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Consider XXXX-XX-XX as missing date #1913

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Consider XXXX-XX-XX as missing date #1913

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victorlin Oct 22, 2025
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Consider XXXX-XX-XX as missing date
victorlin Oct 22, 2025
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21 changes: 15 additions & 6 deletions augur/dates/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -161,28 +161,37 @@ def is_date_ambiguous(date, ambiguous_by):
Note that this can support any date format, not just YYYY-MM-DD.
"""

RE_AUGUR_MISSING_DATE = re.compile(r'^XXXX-XX-XX$')
"""
Matches an Augur-style ambiguous date with all parts masked.
This only supports YYYY-MM-DD format.
"""

@cache
def get_numerical_date_from_value(value, fmt, min_max_year=None) -> Union[float, Tuple[float, float], None]:
value = str(value)

# 1. Check if value is an exact date in the specified format (fmt).
# Check if value is a missing date.
if RE_AUGUR_MISSING_DATE.match(value):
return None
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@victorlin victorlin Oct 22, 2025

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Error from wnv check:

TypeError: unsupported operand type(s) for /: 'NoneType' and 'int'

This is coming from augur frequencies. I'll run locally to investigate.


# Check if value is an exact date in the specified format (fmt).
try:
return date_to_numeric(datetime.datetime.strptime(value, fmt))
except:
pass

# 2. Check if value is an ambiguous date in the specified format (fmt).

# Check if value is an ambiguous date in the specified format (fmt).
if RE_AUGUR_AMBIGUOUS_DATE.match(value):
start, end = AmbiguousDate(value, fmt=fmt).range(min_max_year=min_max_year)
return (date_to_numeric(start), date_to_numeric(end))

# 3. Check formats that are always supported.

# Check if value is a numeric date.
if RE_NUMERIC_DATE.match(value):
return float(value)

# Check if value is an ISO 8601-like date.

if RE_YEAR_ONLY.match(value):
start, end = AmbiguousDate(f"{value}-XX-XX", fmt="%Y-%m-%d").range(min_max_year=min_max_year)
return (date_to_numeric(start), date_to_numeric(end))
Expand All @@ -200,7 +209,7 @@ def get_numerical_date_from_value(value, fmt, min_max_year=None) -> Union[float,
# closest in-bound value.
raise InvalidDate(value, str(error)) from error

# 4. Return none (silent error) if the date does not match any of the checked formats.
# Return none (silent error) if the date does not match any of the checked formats.

return None

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31 changes: 31 additions & 0 deletions tests/functional/filter/cram/filter-missing-date.t
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Original file line number Diff line number Diff line change
@@ -0,0 +1,31 @@
Setup

$ source "$TESTDIR"/_setup.sh

Create metadata TSV file with two date values that should be functionally equivalent.

$ cat >metadata.tsv <<~~
> strain date
> SEQ_1
> SEQ_2 XXXX-XX-XX
> ~~

BUG: SEQ_2 passes for --min-date and --max-date.

$ ${AUGUR} filter \
> --metadata metadata.tsv \
> --min-date 2025 \
> --output-strains filtered_strains.txt
2 strains were dropped during filtering
2 were dropped because they were earlier than 2025.0 or missing a date
ERROR: All samples have been dropped! Check filter rules and metadata file format.
[2]

$ ${AUGUR} filter \
> --metadata metadata.tsv \
> --max-date 2025 \
> --output-strains filtered_strains.txt
2 strains were dropped during filtering
2 were dropped because they were later than 2025.0 or missing a date
ERROR: All samples have been dropped! Check filter rules and metadata file format.
[2]
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