augur.curate.format_dates module

Format date fields to ISO 8601 dates (YYYY-MM-DD).

If the provided --expected-date-formats represent incomplete dates then the incomplete dates are masked with ‘XX’. For example, providing %Y will allow year only dates to be formatted as 2023-XX-XX.

augur.curate.format_dates.directive_is_included(potential_directives, date_format)

Checks if any of the directives in potential_directives is included in date_format string.

If an element within potential_directives is a tuple, then all directives within the tuple must be included in date_format.

Parameters:

potential_directives (set[tuple[str, ...]]) – Set of potential directives to check
date_format (str) – Date format string to check for directives

Returns:

Whether the provided date_format includes any of the potential_directives

Return type:

bool

>>> potential_directives = {('%y', '%b', '%d'), ('%y', '%B', '%d'), ('%y', '%m', '%d'),}
>>> directive_is_included(potential_directives, '%G-%V-%A')
False
>>> directive_is_included(potential_directives, '%y-%m')
False
>>> directive_is_included(potential_directives, '%%y-%m-%d')
False
>>> directive_is_included(potential_directives, '%y-%m-%d')
True
>>> directive_is_included(potential_directives, '%y-%m-%dT%H:%M:%SZ')
True

augur.curate.format_dates.format_date(date_string, expected_formats)

Format date_string to ISO 8601 date (YYYY-MM-DD) by trying to parse it as one of the provided expected_formats.

Parameters:

date_string (str) – Date string to format
expected_formats (list[str]) – List of expected formats for the provided date string

Returns:

Formatted date string or None if the parsing of the date string failed. If date_string is an incomplete date, the date is masked with ‘XX’. Dates without year will be formatted as ‘XXXX-XX-XX’, even if month/day are known. Dates without month will be formatted as ‘YYYY-XX-XX’, even if day is known. Dates without day will be formatted as ‘YYYY-MM-XX’.

Return type:

str or None

>>> expected_formats = ['%Y', '%Y-%m', '%Y-%m-%d', '%Y-%m-%dT%H:%M:%SZ', '%m-%d']
>>> format_date("", expected_formats)
'XXXX-XX-XX'
>>> format_date("  ", expected_formats)
'XXXX-XX-XX'
>>> format_date("01-01", expected_formats)
'XXXX-XX-XX'
>>> format_date("2020", expected_formats)
'2020-XX-XX'
>>> format_date("2020-01", expected_formats)
'2020-01-XX'
>>> format_date("2020-1-15", expected_formats)
'2020-01-15'
>>> format_date("2020-1-1", expected_formats)
'2020-01-01'
>>> format_date("2020-01-15", expected_formats)
'2020-01-15'
>>> format_date("2020-01-15T00:00:00Z", expected_formats)
'2020-01-15'

augur.curate.format_dates.register_parser(parent_subparsers)

augur.curate.format_dates.run(args, records)