Merge pull request #361 from bento-platform/utilspy-cleanup

fix issue with 0-age individuals, use interval notation for public endpoints, and clean up restapi.utils

chord_metadata_service/package.cfg

@@ -1,4 +1,4 @@
 [package]
 name = katsu
-version = 2.15.2
+version = 2.15.3
 authors = Ksenia Zaytseva, David Lougheed, Simon Chénard, Romain Grégoire, Paul Pillot, Son Chau

chord_metadata_service/patients/tests/test_api.py

@@ -420,7 +420,7 @@ def test_public_filtering_extra_properties_invalid_3(self):
     def test_public_filtering_extra_properties_range_1(self):
         # extra_properties range search (both min and max ranges, single value)
         response = self.client.get(
-            '/api/public?lab_test_result_value=200-300'
+            '/api/public?lab_test_result_value=[200, 300)'
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response_obj = response.json()
@@ -433,7 +433,7 @@ def test_public_filtering_extra_properties_range_1(self):
         if db_count <= self.response_threshold:
             self.assertEqual(response_obj, settings.INSUFFICIENT_DATA_AVAILABLE)
         else:
-            self.assertEqual(db_count, response_obj['count'])
+            self.assertEqual(db_count, response_obj["count"])
 
     @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST)
     def test_public_filtering_extra_properties_range_2(self):
@@ -475,7 +475,7 @@ def test_public_filtering_extra_properties_range_3(self):
     def test_public_filtering_extra_properties_wrong_range(self):
         # extra_properties range search, unauthorized range
         response = self.client.get(
-            '/api/public?lab_test_result_value=100-200'
+            '/api/public?lab_test_result_value=[100, 200)'
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response_obj = response.json()
@@ -525,7 +525,7 @@ def test_public_filtering_extra_properties_range_string_2(self):
     def test_public_filtering_extra_properties_multiple_ranges_1(self):
         # extra_properties range search (both min and max range, multiple values)
         response = self.client.get(
-            '/api/public?lab_test_result_value=< 200&baseline_creatinine=100-150'
+            '/api/public?lab_test_result_value=< 200&baseline_creatinine=[100, 150)'
         )
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response_obj = response.json()
@@ -615,7 +615,7 @@ def setUp(self):
     @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST)
     def test_public_filtering_age_range(self):
         # age valid range search
-        response = self.client.get('/api/public?age=20-30')
+        response = self.client.get('/api/public?age=[20, 30)')
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response_obj = response.json()
         db_count = Individual.objects.filter(age_numeric__gte=20, age_numeric__lt=30).count()
@@ -628,23 +628,23 @@ def test_public_filtering_age_range(self):
     @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST)
     def test_public_filtering_age_invalid_range(self):
         # age invalid range max search
-        response = self.client.get('/api/public?age=10-50')
+        response = self.client.get('/api/public?age=[10, 50)')
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response_obj = response.json()
         self.assertEqual(response_obj["code"], 400)
 
     @override_settings(CONFIG_PUBLIC=CONFIG_PUBLIC_TEST_SEARCH_SEX_ONLY)
     def test_public_filtering_age_range_min_and_max_no_age_in_config(self):
         # test with config without age field, returns error
-        response = self.client.get('/api/public?age=20-30')
+        response = self.client.get('/api/public?age=[20, 30)')
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response_obj = response.json()
         self.assertEqual(response_obj["code"], 400)
 
     @override_settings(CONFIG_PUBLIC={})
     def test_public_filtering_age_range_min_and_max_no_config(self):
         # test when config is not provided, returns NO_PUBLIC_DATA_AVAILABLE
-        response = self.client.get('/api/public?age=20-30')
+        response = self.client.get('/api/public?age=[20, 30)')
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response_obj = response.json()
         self.assertIsInstance(response_obj, dict)

chord_metadata_service/restapi/api_views.py

@@ -379,6 +379,8 @@ def public_overview(_request):
             stats = get_range_stats(field_props)
         elif field_props["datatype"] == "date":
             stats = get_date_stats(field_props)
+        else:
+            raise NotImplementedError()
 
         response["fields"][field] = {
             **field_props,

chord_metadata_service/restapi/tests/test_api_utils.py

@@ -24,13 +24,13 @@ def setUp(self):
             }
         }
 
-    def test_config_with_tappers(self):
+    def test_config_with_tapers(self):
         rg = list(labelled_range_generator(self.fp))
         c = self.fp["config"]
         self.assertEqual(rg[0], (c["minimum"], c["taper_left"], f"< {c['taper_left']}"))
         self.assertEqual(rg[-1], (c["taper_right"], c["maximum"], f"≥ {c['taper_right']}"))
         self.assertEqual(rg[1], (c["taper_left"], c["taper_left"] + c["bin_size"],
-                         f"{c['taper_left']}-{c['taper_left'] + c['bin_size']}"))
+                         f"[{c['taper_left']}, {c['taper_left'] + c['bin_size']})"))
 
     def test_config_without_tappers(self):
         self.fp["config"] = {
@@ -39,8 +39,8 @@ def test_config_without_tappers(self):
             "taper_right": 1000
         }
         rg = list(labelled_range_generator(self.fp))
-        self.assertIn("-", rg[0][2])
-        self.assertIn("-", rg[-1][2])
+        self.assertIn("[", rg[0][2])
+        self.assertIn("[", rg[-1][2])
 
     def test_wrong_config_min_max(self):
         self.fp["config"] = {
@@ -81,7 +81,7 @@ def test_custom_bins_config(self):
         rg = list(labelled_range_generator(self.fp))
         self.assertEqual(rg[0], (0, 200, "< 200"))
         self.assertEqual(rg[-1], (2000, None, "≥ 2000"))
-        self.assertEqual(rg[1], (200, 300, "200-300"))
+        self.assertEqual(rg[1], (200, 300, "[200, 300)"))
 
     def test_custom_bins_config_no_open_ended(self):
         c = {
@@ -92,8 +92,8 @@ def test_custom_bins_config_no_open_ended(self):
             }
         }
         rg = list(labelled_range_generator(c))
-        self.assertIn("-", rg[0][2])
-        self.assertIn("-", rg[-1][2])
+        self.assertIn("[", rg[0][2])
+        self.assertIn("[", rg[-1][2])
 
     def test_custom_bins_wrong_min(self):
         c = {