Catch and reissue fluview imputation errors as warnings to avoid failures (#1686)

* catch and reissue imputation errors as warnings to avoid failures

* tests to look for warnings instead

* warn() goes to stderr instead of stdout, so print all messages

* drop warn import

Author: nmdefries

src/acquisition/fluview/impute_missing_values.py

@@ -293,7 +293,11 @@ def impute_missing_values(database, test_mode=False):
             known_values["pr"] = (0, 0, 0)
 
         # get the imputation matrix and lists of known and unknown locations
-        F, known, unknown = get_fusion_parameters(known_values.keys())
+        try:
+            F, known, unknown = get_fusion_parameters(known_values.keys())
+        except StatespaceException as e:
+            print(e)
+            continue
 
         # finally, impute the missing values
         z = np.array([known_values[k] for k in known])

tests/acquisition/fluview/test_impute_missing_values.py

@@ -2,16 +2,17 @@
 
 # standard library
 import argparse
+import sys
 import unittest
 from unittest.mock import MagicMock
+from io import StringIO
 
 # first party
 from delphi.utils.geo.locations import Locations
 from delphi.epidata.acquisition.fluview.impute_missing_values import (
     get_argument_parser,
     get_lag_and_ili,
     impute_missing_values,
-    StatespaceException,
 )
 
 # py3tester coverage target
@@ -87,8 +88,12 @@ def test_impute_missing_values_vipr(self):
         db.get_known_values.return_value = known_data
 
         db.find_missing_rows.return_value = [(201340, 201340)]
-        with self.assertRaises(Exception):
-            impute_missing_values(db, test_mode=True)
+
+        capturedOutput = StringIO()
+        sys.stdout = capturedOutput
+        impute_missing_values(db, test_mode=True)
+        sys.stdout = sys.__stdout__
+        self.assertTrue("system is underdetermined" in capturedOutput.getvalue().split("\n"))
 
         db.find_missing_rows.return_value = [(201339, 201339)]
         impute_missing_values(db, test_mode=True)
@@ -131,5 +136,8 @@ def test_impute_missing_values_underdetermined(self):
         db.find_missing_rows.return_value = [(201740, 201740)]
         db.get_known_values.return_value = known_data
 
-        with self.assertRaises(StatespaceException):
-            impute_missing_values(db, test_mode=True)
+        capturedOutput = StringIO()
+        sys.stdout = capturedOutput
+        impute_missing_values(db, test_mode=True)
+        sys.stdout = sys.__stdout__
+        self.assertTrue("system is underdetermined" in capturedOutput.getvalue().split("\n"))