Merge pull request #176 from WengLab-InformaticsResearch/reload_biolink_mappings

Reload biolink mappings

Author: CaseyTa

cohd/biolink_mapper.py

@@ -150,6 +150,7 @@ def prefetch_mappings():
         mapping_rows = cur.fetchall()
         BiolinkConceptMapper._map_omop = {r['omop_id']:r for r in mapping_rows}
         BiolinkConceptMapper._map_biolink = {r['biolink_id']:r for r in mapping_rows if r['preferred']}
+        logging.info('Biolink mappings prefetch completed')
 
     @staticmethod
     def map_to_omop(curies: List[str]) -> Optional[Tuple[Dict[str, Optional[OmopBiolinkMapping]], Dict[str, Optional[NormalizedNode]]]]:

cohd/cohd_trapi_14.py

@@ -37,7 +37,7 @@ class CohdTrapi140(CohdTrapi):
     edge_types_negative = ['biolink:negatively_correlated_with']
     default_negative_predicate = edge_types_negative[0]
 
-    tool_version = f'{CohdTrapi._SERVICE_NAME} 6.3.6'
+    tool_version = f'{CohdTrapi._SERVICE_NAME} 6.3.7'
     schema_version = '1.4.2'
     biolink_version = bm_version
 

cohd/scheduled_tasks.py

@@ -10,17 +10,20 @@ def task_build_cache():
     print('Running scheduled task to build cache')
     BiolinkConceptMapper.build_mappings()
 
+# Schedule a task to update the Biolink Mapping cache nightly (all environments)
+scheduler = BackgroundScheduler()
+scheduler.add_job(func=BiolinkConceptMapper.prefetch_mappings, trigger='cron', hour=6)
 
 # Schedule a task to build the cache every first Saturday of the month (in ITRB-CI and Dev only)
 deployment_env = app.config.get('DEPLOYMENT_ENV', 'dev').lower()
-if deployment_env in ('itrb-ci', 'dev'):
-    scheduler = BackgroundScheduler()
-    scheduler.add_job(func=task_build_cache, trigger='cron', day='1st sat', hour=0)
-    scheduler.start()
+if False:    
+    scheduler.add_job(func=task_build_cache, trigger='cron', day='1st sat', hour=0)    
     logging.info(f'Background task scheduled to build Biolink mappings (env: {deployment_env})')
 else:
     logging.info(f'Background task NOT scheduled to build Biolink mappings (env: {deployment_env})')
 
+scheduler.start()
+
 
 # Registering a shutdown seems to cause UWSGI to have issues shutting down COHD, even with the wait=False option.
 # Since the default job store does not persist jobs anyway, remove this line for now