Foresyn

iGEM project by USTC Software 2019.

Installation

Assuming that you are using Debian Buster and Python 3.7.

Initialization

1. Use git to clone this project to your computer.

After cloning the repo, use this command to fetch the submodule

git submodule update --init

2. Install MySQL (or MariaDB), PostgreSQL and RabbitMQ.

   $ apt update && apt upgrade
   $ apt install mariadb-server rabbitmq-server p7zip-full libmysqlclient-dev
   $ mysql_secure_installation  # setting mysql/mariadb
   $ mysql  
   (and then type `GRANT ALL ON *.* TO 'set_your_admin_user_name_here'@'localhost' IDENTIFIED BY 'set_your_admin_password_here' WITH GRANT OPTION;` and `FLUSH PRIVILEGES;` inside, to let our project access mysql database)
   $ cd my_trgm # Configure the 3-gram algorithm implment for MySQL for searching
   $ gcc -o my_trgm.so -fPIC -shared my_trgm.c `mysql_config --include` # Compile the shared library for MySQL
   $ cp my_trgm.so `mysql_config --plugindir` # Copy the shared library to the MySQL plugin folder. Maybe sudo required
   $ echo "CREATE FUNCTION trgm_similarity RETURNS REAL SONAME \"my_trgm.so\";" | sudo mysql

3. Enter into project folder, create a Python virtual environment by:

   $ python3 -m venv venv
   $ source venv/bin/activate
   (venv) $ pip install wheel  # to prevent installation failure
   (venv) $ pip install -r requirements.txt
   (venv) $ sed -i '34 s/^/#/; 35 s/^/#/; 36 s/^/#/' venv/lib/python3.7/site-packages/django/db/backends/mysql/base.py && sed -i 's/.decode(errors/.encode(errors/g' venv/lib/python3.7/site-packages/django/db/backends/mysql/operations.py

4. Write project configuration. Copy backend/backend/config.example.py to backend/backend/config.py, and modify according to your environment.

5. Create and migrate database, and load SQL data by using mysql

   $ echo "CREATE DATABASE igem_backend CHARACTER SET utf8 COLLATE utf8_bin;" | sudo mysql # Create database with name "igem_backend" for mysql
   (venv) $ python manage.py migrate
   $ echo "SET GLOBAL max_allowed_packet=107374182;" | sudo mysql # ensure the large dump imported successfully
   $ sudo mysql < data/all.sql

Run This Project

1. Load Celery computation tasks.

   (venv) $ cd backend/cobra_wrapper/remote/
   (venv) $ env PYTHONOPTIMIZE=1 celery worker -l info -A cobra_computation -Q cobra_feeds
   (a new shell)
   (venv) $ cd backend
   (venv) $ env PYTHONOPTIMIZE=1 celery worker -l info -A backend -Q cobra_results
   (a new shell)
   (venv) $ cd backend
   (venv) $ env PYTHONOPTIMIZE=1 celery worker -l info -A backend -Q cobra_locals

2. Run this project.

   (venv) $ python manage.py runserver