1. Installation¶
machado is a Django framework for Chado.
1.1. Prerequisite¶
The list bellow contains the softwares and versions required by machado.
PostgreSQL 12
Install PostgreSQL and create a database and user for loading the Chado schema. As postgres user run:
psql
create user username with encrypted password 'password';
create database yourdatabase with owner username;
alter user username createdb;
Don’t forget to configure the PostgreSQL server to allow regular users to connect (pg_hba.conf).
Linux dependencies
Be sure to have the following dependencies installed
sudo apt install zlib1g-dev libbz2-dev liblzma-dev python3-dev
Python 3.8
We strongly recommend creating a new virtualenv for your project
virtualenv -p /usr/bin/python3.8 YOURPROJECT
cd YOURPROJECT
source bin/activate
machado
Just grab the code using GIT and install it:
git clone https://github.com/lmb-embrapa/machado.git src/machado
pip install ./src/machado
1.2. Preparation¶
From this point on it is assumed you have read the Django introduction and tutorial on the Django project website.
Create a Django project
Inside YOURPROJECT directory create a Django project with the following command:
django-admin startproject WEBPROJECT
cd WEBPROJECT
Then, configure the WEBPROJECT/settings.py file to connect to your Chado database.
DATABASES = {
'default': {
'ENGINE': 'django.db.backends.postgresql', # 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
},
}
Let Django know about your machado
In the WEBPROJECT/settings.py file, add chado to INSTALLED_APPS section.
INSTALLED_APPS = [
...
'machado',
'rest_framework',
'drf_yasg',
...
]
(Additional information here: https://docs.djangoproject.com/en/2.1/intro/tutorial02/)
List the machado commands
python manage.py
1.3. Start you app and open the admin interface¶
You have to run the following command to create django admin tables:
python manage.py migrate
Run tests to check the instalation:
python manage.py test machado
Now, just run the DJango server to access the web interface:
python manage.py runserver
The API interface will be available at http://localhost:8000/machado/api