docker-compose-django-rdkit

Docker-compose to use compound database easily.

For an explanation of Japanese please see this article.
(日本語の説明はこちらの記事をご覧ください)
Django + RDKit database cartridge のDocker-composeで化合物データベースを作った話

Docker image

db

PostgreSQL with RDKit database cartridge for compound database

• PostsgreSQL (version 9.5)
• RDKit database cartridge (latest)

web

Django with django-rdkit for creating database and using database with Python

• Python (version 3.6.0)
  • Django (version 1.11.7)
  • django-rdkit (version 0.0.5)
  • psycopg2 (version 2.7.3.2)
  • Pillow (version 4.3.0)
  • RDKit (version 2017.03.1)

How to use

1. git clone

git clone https://github.com/yamasakih/docker-compose-django-rdkit
cd docker-compose-django-rdkit

2. docker-compose up

docker-compose up -d

Just to do this.

> $ docker-compose up -d
Creating network "dockercomposedjangordkit_default" with the default driver
Creating volume "dockercomposedjangordkit_dbdata" with default driver
Building web
Step 1/9 : FROM kubor/alpine-rdkit
 ---> e204cd64867b
Step 2/9 : RUN apk add --no-cache git
 ---> Using cache
 ---> 6f0e09b5f69e
Step 3/9 : ENV PYTHONUNBUFFERED 1
 ---> Running in 982f015c0877
 ---> 58d9165cab2a
Removing intermediate container 982f015c0877
Step 4/9 : RUN mkdir /code
 ---> Running in 7b035348c449
 ---> 708259c183bb
Removing intermediate container 7b035348c449
Step 5/9 : WORKDIR /code
 ---> 3b5c539129fa
Removing intermediate container 480ea5c995f3
Step 6/9 : ADD requirements.txt /code/
 ---> 077e3641fbc3
Step 7/9 : RUN pip install -r requirements.txt
 ---> Running in 561f24e020db
Collecting Django==1.11.7 (from -r requirements.txt (line 1))
  Downloading Django-1.11.7-py2.py3-none-any.whl (6.9MB)
Collecting psycopg2==2.7.3.2 (from -r requirements.txt (line 2))
  Downloading psycopg2-2.7.3.2-cp36-cp36m-manylinux1_x86_64.whl (2.7MB)
Collecting pillow==4.3.0 (from -r requirements.txt (line 3))
  Downloading Pillow-4.3.0-cp36-cp36m-manylinux1_x86_64.whl (5.8MB)
Collecting pytz (from Django==1.11.7->-r requirements.txt (line 1))
  Downloading pytz-2017.3-py2.py3-none-any.whl (511kB)
Collecting olefile (from pillow==4.3.0->-r requirements.txt (line 3))
  Downloading olefile-0.44.zip (74kB)
Building wheels for collected packages: olefile
  Running setup.py bdist_wheel for olefile: started
  Running setup.py bdist_wheel for olefile: finished with status 'done'
  Stored in directory: /root/.cache/pip/wheels/20/58/49/cc7bd00345397059149a10b0259ef38b867935ea2ecff99a9b
Successfully built olefile
Installing collected packages: pytz, Django, psycopg2, olefile, pillow
Successfully installed Django-1.11.7 olefile-0.44 pillow-4.3.0 psycopg2-2.7.3.2 pytz-2017.3
 ---> 2cb6ac1ae78d
Removing intermediate container 561f24e020db
Step 8/9 : RUN pip install git+https://github.com/rdkit/django-rdkit.git
 ---> Running in 04157c63862e
Collecting git+https://github.com/rdkit/django-rdkit.git
  Cloning https://github.com/rdkit/django-rdkit.git to /tmp/pip-tju8uk22-build
Installing collected packages: django-rdkit
  Running setup.py install for django-rdkit: started
    Running setup.py install for django-rdkit: finished with status 'done'
Successfully installed django-rdkit-0.0.5
 ---> 75c0a26d8fbe
Removing intermediate container 04157c63862e
Step 9/9 : ADD . /code/
 ---> 7dc60211c63c
Successfully built 7dc60211c63c
Successfully tagged dockercomposedjangordkit_web:latest
WARNING: Image for service web was built because it did not already exist. To rebuild this image you must use `docker-compose build` or `docker-compose up --build`.
Creating dockercomposedjangordkit_db_1 ... 
Creating dockercomposedjangordkit_db_1 ... done
Creating dockercomposedjangordkit_web_1 ... 
Creating dockercomposedjangordkit_web_1 ... done

Please access http://0.0.0.0:8000 or http://localhost:8000, then you can see It worked!

If you can't, please restart docker-compose.

> $ docker-compose stop
Stopping dockercomposedjangordkit_web_1 ... done
Stopping dockercomposedjangordkit_db_1  ... done

> $ docker-compose restart
Restarting dockercomposedjangordkit_web_1 ... done
Restarting dockercomposedjangordkit_db_1  ... done

3. Initialize the database

First, initialize the database by doing migrate.
You can use Django's manage.py command by simply adding docker-compose run web at the beginning.

> $ docker-compose run web ./manage.py migrate
Starting dockercomposedjangordkit_db_1 ... done
Operations to perform:
  Apply all migrations: admin, auth, contenttypes, django_rdkit, sessions
Running migrations:
  Applying contenttypes.0001_initial... OK
  Applying auth.0001_initial... OK
  Applying admin.0001_initial... OK
  Applying admin.0002_logentry_remove_auto_add... OK
  Applying contenttypes.0002_remove_content_type_name... OK
  Applying auth.0002_alter_permission_name_max_length... OK
  Applying auth.0003_alter_user_email_max_length... OK
  Applying auth.0004_alter_user_username_opts... OK
  Applying auth.0005_alter_user_last_login_null... OK
  Applying auth.0006_require_contenttypes_0002... OK
  Applying auth.0007_alter_validators_add_error_messages... OK
  Applying auth.0008_alter_user_username_max_length... OK
  Applying django_rdkit.0001_setup... OK
  Applying sessions.0001_initial... OK```

4. Delete mount volume

This Docker-compose uses named volume.
If it becomes unnecessary, delete it with the following command.

> $ docker volume list
DRIVER              VOLUME NAME
local               dockercomposedjangordkit_dbdata

> $ docker volume rm dockercomposedjangordkit_dbdata 
dockercomposedjangordkit_dbdata

> $ docker volume list                        
DRIVER              VOLUME NAME

For more information, see branch add-mol-table or django-rdkit's tutorial.rst.