Merge pull request #5107 from broadinstitute/dev

Dev

Author: hanars

panelapp/pa_locus_list_api_tests.py

@@ -71,6 +71,7 @@ def test_import_all_panels(self):
 
         responses.add(responses.GET, au_panels_p1_url, json=au_panels_p1_json, status=200)
         responses.add(responses.GET, au_panels_p2_url, json=au_panels_p2_json, status=200)
+        responses.add(responses.GET, au_genes_url, status=429)
         responses.add(responses.GET, au_genes_url, json=au_genes_json, status=200)
         responses.add(responses.GET, uk_panels_p1_url, json=uk_panels_p1_json, status=200)
         responses.add(responses.GET, uk_genes_url, json=uk_genes_json, status=200)

panelapp/panelapp_utils.py

@@ -4,6 +4,7 @@
 from django.db import transaction
 from django.utils import timezone
 from tenacity import retry, wait_exponential, stop_after_attempt, retry_if_exception_type
+from time import sleep
 from urllib3.exceptions import MaxRetryError
 
 from panelapp.models import PaLocusList, PaLocusListGene
@@ -17,6 +18,8 @@
 
 REQUEST_TIMEOUT_S = 300
 
+class TooManyRequestsError(Exception):
+    pass
 
 def import_all_panels(user, panel_app_api_url, label=None):
     def _extract_ensembl_id_from_json(raw_gene_json):
@@ -118,12 +121,15 @@ def _get_all_panels(panels_url, all_results):
 
 def _get_all_genes(genes_url: str, results_by_panel_id: dict):
     @retry(
-        retry=retry_if_exception_type(MaxRetryError),
+        retry=retry_if_exception_type((MaxRetryError, TooManyRequestsError)),
         wait=wait_exponential(multiplier=1, min=4, max=10),
         stop=stop_after_attempt(5),
     )
     def _get(url):
         resp = requests.get(url, timeout=REQUEST_TIMEOUT_S)
+        if resp.status_code == 429:
+            sleep(10)
+            raise TooManyRequestsError()
         return resp.json()
 
     resp_json = _get(genes_url)

seqr/management/commands/reload_clinvar_all_variants.py

@@ -123,6 +123,9 @@ def parse_pathogenicity_and_assertions(classified_record_node: xml.etree.Element
     ).replace(
         ', low penetrance',
         '; low penetrance'
+    ).replace(
+        'Likely pathogenic/Likely pathogenic',
+        'Likely pathogenic'
     )
 
     pathogenicity = pathogenicity_string.split(';')[0].strip()

seqr/views/apis/individual_api_tests.py

@@ -245,6 +245,20 @@ def test_edit_individuals(self, mock_pm_group):
         self.assertEqual(response_json['individualsByGuid'][ID_UPDATE_GUID]['individualId'], UPDATED_ID)
         self.assertEqual(response_json['individualsByGuid'][ID_UPDATE_GUID]['maternalId'], 'NA19679')
 
+        response = self.client.post(edit_individuals_url, content_type='application/json', data=json.dumps({
+            'individuals': [{
+                'individualGuid': INDIVIDUAL_GUID,
+                'familyId': '1',
+                'individualId': 'NA19675_1',
+                'paternalId': '',
+            }]
+        }))
+        self.assertEqual(response.status_code, 200)
+        response_json = response.json()
+        self.assertSetEqual({INDIVIDUAL_GUID}, set(response_json['individualsByGuid']))
+        self.assertIsNone(response_json['individualsByGuid'][INDIVIDUAL_GUID]['paternalId'])
+        self.assertEqual(response_json['individualsByGuid'][INDIVIDUAL_GUID]['maternalId'], 'NA19679')
+
         # Test PM permission
         pm_required_edit_individuals_url = reverse(edit_individuals_handler, args=[PM_REQUIRED_PROJECT_GUID])
         response = self.client.post(pm_required_edit_individuals_url, content_type='application/json', data=json.dumps({

seqr/views/utils/individual_utils.py

@@ -143,7 +143,7 @@ def _update_from_record(record, user, families_by_id, individual_lookup, updated
             'mother': record.pop('mother', None),
             'father': record.pop('father', None),
         })
-    elif record.get('maternalId') or record.get('paternalId'):
+    elif record.get('maternalId') is not None or record.get('paternalId') is not None:
         parent_updates.append({
             'individual': individual,
             'maternalId': record.pop('maternalId', None),

seqr/views/utils/json_to_orm_utils.py

@@ -55,10 +55,14 @@ def update_individual_parents(individual, json, user):
 
 def _parse_parent_field(update_json, all_json, individual, parent_key, parent_id_key):
     updated_parent = all_json.get(parent_id_key) if parent_id_key else all_json.get(parent_key)
+    if updated_parent is None:
+        return
     parent = getattr(individual, parent_key, None)
     if parent_id_key:
         parent = parent.individual_id if parent else None
-    if updated_parent != parent:
+    if parent and not updated_parent:
+        update_json[parent_key] = None
+    elif updated_parent != parent:
         if parent_id_key:
             updated_parent = Individual.objects.get(individual_id=updated_parent, family=individual.family) if updated_parent else None
         update_json[parent_key] = updated_parent