catch and reissue imputation errors as warnings to avoid failures

Author: nmdefries

src/acquisition/fluview/impute_missing_values.py

@@ -51,13 +51,16 @@
 # third party
 import mysql.connector
 import numpy as np
+from warnings import warn
 
 # first party
 import delphi.operations.secrets as secrets
 from delphi.utils.epiweek import delta_epiweeks
 from delphi.utils.geo.locations import Locations
 
 
+UNDERDETERMINED_MSG = "system is underdetermined"
+
 class Database:
     """Database wrapper and abstraction layer."""
 
@@ -107,14 +110,7 @@ class Sql:
         # epiweek.
         get_known_values = """
         SELECT
-          `region`, `num_ili`, `num_patients`, `num_providers`,
-          -- TODO
-          -- `num_age_0`,
-          -- `num_age_1`,
-          -- `num_age_2`,
-          -- `num_age_3`,
-          -- `num_age_4`,
-          -- `num_age_5`
+          `region`, `num_ili`, `num_patients`, `num_providers`
         FROM
           `fluview`
         WHERE
@@ -181,24 +177,8 @@ def get_known_values(self, issue, epiweek):
 
         self.cur.execute(Database.Sql.get_known_values, (issue, epiweek))
         return {
-            loc: (n_ili, n_pat, n_prov,
-                ## TODO
-                # num_age_0,
-                # num_age_1,
-                # num_age_2,
-                # num_age_3,
-                # num_age_4,
-                # num_age_5,
-            )
-            for (loc, n_ili, n_pat, n_prov,
-                ## TODO
-                # num_age_0,
-                # num_age_1,
-                # num_age_2,
-                # num_age_3,
-                # num_age_4,
-                # num_age_5,
-            )
+            loc: (n_ili, n_pat, n_prov,)
+            for (loc, n_ili, n_pat, n_prov,)
             in self.cur
         }
 
@@ -267,7 +247,7 @@ def get_fusion_parameters(known_locations):
     H = graph[is_known, :]
     W = graph[is_unknown, :]
     if np.linalg.matrix_rank(H) != len(atoms):
-        raise StatespaceException("system is underdetermined")
+        raise StatespaceException(UNDERDETERMINED_MSG)
 
     HtH = np.dot(H.T, H)
     HtH_inv = np.linalg.inv(HtH)
@@ -320,7 +300,15 @@ 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:
+            message = str(e)
+            if message == UNDERDETERMINED_MSG:
+                warn(message)
+            else:
+                print(message)
+            continue
 
         # finally, impute the missing values
         z = np.array([known_values[k] for k in known])