ftirdb

Introduction

ftirdb is a databank application for uploading and retrieving infrared spectra for biomolecules. Anything from tissue samples to proteins.

Installation

1. Create a new Python 3 environment python3 -m venv ftirdb_env
2. Enter the environment by running ./ftirdb_env/bin/activate
3. Install and upgrade the packaging tools: pip install --upgrade pip setuptools
4. Install the project in editable mode pip install -e ".[testing]"
5. Create a new database

mysql -u root
create database mydb;
exit

6. Initialize and upgrade the database using Alembic: alembic -c development.ini revision --autogenerate -m "init"
7. Upgrade to that revision: alembic -c development.ini upgrade head
8. Load default data into the database using a script: initialize_ftirdb_db development.ini
9. Run your project's tests with pytest
10. Run your project pserve development.ini