LAHMA

LAHMA stands for Local Annotation of Homology Matched Aminoacids.

LAHMA is a web application that facilitates protein crystallography research. In this repository you can find the core of the application.

You can visit the complete site https://lahma.pdb-redo.eu

Basic web software used in this project:

• Flask
• JQuery
• AJAX
• Google Material Design
• Bootstrap
• SQL

Installation for development on your computer

Prerequisites

First of all, you must be running a Debian Operating System like Ubuntu.

The following prerequisites are required and must be installed manually if not present:

• git (e.g. apt-get install git on a Debian-like OS)
• python 3.8, follow this tutorial to prepare https://www.digitalocean.com/community/tutorials/how-to-install-python-3-and-set-up-a-programming-environment-on-ubuntu-20-04-quickstart

Steps for setting up the development environment

Clone the repository from github and go to the ccd directory:

git clone https://github.com/gdamaskos/flask_with_sql_connector.git

cd flask_with_sql_connector

Install Mariadb following this tutorial https://www.digitalocean.com/community/tutorials/how-to-install-mariadb-on-ubuntu-20-04

Log in the database as root or administrator and create a database:

$ mysql -u admin -p
mysql> CREATE DATABASE LahmaDB1;
mysql> exit

Import the demo databse provided in the repository:

mysql -u admin -p LahmaDB1 < data/LahmaDB1.sql 

Create a python3.8 virtual environment containing the dependences found in requirements.txt:

python3 -m venv ~/virtual_environments/lahma
source ~/virtual_environments/lahma/bin/activate

Install python dependencies:

pip install wheel
pip install -r requirements.txt

Modify the settings in config/lahma_settings.example to your needs and rename the file to config/lahma_settings.cfg. Make sure you generate a new secret key, and fill in a valid email. Make sure you put the right credentils to access the database (IP, Username, Password, Database_name).

The secret key can be generated using a python shell, for example:

$ python
>>> import os
>>> os.urandom(96)

Start the app!

./run.sh

Visit the address:

http://localhost:8080