
        elif contents == self._male_symbol:
            return Constants.MALE_SYMBOL
        elif contents == self._other_symbol:
            return Constants.OTHER_SEX_SYMBOL
        elif contents == self._unknown_symbol:
            return Constants.UNKNOWN_SEX_SYMBOL
        else:
            self._erroneous_input_counter[contents] += 1
            return Constants.UNKNOWN_SEX_SYMBOL

    def preview_column(self, df:pd.DataFrame):
        if not isinstance(df, pd.DataFrame):
            raise ValueError("df argument must be pandas DataFrame, but was {type(column)}")
        column = df[self.get_column_name()]
        dlist = []
        for _, value in column.items():
            result = self.map_cell(str(value))
            if result is None:
                dlist.append({"original column contents": value, "sex": "n/a"})
            else:
                dlist.append({"original column contents": value, "sex": result})
        return pd.DataFrame(dlist)

    def get_column_name(self):
        return self._column_name

    def has_error(self):
        return len(self._erroneous_input_counter) > 0

    def error_summary(self):
        items = []
        for k, v in self._erroneous_input_counter.items():
            items.append(f"{k} (n={v})")
        return f"Could not parse the following as sex descriptors: {', '.join(items)}"

    @staticmethod
    def not_provided():
        """Create an object for cases where sex is not indicated.
        """
        return SexColumnMapper(male_symbol=Constants.NOT_PROVIDED,
                            female_symbol=Constants.NOT_PROVIDED,
                            not_provided=True,
                            column_name=Constants.NOT_PROVIDED)

__init__(male_symbol, female_symbol, column_name, other_symbol=None, unknown_symbol=None, not_provided=False)

Constructor

Source code in pyphetools/creation/sex_column_mapper.py 
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def __init__(self, male_symbol, female_symbol, column_name, other_symbol=None, unknown_symbol=None, not_provided=False) -> None:
    """
    Constructor
    """
    self._male_symbol = male_symbol
    self._female_symbol = female_symbol
    self._other_symbol = other_symbol
    self._unknown_symbol = unknown_symbol
    if column_name is None:
        raise ValueError("Must provide non-null column_name argument")
    self._column_name = column_name
    self._not_provided = not_provided
    self._erroneous_input_counter = defaultdict(int)

not_provided() staticmethod

Create an object for cases where sex is not indicated.

Source code in pyphetools/creation/sex_column_mapper.py 
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@staticmethod
def not_provided():
    """Create an object for cases where sex is not indicated.
    """
    return SexColumnMapper(male_symbol=Constants.NOT_PROVIDED,
                        female_symbol=Constants.NOT_PROVIDED,
                        not_provided=True,
                        column_name=Constants.NOT_PROVIDED)