sampledb

This is a alpha-stage Django application to store metadata of biological samples and associated high-throughput sequencing datasets.

Data Model

How to run

Build Docker image

docker build -t sampledb .

Run container

MYSECRETKEY="mysecretkey"

docker run -it -p 8020:8010 -e SECRET_KEY="$MYSECRETKEY" -v $(pwd):/opt/app/ sampledb:test

Using conda

Alternatively, you can also create a conda/mamba environment using environment.yml file, activate it and start start-server.sh.

Deployment

Production deployment is done on heroku using a basic dyno with a Mini Postgres database.

The heroku setup was done as follows:

heroku stack:set heroku-22
heroku config:set DISABLE_COLLECTSTATIC=1

heroku config:set DJANGO_SETTINGS_MODULE=sampledb.settings.production


# set dyno
heroku ps:resize web=basic

# set domain

heroku domains:add $MYDOMAIN
heroku certs:auto
heroku config:set DJANGO_ALLOWED_HOSTS=$MYDOMAIN

# activate postgres
heroku addons:create heroku-postgresql

Django settings for deployment are defined in sampledb/settings/production.py and imported by setting the environment variable via

Populate PostgresSQL on Heroku

Create a local PostgresSQL server, initiate tables/app and import data. Then, create a database dump using pg_dump and push to Heroku.

Alternatively, push from local DB dirgit push --set-upstream origin devectly to Heroku.

 heroku pg:push local database:PGUSER=sampledb PGPASSWORD=sampledb@postgres  sampledb pg:push $POSTGRES_URI $POSTGRES_DB_NAME
 pg_dump --user sampledb postgres://localhost > pg_dump.sql
 PGUSER=sampledb PGPASSWORD="sampledb@postgres" && heroku pg:push postgres://localhost/sampledb $POSTGRES_DB_NAME --app sampledb
 

Applying migration on Heroku

Applying database migrations on the Heroku production database