Merge pull request #3449 from broadinstitute/actually-save-mondo-id

Save mondo ID updates

seqr/views/apis/individual_api_tests.py

@@ -669,8 +669,8 @@ def _send_request_data(data):
         self.assertEqual(len(response_json['familiesByGuid']), 1)
         family_guid = next(iter(response_json['familiesByGuid'].keys()))
         self.assertEqual(response_json['familiesByGuid'][family_guid]['familyId'], 'PED073')
-        self.assertEqual(response_json['familiesByGuid'][family_guid]['codedPhenotype'], None)
-        self.assertEqual(response_json['familiesByGuid'][family_guid]['mondoId'], None)
+        self.assertEqual(response_json['familiesByGuid'][family_guid]['codedPhenotype'], 'Perinatal death')
+        self.assertEqual(response_json['familiesByGuid'][family_guid]['mondoId'],  'MONDO:0100086')
         self.assertSetEqual(set(
             response_json['familiesByGuid'][family_guid]['individualGuids']),
             set(response_json['individualsByGuid'].keys())

seqr/views/utils/individual_utils.py

@@ -6,7 +6,8 @@
 from matchmaker.models import MatchmakerSubmission, MatchmakerResult
 from seqr.models import Sample, IgvSample, Individual, Family, FamilyNote
 from seqr.utils.middleware import ErrorsWarningsException
-from seqr.views.utils.json_to_orm_utils import update_individual_from_json, update_individual_parents, create_model_from_json
+from seqr.views.utils.json_to_orm_utils import update_individual_from_json, update_individual_parents, create_model_from_json, \
+    update_family_from_json
 from seqr.views.utils.orm_to_json_utils import _get_json_for_individuals, _get_json_for_families, get_json_for_family_notes
 from seqr.views.utils.pedigree_info_utils import JsonConstants
 
@@ -143,6 +144,14 @@ def _update_from_record(record, user, families_by_id, individual_lookup, updated
         note = create_model_from_json(FamilyNote, {'note': family_notes, 'note_type': 'C', 'family': family}, user)
         updated_note_ids.append(note.id)
 
+    family_record = {
+        k: record.pop(k) for k in [JsonConstants.CODED_PHENOTYPE_COLUMN, JsonConstants.MONDO_ID_COLUMN] if k in record
+    }
+    if family_record:
+        is_updated = update_family_from_json(family, family_record, user=user)
+        if is_updated:
+            updated_family_ids.add(family.id)
+
     is_updated = update_individual_from_json(individual, record, user=user, allow_unknown_keys=True)
     if is_updated:
         updated_individuals.add(individual)

seqr/views/utils/json_to_orm_utils.py

@@ -21,7 +21,7 @@ def update_family_from_json(family, json, user, allow_unknown_keys=False, immuta
 
     immutable_keys = (immutable_keys or []) + ['pedigree_image', 'assigned_analyst', 'case_review_summary', 'case_review_notes', 'guid']
 
-    update_model_from_json(
+    return update_model_from_json(
         family, json, user=user, allow_unknown_keys=allow_unknown_keys, immutable_keys=immutable_keys,
     )