BARM_web_server
Baltic sea Reference Metagenome web server
running at https://barm.scilifelab.se
Installation instructions
conda create -n barm_run_env python=3.9
conda activate barm_run_env
git clone https://github.com/EnvGen/BARM_web_server.git
cd BARM_web_server/
conda install psycopg2
pip install -r requirements.txt
Install postgresql locally: https://www.postgresql.org/download/
Log in with default postgres user:
sudo -u postgres /Library/PostgreSQL/13/bin/psql
The first password it asks for is for the sudo. The second password is postgres psql password.
Create database user for local user: sudo -u postgres /Library/PostgreSQL/13/bin/createuser --createdb --password --role=pg_read_server_files $USER
Sudo and then postgres password.
sudo -u postgres /Library/PostgreSQL/13/bin/psql
postgres password.
ALTER ROLE "<username>" WITH PASSWORD '<password>';
\q;
Then create an empty database for unit tests:
python manage.py create_empty --db barm_web_test
Run unittests:
python run_test.py unit
Integration tests exist and should work, but they are a bit difficult to set up so that's not done currently.
Dev note
I always forget this, to log in to psql on local mac:
sudo -u postgres /Library/PostgreSQL/13/bin/psql
The first password it asks for is for the sudo. The second password is postgres psql password.
When creating a new database:
sudo -u postgres /Library/PostgreSQL/13/bin/createdb -U $USER --locale=en_US.utf-8 -E utf-8 -O $USER barm_web_dev -T template0
The first password is for sudo, the second is for user $USER (not postgres) for psql.
Drop stage database and recreate it with new data:
Check the manage.py or the setup_test_database.py files for useful commands.
Export database to the server:
pg_dump dbname >file.sql
scp file.sql username.login@barm.scilifelab.se:~/
On the actual server
Loading in a new databse:
createdb -U db_user -O db_owner barm_web_prod -T template0
psql -U db_user -d barm_web_prod -f file.sql
Shutdown current process:
pkill -f runserver
Start running the server manually:
bash /home/<user>/starta_barm.sh >> /var/log/barm.log 2>&1 &