Merge pull request #4245 from broadinstitute/empty-family-error

properly populate individual aggregate fields for families with no individuals

seqr/views/apis/project_api.py

@@ -181,6 +181,35 @@ def project_page_data(request, project_guid):
     })
 
 
+FAMILY_INDIVIDUAL_FIELDS = {
+    'caseReviewStatuses': {'agg': ArrayAgg('case_review_status', distinct=True, filter=~Q(case_review_status=''))},
+    'caseReviewStatusLastModified': {'agg': Max('case_review_status_last_modified_date'), 'default': None},
+    'parental_ids': {
+        'agg': ArrayAgg(JSONObject(**{k: k for k in ['id', 'guid', 'father_id', 'mother_id']})),
+        'format': lambda parental_ids, id_guid_map: [
+            {'paternalGuid': id_guid_map.get(p['father_id']), 'maternalGuid': id_guid_map.get(p['mother_id'])}
+            for p in parental_ids if p['father_id'] or p['mother_id']
+        ],
+        'response_key': 'parents',
+    },
+    'metadata_count': {
+        'agg': Count('id', filter=Q(
+            features__0__isnull=False, birth_year__isnull=False,
+            population__isnull=False, proband_relationship__isnull=False,
+        )),
+        'format': lambda metadata_count, *args: bool(metadata_count),
+        'response_key': 'hasRequiredMetadata',
+    },
+}
+
+
+def _get_formatted_value(value, config, *args):
+    value = value or config.get('default', [])
+    if config.get('format'):
+        value = config['format'](value, *args)
+    return value
+
+
 @login_and_policies_required
 def project_families(request, project_guid):
     project = get_project_and_check_permissions(project_guid, request.user)
@@ -197,30 +226,24 @@ def project_families(request, project_guid):
     )
     families_by_id = {f.pop('id'): f for f in families}
 
-    phenotype_priority_families = set(PhenotypePrioritization.objects.filter(
-        individual__family_id__in=families_by_id).values_list('individual__family_id', flat=True).distinct())
-    family_individuals = Individual.objects.filter(family_id__in=families_by_id).values('family_id').annotate(
-        caseReviewStatuses=ArrayAgg('case_review_status', distinct=True, filter=~Q(case_review_status='')),
-        caseReviewStatusLastModified=Max('case_review_status_last_modified_date'),
-        parental_ids=ArrayAgg(JSONObject(**{k: k for k in ['id', 'guid', 'father_id', 'mother_id']})),
-        metadata_count=Count('id', filter=Q(
-            features__0__isnull=False, birth_year__isnull=False,
-            population__isnull=False, proband_relationship__isnull=False,
-        )),
-    )
-    for individual_agg in family_individuals:
-        family_id = individual_agg.pop('family_id')
-        parental_ids = individual_agg.pop('parental_ids')
-        id_guid_map = {i['id']: i['guid'] for i in parental_ids}
-        families_by_id[family_id].update({
+    has_data_families = {
+        'hasPhenotypePrioritization': set(PhenotypePrioritization.objects.filter(
+            individual__family_id__in=families_by_id).values_list('individual__family_id', flat=True).distinct()),
+    }
+
+    family_individual_aggs = {
+        agg.pop('family_id'): agg for agg in Individual.objects.filter(family_id__in=families_by_id).values('family_id').annotate(
+            **{k: v['agg'] for k, v in FAMILY_INDIVIDUAL_FIELDS.items()}
+        )
+    }
+    for family_id, family in families_by_id.items():
+        individual_agg = family_individual_aggs.get(family_id, {})
+        id_guid_map = {i['id']: i['guid'] for i in individual_agg.get('parental_ids', [])}
+        family.update({
             'individualGuids': sorted(id_guid_map.values()),
-            'hasPhenotypePrioritization': family_id in phenotype_priority_families,
-            'hasRequiredMetadata': individual_agg.pop('metadata_count') > 0,
-            'parents': [
-                {'paternalGuid': id_guid_map.get(p['father_id']), 'maternalGuid': id_guid_map.get(p['mother_id'])}
-                for p in parental_ids if p['father_id'] or p['mother_id']
-            ],
-            **individual_agg,
+            **{config.get('response_key', key): _get_formatted_value(individual_agg.get(key), config, id_guid_map)
+               for key, config in FAMILY_INDIVIDUAL_FIELDS.items()},
+            **{key: family_id in data_families for key, data_families in has_data_families.items()},
         })
 
     response = families_discovery_tags(families, project=project)

seqr/views/apis/project_api_tests.py

@@ -380,27 +380,36 @@ def test_project_families(self):
 
         family_1 = response_json['familiesByGuid']['F000001_1']
         family_3 = response_json['familiesByGuid']['F000003_3']
+        empty_family = response_json['familiesByGuid']['F000013_13']
         family_fields = {
             'individualGuids', 'discoveryTags', 'caseReviewStatuses', 'caseReviewStatusLastModified', 'hasRequiredMetadata',
             'parents', 'hasPhenotypePrioritization',
         }
         family_fields.update(SUMMARY_FAMILY_FIELDS)
         self.assertSetEqual(set(family_1.keys()), family_fields)
+        self.assertSetEqual(set(empty_family.keys()), family_fields)
 
         self.assertEqual(len(family_1['individualGuids']), 3)
         self.assertEqual(len(family_3['individualGuids']), 1)
+        self.assertEqual(len(empty_family['individualGuids']), 0)
         self.assertListEqual(family_1['caseReviewStatuses'], ['A', 'I', 'U'])
         self.assertListEqual(family_3['caseReviewStatuses'], [])
+        self.assertListEqual(empty_family['caseReviewStatuses'], [])
         self.assertEqual(family_1['caseReviewStatusLastModified'], '2017-03-12T22:34:49.964Z')
         self.assertIsNone(family_3['caseReviewStatusLastModified'])
+        self.assertIsNone(empty_family['caseReviewStatusLastModified'])
         self.assertTrue(family_1['hasRequiredMetadata'])
         self.assertFalse(family_3['hasRequiredMetadata'])
+        self.assertFalse(empty_family['hasRequiredMetadata'])
         self.assertListEqual(family_1['parents'], [{'maternalGuid': 'I000003_na19679', 'paternalGuid': 'I000002_na19678'}])
         self.assertListEqual(family_3['parents'], [])
+        self.assertListEqual(empty_family['parents'], [])
         self.assertEqual(family_1['hasPhenotypePrioritization'], True)
         self.assertFalse(family_3['hasPhenotypePrioritization'], False)
+        self.assertFalse(empty_family['hasPhenotypePrioritization'], False)
 
         self.assertListEqual(family_3['discoveryTags'], [])
+        self.assertListEqual(empty_family['discoveryTags'], [])
         self.assertSetEqual({tag['variantGuid'] for tag in family_1['discoveryTags']}, {'SV0000001_2103343353_r0390_100'})
         self.assertSetEqual(
             {tag['variantGuid'] for tag in response_json['familiesByGuid']['F000002_2']['discoveryTags']},