added env variable to toggle startup update

Former-commit-id: da8017732756d3bd9956f1da010b3187b34c4d16 [formerly ea203bffa93fcb1941bc3ceb7221bcb85b5dd4e8]
Former-commit-id: 57f29f748fe0ecb1b857be59a827eab886e2c0d8

docker-django.env

@@ -12,4 +12,5 @@ REDIS_HOST=redis
 REDIS_PORT=6379
 GT_THREADS=16
 DJANGO_SETTINGS_MODULE=drugstone.settings
-CELERY_BROKER_URL=redis://redis:6379/0
+CELERY_BROKER_URL=redis://redis:6379/0
\ No newline at end of file
+DB_UPDATE_ON_START=0
\ No newline at end of file

docker-django.env.dev

@@ -14,4 +14,5 @@ DJANGO_SETTINGS_MODULE=drugstone.settings
 CELERY_BROKER_URL=redis://redis:6379/0
 FLOWER_PORT=8888
 FLOWER_BASIC_AUTH=drugstone:test
-GT_THREADS=2
+GT_THREADS=2
\ No newline at end of file
+DB_UPDATE_ON_START=0
\ No newline at end of file

drugstone/management/commands/populate_db.py

@@ -150,20 +150,20 @@ def populate(kwargs):
         print(f'Populated {n} Expressions.')
 
     if kwargs['protein_drug']:
-        print('Importing PDIs from unlicenced NeDRexDB...')
+        print('Importing PDIs from unlicensed NeDRexDB...')
         n = NedrexImporter.import_drug_target_interactions(importer,
                                                            DatasetLoader.get_drug_target_nedrex(nedrex_api_url_open, False),
                                                            update)
         total_n += n
-        print(f'Imported {n} PDIs from unlicenced NeDRexDB')
+        print(f'Imported {n} PDIs from unlicensed NeDRexDB')
 
-        print('Importing PDIs from licenced NeDRexDB...')
+        print('Importing PDIs from licensed NeDRexDB...')
         n = NedrexImporter.import_drug_target_interactions(importer,
                                                            DatasetLoader.get_drug_target_nedrex(nedrex_api_url_licensed, True),
                                                            update)
         total_n += n
         nedrex_update = True
-        print(f'Imported {n} PDIs from licenced NeDRexDB')
+        print(f'Imported {n} PDIs from licensed NeDRexDB')
 
         print('Populating PDIs from Chembl...')
         n = DataPopulator.populate_pdi_chembl(populator, DatasetLoader.get_drug_target_chembl(), update)
@@ -176,13 +176,13 @@ def populate(kwargs):
         print(f'Populated {n} PDIs from DGIdb.')
 
     if kwargs['protein_disorder']:
-        print('Importing PDis from unlicenced NeDRexDB...')
+        print('Importing PDis from unlicensed NeDRexDB...')
         n = NedrexImporter.import_protein_disorder_associations(importer,
                                                                 DatasetLoader.get_protein_disorder_nedrex(
                                                                     nedrex_api_url_open, False),
                                                                 update)
         total_n += n
-        print(f'Imported {n} PDis from unlicenced NeDRexDB')
+        print(f'Imported {n} PDis from unlicensed NeDRexDB')
 
         print('Importing PDis from licenced NeDRexDB...')
         n = NedrexImporter.import_protein_disorder_associations(importer,
@@ -194,12 +194,12 @@ def populate(kwargs):
         print(f'Imported {n} PDis from licenced NeDRexDB')
 
     if kwargs['drug_disorder']:
-        print('Importing DrDis from unlicenced NeDRexDB...')
+        print('Importing DrDis from unlicensed NeDRexDB...')
         n = NedrexImporter.import_drug_disorder_indications(importer,
                                                             DatasetLoader.get_drug_disorder_nedrex(nedrex_api_url_open, False),
                                                             update)
         total_n += n
-        print(f'Imported {n} DrDis from unlicenced NeDRexDB')
+        print(f'Imported {n} DrDis from unlicensed NeDRexDB')
 
         print('Importing DrDis from licenced NeDRexDB...')
         n = NedrexImporter.import_drug_disorder_indications(importer,
@@ -215,12 +215,12 @@ def populate(kwargs):
         print(f'Populated {n} DrDi associations from DrugBank.')
 
     if kwargs['protein_protein']:
-        print('Importing PPIs from unlicenced NeDRexDB...')
+        print('Importing PPIs from unlicensed NeDRexDB...')
         n = NedrexImporter.import_protein_protein_interactions(importer,
                                                                DatasetLoader.get_ppi_nedrex(nedrex_api_url_open, False),
                                                                update)
         total_n += n
-        print(f'Imported {n} PPIs from unlicended NeDRexDB')
+        print(f'Imported {n} PPIs from unlicensed NeDRexDB')
         print('Importing PPIs from licenced NeDRexDB...')
         n = NedrexImporter.import_protein_protein_interactions(importer,
                                                                DatasetLoader.get_ppi_nedrex(nedrex_api_url_licensed,
@@ -228,7 +228,7 @@ def populate(kwargs):
                                                                update)
         total_n += n
         nedrex_update = True
-        print(f'Imported {n} PPIs from licended NeDRexDB')
+        print(f'Imported {n} PPIs from licensed NeDRexDB')
         print('Populating PPIs from STRING...')
         n = DataPopulator.populate_ppi_string(populator, DatasetLoader.get_ppi_string(), update)
         total_n += n

drugstone/settings/celery_schedule.py

@@ -3,7 +3,7 @@ from celery.schedules import crontab
 CELERY_BEAT_SCHEDULE = {
     'update_db': {
         'task': 'drugstone.tasks.task_update_db_from_nedrex',
-        'schedule': crontab(day_of_week=1, hour=5, minute=0),
+        'schedule': crontab(day_of_week=2, hour=3, minute=0),
         # 'schedule': crontab(minute='*/1'),
     },
 }

scripts/docker-entrypoint.sh

@@ -4,7 +4,11 @@ python3 manage.py makemigrations drugstone
 python3 manage.py migrate
 python3 manage.py createfixtures
 python3 manage.py cleanuptasks
-python3 manage.py populate_db --update -a
-python3 manage.py make_graphs
-
+if [[ -z "$DB_UPDATE_ON_START" ]] || [[ "$DB_UPDATE_ON_START" = "0" ]]
+then
+echo "Update on startup disabled!"
+else
+ python3 manage.py populate_db --update -a
+ python3 manage.py make_graphs
+fi
 /usr/bin/supervisord -c "/etc/supervisor/conf.d/supervisord.conf"