SynBio Glyph repository

A Registry of Synthetic Biology Glyphs, created for the IWBDA 2017 BDAthlon competition

It was built using Flask as a web framework, SQLAlchemy as an ORM layer, and various Flask packages (most notably Flask-Login, WTForms and Flask-WTF, but see requirements/prod.txt for a complete list). The front-end uses Boostrap for layout, FontAwesome for icons, jQuery as a dependendy for Bootstrap, and the selectize library for fuzzy-filtering of lists. As a starting point, `cookiecutter-flask https://github.com/sloria/cookiecutter-flask`_ was used to create the boilerplate for a site with user management but no other interactivity.

Project Structure

The project consists of many files. These are some of the most significant ones

autoapp.py    - main entrypoint that creates an application instance
requirements/ - list of project requirements in format readable by ``pip -r``

glyphrepository/
    app.py      - app factory function
    assets.py   - lists JS and CSS files to be included
    settings.py - main configuration file
    static/     - JS and CSS files, as well as the images of glyphs
    templates/  - directory of template files (in Jinja2 format)

The bulk of the non-boilerplate code is in one of:

comment/
glyph/
public/
soterm/
user/

which contain a model.py file (which defines a database table using SQLAlchemy), a forms.py file, and a views.py file (which defines the routes/URLs for the application, and the functions that actually handle requests).

Quickstart

This project is written in Python using the Flask framework. If you have Python and pip installed, you can get the code and install its dependencies (including Flask)

git clone https://github.com/BDAthlon/2017-Triple_Helix-1
cd glyphrepository
pip install -r requirements/dev.txt

Before running shell commands, set the FLASK_APP and FLASK_DEBUG environment variables

export FLASK_APP=/path/to/autoapp.py
export FLASK_DEBUG=1

You then need to setup the database. The repository includes a SQLite database (dev.db) that should `just work' when debugging mode is enabled, but you can alternatively created the database from scratch

flask db init
flask db migrate
flask db upgrade
flask run

You will then also need to load the SO data in so.sql into the database.

You can then run the site using

flask run

and nvaigate to 127.0.0.1:5000 in your favourite browser.

Deployment

You need to set a secret key as an environment variable. For example, add the following to .bashrc or .bash_profile.

export glyphrepository_SECRET='something-really-secret'

In your production environment, make sure the FLASK_DEBUG environment variable is unset or is set to 0, so that ProdConfig is used.

Shell

To open the interactive shell, run

flask shell

By default, you will have access to the flask app.

Running Tests

This project was written quickly at a hackathon, so contains few tests; only those that came with the scaffolding.

To run all tests, run

flask test

Migrations

Whenever a database migration needs to be made. Run the following commands

flask db migrate

This will generate a new migration script. Then run

flask db upgrade

To apply the migration.

For a full migration command reference, run flask db --help.