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Improve error handling in curate apply-geolocation-rules #1905

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Improve error handling in curate apply-geolocation-rules #1905

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18 changes: 16 additions & 2 deletions augur/curate/apply_geolocation_rules.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,8 @@
Applies user curated geolocation rules to the geolocation fields.
"""
from collections import defaultdict
from typing import Optional

from augur.data import as_file
from augur.errors import AugurError
from augur.io.print import print_err
Expand Down Expand Up @@ -76,7 +78,7 @@ def load_geolocation_rules(geolocation_rules_file, case_sensitive):
return geolocation_rules


def get_annotated_geolocation(geolocation_rules, raw_geolocation, case_sensitive, rule_traversal = None):
def get_annotated_geolocation(geolocation_rules, raw_geolocation, case_sensitive, rule_traversal: Optional[list[str]] = None):
"""
Gets the annotated geolocation for the *raw_geolocation* in the provided
*geolocation_rules*.
Expand All @@ -98,7 +100,12 @@ def get_annotated_geolocation(geolocation_rules, raw_geolocation, case_sensitive
# Traverse the geolocation rules based using the rule_traversal values
for field_value in rule_traversal:
# Use lowercase for field_value for case-insensitive rule matching
current_rules = current_rules.get(field_value.lower())
try:
lower_field_value = field_value.lower()
except AttributeError:
print_err(f"WARNING: Could not convert {field_value!r} to lowercase.")
continue
current_rules = current_rules.get(lower_field_value)
Comment on lines +103 to +108
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@victorlin victorlin Oct 18, 2025

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No need for try/except – the case of field_value not being a string should be handled elsewhere (done in this PR).

# If we hit `None`, then we know there are no matching rules, so stop the rule traversal
if current_rules is None:
break
Expand All @@ -111,6 +118,13 @@ def get_annotated_geolocation(geolocation_rules, raw_geolocation, case_sensitive
# so try to traverse the rules with the next target in raw_geolocation
if isinstance(current_rules, dict):
next_traversal_target = raw_geolocation[len(rule_traversal)]
if type(next_traversal_target) is not str:
# Error out if the next traversal target is not a string
raise Exception(
f"Expected the next traversal target to be a string, but got {type(next_traversal_target)} instead. " +
f"Raw geolocation: {raw_geolocation}, rule traversal: {rule_traversal}. " +
f"Current rules: {current_rules}."
Comment on lines +123 to +126
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@victorlin victorlin Oct 18, 2025

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Suggested rewording that points directly to the problem:

ERROR: The 'location' field has a null value. Please use an empty string ""
instead of null for missing values.

Input values:
  region: ''
  country: 'Democratic Republic of the Congo'
  division: 'Tshopo,Yahuma'
  location: null

)
rule_traversal.append(next_traversal_target)
return get_annotated_geolocation(geolocation_rules, raw_geolocation, case_sensitive, rule_traversal)

Expand Down
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