Merge pull request #313 from bento-platform/patch/type-exception

Add type exception for public overview count

chord_metadata_service/package.cfg

@@ -1,4 +1,4 @@
 [package]
 name = katsu
-version = 2.9.1
+version = 2.9.2
 authors = Ksenia Zaytseva, David Lougheed, Simon Chénard, Romain Grégoire

chord_metadata_service/restapi/api_views.py

@@ -1,4 +1,6 @@
 import math
+import logging
+
 from collections import Counter
 from django.conf import settings
 from django.views.decorators.cache import cache_page
@@ -17,6 +19,10 @@
 from chord_metadata_service.mcode.api_views import MCODEPACKET_PREFETCH, MCODEPACKET_SELECT
 
 
+logger = logging.getLogger("restapi_api_views")
+logger.setLevel(logging.INFO)
+
+
 @api_view()
 @permission_classes([AllowAny])
 def service_info(_request):
@@ -339,7 +345,12 @@ def public_overview(_request):
                         # add new Counter()
                         if key not in extra_properties:
                             extra_properties[key] = Counter()
-                        extra_properties[key].update((individual.extra_properties[key],))
+                        try:
+                            extra_properties[key].update((individual.extra_properties[key],))
+                        except TypeError:
+                            logger.error(f"The extra_properties {key} value is not of type string or number.")
+                            pass
+
                         individuals_extra_properties[key] = dict(extra_properties[key])
         # Experiments
         for experiment in experiments:
@@ -367,13 +378,14 @@ def public_overview(_request):
                         if "bin_size" in settings.CONFIG_FIELDS["extra_properties"][key] else None
                     # retrieve the values from extra_properties counter
                     values = individuals_extra_properties[key]
-                    kwargs = dict(values=values, bin_size=field_bin_size)
-                    # sort into bins and remove numeric values where count <= threshold
-                    extra_prop_values_in_bins = sort_numeric_values_into_bins(
-                        **{k: v for k, v in kwargs.items() if v is not None}
-                    )
-                    # rewrite with sorted values
-                    individuals_extra_properties[key] = extra_prop_values_in_bins
+                    if values:
+                        kwargs = dict(values=values, bin_size=field_bin_size)
+                        # sort into bins and remove numeric values where count <= threshold
+                        extra_prop_values_in_bins = sort_numeric_values_into_bins(
+                            **{k: v for k, v in kwargs.items() if v is not None}
+                        )
+                        # rewrite with sorted values
+                        individuals_extra_properties[key] = extra_prop_values_in_bins
                     # add missing value count
                     individuals_extra_properties[key][missing] = len(individuals_set) - sum(v for v in value.values())
                 else:

chord_metadata_service/restapi/tests/constants.py

@@ -1,3 +1,6 @@
+from copy import deepcopy
+
+
 INVALID_FHIR_BUNDLE_1 = {
     "resourceType": "NotBundle",
     "entry": [
@@ -209,6 +212,40 @@
 VALID_INDIVIDUALS = [VALID_INDIVIDUAL_1, VALID_INDIVIDUAL_2, VALID_INDIVIDUAL_3, VALID_INDIVIDUAL_4,
                      VALID_INDIVIDUAL_5, VALID_INDIVIDUAL_6, VALID_INDIVIDUAL_7, VALID_INDIVIDUAL_8]
 
+
+extra_properties_with_list = {
+        "smoking": "Former smoker",
+        "covidstatus": "Positive",
+        "death_dc": "Alive",
+        "mobility": "I have slight problems in walking about",
+        "date_of_consent": "2021-03-03",
+        "lab_test_result_value": 699.86,
+        "baseline_creatinine": [100, 120]
+    }
+
+extra_properties_with_dict = {
+        "smoking": "Former smoker",
+        "covidstatus": "Positive",
+        "death_dc": "Alive",
+        "mobility": "I have slight problems in walking about",
+        "date_of_consent": "2021-03-03",
+        "lab_test_result_value": 699.86,
+        "baseline_creatinine": {
+            "test_key_1": 120,
+            "test_key_2": "test_value_2"
+        }
+    }
+
+
+INDIVIDUALS_NOT_ACCEPTED_DATA_TYPES_LIST = [
+    {**item, "extra_properties": extra_properties_with_list} for item in deepcopy(VALID_INDIVIDUALS)
+]
+
+INDIVIDUALS_NOT_ACCEPTED_DATA_TYPES_DICT = [
+    {**item, "extra_properties": extra_properties_with_dict} for item in deepcopy(VALID_INDIVIDUALS)
+]
+
+
 CONFIG_FIELDS_TEST = {
     "sex": {
         "type": "string",

chord_metadata_service/restapi/tests/test_api.py

@@ -1,4 +1,5 @@
 from copy import deepcopy
+
 from django.conf import settings
 from django.urls import reverse
 from django.test import override_settings
@@ -12,9 +13,13 @@
 from chord_metadata_service.experiments.tests import constants as exp_c
 from chord_metadata_service.mcode import models as mcode_m
 from chord_metadata_service.mcode.tests import constants as mcode_c
-from .constants import CONFIG_FIELDS_TEST
 
-from .constants import VALID_INDIVIDUALS
+from .constants import (
+    CONFIG_FIELDS_TEST,
+    VALID_INDIVIDUALS,
+    INDIVIDUALS_NOT_ACCEPTED_DATA_TYPES_LIST,
+    INDIVIDUALS_NOT_ACCEPTED_DATA_TYPES_DICT
+)
 
 
 class ServiceInfoTest(APITestCase):
@@ -227,3 +232,48 @@ def test_overview_response_no_config(self):
         response_obj = response.json()
         self.assertIsInstance(response_obj, dict)
         self.assertEqual(response_obj, settings.NO_PUBLIC_DATA_AVAILABLE)
+
+
+class PublicOverviewNotSupportedDataTypesListTest(APITestCase):
+    # individuals (count 8)
+    def setUp(self) -> None:
+        # create individuals including those who have not accepted data types
+        for ind in INDIVIDUALS_NOT_ACCEPTED_DATA_TYPES_LIST:
+            ph_m.Individual.objects.create(**ind)
+
+    @override_settings(CONFIG_FIELDS=CONFIG_FIELDS_TEST)
+    def test_overview_response(self):
+        # test overview response with passing TypeError exception
+        response = self.client.get('/api/public_overview')
+        response_obj = response.json()
+        print(response_obj)
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertIsInstance(response_obj, dict)
+        # the field name is present, but the keys are not (except 'missing')
+        self.assertIn("baseline_creatinine", response_obj["extra_properties"])
+        self.assertIn("missing", response_obj["extra_properties"]["baseline_creatinine"])
+        self.assertEqual(8, response_obj["extra_properties"]["baseline_creatinine"]["missing"])
+        # if we add support for an array values for the public_overview
+        # then this assertion will fail, so far there is no support for it
+        self.assertNotIn(100, response_obj["extra_properties"]["baseline_creatinine"])
+
+
+class PublicOverviewNotSupportedDataTypesDictTest(APITestCase):
+    # individuals (count 8)
+    def setUp(self) -> None:
+        # create individuals including those who have not accepted data types
+        for ind in INDIVIDUALS_NOT_ACCEPTED_DATA_TYPES_DICT:
+            ph_m.Individual.objects.create(**ind)
+
+    @override_settings(CONFIG_FIELDS=CONFIG_FIELDS_TEST)
+    def test_overview_response(self):
+        # test overview response with passing TypeError exception
+        response = self.client.get('/api/public_overview')
+        response_obj = response.json()
+        print(response_obj)
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        self.assertIsInstance(response_obj, dict)
+        # the field name is present, but the keys are not (except 'missing')
+        self.assertIn("baseline_creatinine", response_obj["extra_properties"])
+        self.assertIn("missing", response_obj["extra_properties"]["baseline_creatinine"])
+        self.assertEqual(8, response_obj["extra_properties"]["baseline_creatinine"]["missing"])