CRUISE-screening

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Table of contents

1. Installation
2. Running

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1. Installation

This project contains four parts:

• Python Django backend serving the web application
• Postgres database for storing user data
• ElasticSearch database for documents with search API [docker]
• Text2Text API for automatic screening

As a minimum, you need to install the first two parts.

1.1 Python Django Backend

Project was tested on Python 3.9+. It will not run on Python 3.8 and below because of type hints for generics.

Create conda environment:

$ conda create --name cruise-literature python==3.9.12

Activate the environment:

$ source activate cruise-literature

Use pip to install requirements (you will need g++ to install fasttext):

(cruise-literature)$ pip install -r requirements.txt

npm install bulma-calendar

1.2 Postgres database

Install PostgreSQL

macOS

Based on this gist

brew install postgresql@14

Run server:

pg_ctl -D /opt/homebrew/var/postgresql@14 start

Note: if you’re on Intel, the /opt/homebrew probably is /usr/local.

Start psql and open database postgres, which is the database postgres uses itself to store roles, permissions, and structure:

$ psql postgres

Ubuntu

$ sudo apt install postgresql postgresql-contrib

$ service postgresql start

Start postgres server

$ sudo systemctl start postgresql.service

Configuration

Next steps common for Ubuntu and macOS.

Replace SYSTEM_USERNAME with your system username and YOUR_PASSWORD with your desired database password.

You can check what is your SYSTEM_USERNAME with the following command:

$ whoami

Start psql and open database:

$ sudo -u postgres psql

Create new role for cruise application, set its name same as your SYSTEM_USERNAME, give LOGIN and CREATEDB permissions; set YOUR_PASSWORD password:

postgres-# CREATE ROLE SYSTEM_USERNAME WITH LOGIN;
postgres-# ALTER ROLE SYSTEM_USERNAME CREATEDB;
postgres-# ALTER  USER SYSTEM_USERNAME WITH  PASSWORD 'YOUR_PASSWORD';

Quit psql, because we will log in with the new role (=cruise_literature_user) to create a database:

postgres-# \q

On shell, open psql with postgres database with our new user.

$ psql postgres

Note that the postgres prompt looks different, because you’re not logged in as a root user anymore. Create a cruise_literature database and grant all privileges to our SYSTEM_USERNAME user:

postgres-> CREATE DATABASE cruise_literature;
postgres-> GRANT ALL PRIVILEGES ON DATABASE cruise_literature TO SYSTEM_USERNAME;

Update the DATABASE_URL entry in the .env file (see 2.1 Before first run). Replace SYSTEM_USERNAME with your system username and YOUR_PASSWORD with your desired database password.

DATABASE_URL=postgres://SYSTEM_USERNAME:YOUR_PASSWORD@localhost:5432/cruise_literature

1.3 ElasticSearch and Search API

Check backend API documentation to learn more about installation.

In order to use CORE search API create a file data/core_api_key.txt and insert your API key. Next, change SEARCH_WITH_CORE to True in cruise_literature/settings.py.

1.4 Text to text API

It is a separate flask application that can be used to generate text predictions (question answering, summarisation) for a given text. It is not necessary and can be switched off in the cruise_literature/settings.py by setting:

TEXT_TO_TEXT_API = False

Check prompt_API documentation to learn more about installation.

2. Running

2.1 Before first run

This fields will also apply after making some changes or updating the code, when the database could be out of sync with the code.

Go into src/cruise_literature/ directory:

(cruise-literature)$ cd src/cruise_literature/

Create .env file in that directory and fill it with the following fields (read more):

DEBUG=True
SECRET_KEY=your-secret-django-key
ALLOWED_HOSTS=
DATABASE_URL=postgres://user:password@host:port/dbname

Make migrations and migrate the database

(cruise-literature)$ python manage.py makemigrations
(cruise-literature)$ python manage.py migrate

Create superuser:

(cruise-literature)$ python manage.py createsuperuser

Fill in sample data into the database

(cruise-literature)$ python manage.py loaddata users_data.json
(cruise-literature)$ python manage.py loaddata search_engines.json

2.2 On a local host

Postgres database

To start the Postgres database, run on macOS:

$ pg_ctl -D /opt/homebrew/var/postgresql@14 start

Django server

Finally, run Django server

(cruise-literature)$ python manage.py runserver 8000

Server should be available at http://127.0.0.1:8000/

2.3 Deployment on prod server

Add YOUR_IP to ALLOWED_HOSTS in .env file, for example:

ALLOWED_HOSTS=123.456.789.0

Run Django server:

(cruise-literature)$ python manage.py runserver YOUR_IP:YOUR_PORT