5. Models

This document describes how the Django models.py file for the Chado schema was created. You don’t need to create it again since machado already contains a copy of this file.

5.1. Prerequisite

The list bellow contains the softwares and versions required by machado.

PostgreSQL 9.5

Install PostgreSQL and create a database and user for loading the Chado schema. As postgres user run:

create user username with encrypted password 'password';
create database yourdatabase with owner username;

Chado 1.31

Download Chado schema, unpack the file and load the chado-1.31/schemas/1.31/default_schema.sql to the database.

psql -h localhost -U username -W -d yourdatabase < chado-1.31/schemas/1.31/default_schema.sql

Python 3.5.2

We strongly recommend creating a new virtualenv for your project

virtualenv -p /usr/bin/python3 YOURPROJECT
source bin/activate


Just grab the code using GIT and install it:

git clone https://github.com/lmb-embrapa/machado.git src/machado
python src/machado/setup.py install

5.2. The Django project

Inside YOURPROJECT directory create a Django project with the following command:

django-admin startproject WEBPROJECT

Then, configure the WEBPROJECT/settings.py file to connect to your Chado database.

    'default': {
        'ENGINE': 'django.db.backends.postgresql_psycopg2',    # Set the DB driver
        'NAME': 'yourdatabase',                                # Set the DB name
        'USER': 'username',                                    # Set the DB user
        'PASSWORD': 'password',                                # Set the DB password
        'HOST': 'localhost',                                   # Set the DB host
        'PORT': '',                                            # Set the DB port

5.3. The model

Django has a command to generate a Models file:

python manage.py inspectdb > unsortedmodels.py

This will create a raw models.py with a model for each table and view in the specified Postgres database. This file needs to be fixed as each foreign key relation should have a unique name in Django to support reverse relationships. The following Python code will create these unique names. The code rewrites the models and also generate a admin.py file:

fixChadoModel.py --input unsortedmodels.py

The resulting files, models.py and admin.py, are ready.