From 2b58a3b50c74c956678a21fc61909c8a13fb1098 Mon Sep 17 00:00:00 2001
From: AndiMajore <andi.majore@googlemail.com>
Date: Mon, 5 Dec 2022 10:51:49 +0100
Subject: [PATCH] added env variable to toggle startup update
Former-commit-id: da8017732756d3bd9956f1da010b3187b34c4d16 [formerly ea203bffa93fcb1941bc3ceb7221bcb85b5dd4e8]
Former-commit-id: 57f29f748fe0ecb1b857be59a827eab886e2c0d8
---
docker-django.env | 3 ++-
docker-django.env.dev | 3 ++-
drugstone/management/commands/populate_db.py | 22 ++++++++++----------
drugstone/settings/celery_schedule.py | 2 +-
scripts/docker-entrypoint.sh | 10 ++++++---
5 files changed, 23 insertions(+), 17 deletions(-)
diff --git a/docker-django.env b/docker-django.env
index 9bf4bf3..defd3e7 100755
--- a/docker-django.env
+++ b/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
\ No newline at end of file
+CELERY_BROKER_URL=redis://redis:6379/0
+DB_UPDATE_ON_START=0
\ No newline at end of file
diff --git a/docker-django.env.dev b/docker-django.env.dev
index 1f3d65d..91d6c04 100644
--- a/docker-django.env.dev
+++ b/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
\ No newline at end of file
+GT_THREADS=2
+DB_UPDATE_ON_START=0
\ No newline at end of file
diff --git a/drugstone/management/commands/populate_db.py b/drugstone/management/commands/populate_db.py
index 497b3d1..690ec3b 100755
--- a/drugstone/management/commands/populate_db.py
+++ b/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
diff --git a/drugstone/settings/celery_schedule.py b/drugstone/settings/celery_schedule.py
index d33a3a0..6c06894 100644
--- a/drugstone/settings/celery_schedule.py
+++ b/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'),
},
}
diff --git a/scripts/docker-entrypoint.sh b/scripts/docker-entrypoint.sh
index 43bf32d..8ce3250 100755
--- a/scripts/docker-entrypoint.sh
+++ b/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"
--
GitLab