Consider XXXX-XX-XX as missing date

Previously, this was considered an ambiguous date with a range of
'[0001-01-01, present]'. That may be somewhat correct, but it has the
side effect of passing min/max date filters. Other missing dates such as
empty string are dropped by those date filters, and it seems more
reasonable to consider XXXX-XX-XX the same way.

Author: victorlin

augur/dates/__init__.py

@@ -161,6 +161,12 @@ 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$')
+"""
+Matches an Augur-style ambiguous date with all parts masked.
+This only supports YYYY-MM-DD format.
+"""
+
 RE_DATE_RANGE = re.compile(r'^\d{4}-\d{2}-\d{2}/\d{4}-\d{2}-\d{2}$')
 """
 Matches a date range in YYYY-MM-DD/YYYY-MM-DD format.
@@ -171,6 +177,10 @@ def is_date_ambiguous(date, ambiguous_by):
 def get_numerical_date_from_value(value, fmt, min_max_year=None) -> Union[float, Tuple[float, float], None]:
     value = str(value)
 
+    # Check if value is a missing date.
+    if RE_AUGUR_MISSING_DATE.match(value):
+        return None
+
     # Check if value is an exact date in the specified format (fmt).
     try:
         return date_to_numeric(datetime.datetime.strptime(value, fmt))

tests/functional/filter/cram/filter-missing-date.t

@@ -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]