Merge pull request #530 from bento-platform/fix/sampled-tissue-autoco…

…mplete

fix(phenopackets): sampled tissue autocomplete crash w/ None + no q

chord_metadata_service/phenopackets/autocomplete_views.py

@@ -56,7 +56,13 @@ def get_result_label(self, item):
         return item.sampled_tissue["label"]
 
     def get_queryset(self):
-        qs = Biosample.objects.all().distinct("sampled_tissue__label").order_by("sampled_tissue__label")
+        qs = (
+            Biosample.objects
+            .filter(sampled_tissue__isnull=False)
+            .distinct("sampled_tissue__label")
+            .order_by("sampled_tissue__label")
+        )
+
         if self.q:
             # looks for a matching string everywhere in sampled_tissue label field
             qs = qs.filter(sampled_tissue__label__icontains=self.q)

chord_metadata_service/phenopackets/tests/constants.py

@@ -439,14 +439,19 @@ def valid_biosample_1(individual, procedure=VALID_PROCEDURE_1):
     )
 
 
-def valid_biosample_2(individual, procedure=VALID_PROCEDURE_2):
+def valid_biosample_2(individual, procedure=VALID_PROCEDURE_2, **kwargs):
+    if "sampled_tissue" in kwargs:
+        sampled_tissue = kwargs["sampled_tissue"]
+    else:
+        sampled_tissue = {
+            "id": "UBERON_0001256",
+            "label": "urinary bladder"
+        }
+
     return dict(
         id='biosample_id:2',
         individual=individual,
-        sampled_tissue={
-            "id": "UBERON_0001256",
-            "label": "urinary bladder"
-        },
+        sampled_tissue=sampled_tissue,
         description='This is a test biosample.',
         taxonomy={
             "id": "NCBITaxon:9606",

chord_metadata_service/phenopackets/tests/test_autocomplete.py

@@ -51,6 +51,12 @@ def setUp(self):
         self.biosample_1 = m.Biosample.objects.create(**c.valid_biosample_1(self.individual))
         self.biosample_2 = m.Biosample.objects.create(**c.valid_biosample_2(self.individual))
 
+    def test_autocomplete_response_no_q(self):
+        response = self.client.get('/api/biosample_sampled_tissue_autocomplete')
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        response_data = response.json()
+        self.assertEqual(len(response_data["results"]), 2)
+
     def test_autocomplete_response(self):
         response = self.client.get('/api/biosample_sampled_tissue_autocomplete', {'q': 'bladder'})
         self.assertEqual(response.status_code, status.HTTP_200_OK)
@@ -62,3 +68,26 @@ def test_autocomplete_response_2(self):
         self.assertEqual(response.status_code, status.HTTP_200_OK)
         response_data = response.json()
         self.assertEqual(len(response_data["results"]), 1)
+
+
+class BiosapleSampledTissueAutocompleteWithNoneTest(APITestCase):
+    """ Test module for sampled tissue label autocomplete with None present for sampled tissue. """
+
+    def setUp(self):
+        self.individual = m.Individual.objects.create(**c.VALID_INDIVIDUAL_1)
+        self.biosample_1 = m.Biosample.objects.create(**c.valid_biosample_1(self.individual))
+        self.biosample_2 = m.Biosample.objects.create(**c.valid_biosample_2(self.individual, sampled_tissue=None))
+
+    def test_autocomplete_response_no_q(self):
+        # no q set used to trigger an error, since it was assumed sampled_tissue would be set; this is a regression test
+        # for that case.
+        response = self.client.get('/api/biosample_sampled_tissue_autocomplete')
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        response_data = response.json()
+        self.assertEqual(len(response_data["results"]), 1)
+
+    def test_autocomplete_response(self):
+        response = self.client.get('/api/biosample_sampled_tissue_autocomplete', {'q': 'bladder'})
+        self.assertEqual(response.status_code, status.HTTP_200_OK)
+        response_data = response.json()
+        self.assertEqual(len(response_data["results"]), 1)