fix problems after merging fastapi and cohort_year

app.py

@@ -7,6 +7,7 @@
 import os
 from time import strftime
 from typing import Any
+from jsonschema import ValidationError
 
 from fastapi import FastAPI, Request
 from fastapi.encoders import jsonable_encoder
@@ -114,9 +115,13 @@ def wrapper(*args, request=None, **kwargs):
         # run func, logging errors
         try:
             return_value = func(*args, **kwargs)
+
+        except ValidationError as err:
+            LOGGER.exception(err)
+            return_value = {"return value": e.message}
         except Exception as err:
             LOGGER.exception(err)
-            raise err
+            return_value = {"return value": str(err)}
 
         # return tabular data, if requested
         if request.headers["accept"] == "text/tabular":

dbutils.py

@@ -30,8 +30,6 @@ def create_indices():
     itrunc = 0
     def truncate(a, length=63):
         logger.info("creating index " + a)
-        sys.stdout.flush()
-        sys.stderr.flush()
         nonlocal itrunc
         prefix = "index" + str(itrunc)
         itrunc += 1

features/model.py

@@ -437,7 +437,7 @@ def select_feature_matrix(conn, table_name, year, cohort_features, cohort_year,
         yb = feature_b_norm["year"]
 
         table, table_matrices = generate_tables_from_features(table_name, cohort_features_norm, cohort_year, [(ka, ya), (kb, yb)])
-        
+
         selections = [
             case_select2(table_matrices[yb], table_matrices[ya], kb, vb, ka, va, table_name=table_name) for vb, va in product(vbs, vas)
         ] + [
@@ -567,7 +567,7 @@ def select_feature_count(conn, table_name, year, cohort_features, cohort_year, f
 
 
 def get_feature_levels(conn, table, year, feature):
-    s = select([table.c[feature]]).where(table.c.year == year).distinct().order_by(table.c[feature])
+    s = select([table.c[feature]]).where(table.c.year == year).where(table.c[feature] != None).distinct().order_by(table.c[feature])
     return list(map(lambda row: row[0], conn.execute((s))))
 
 

sample.py

@@ -1,7 +1,6 @@
 from features import features
 import pandas as pd
 import numpy as np
-from sqlalchemy import Integer, String, Enum
 import sys
 import argparse
 
@@ -18,12 +17,12 @@ def generate_data(table_name, years, n, fn):
             col = f.name
             levels = f.options
             if levels is None:
-                if t == Integer:
+                if t == int:
                     df[col] = np.random.randint(10, size=n)
-                elif t == String:
+                elif t == str:
                     df[col] = [''.join(chr(x + 97) for x in np.random.randint(26, size=2)) for _ in range(n)]
                 else:
-                    print ("error: " + col)
+                    print ("error: " + col + " " + str(t))
             else:
                 df[col] = np.random.choice(levels, size=n)
         if df_all is None:

test/docker-compose.yml

@@ -5,7 +5,7 @@ services:
       context: .
       dockerfile: test/Dockerfile
     image: icees-api-test:0.2.0
-    command: ["-s", "-vv"] # , "test/test_api.py::test_feature_association2_explicit_check_coverage_is_full"]
+    command: ["-s", "-vv"] # , "test/test_api.py::test_cohort_dictionary_explicit_tabular"]
     environment:
       WAIT: 60
     depends_on:

test/test_api.py

@@ -905,7 +905,7 @@ def test_cohort_dictionary_explicit_tabular():
             }
         }]
         resp = requests.post(prot + "://"+host+":"+str(port)+"/{0}/{1}/cohort".format(table, year), json=feature_variables, headers = json_headers, verify = False)
-        resp2 = requests.post(prot + "://"+host+":"+str(port)+"/{0}/{1}/cohort".format(table, year), headers = {"Accept": "text/tabular"}, verify = False)
+        resp2 = requests.post(prot + "://"+host+":"+str(port)+"/{0}/{1}/cohort".format(table, year), json=feature_variables, headers = {"Content-Type": "application/json", "Accept": "text/tabular"}, verify = False)
 
         assert resp2.status_code == 200