thehyve/cookiecutter

Name: cookiecutter

Owner: The Hyve

Description: Cookiecutter boilerplate for tranSMART data portal. Based on hack4impact flask-base

Created: 2017-05-05 13:15:02.0

Updated: 2017-05-26 16:59:40.0

Pushed: 2017-06-23 10:32:52.0

Homepage: null

Size: 8199

Language: Python

GitHub Committers

User	Most Recent Commit	# Commits
Piotr Zakrzewski	2017-05-26 12:24:47.0	12

Other Committers

User	Email	Most Recent Commit	# Commits
Piotr Zakrzewski	piotr@thehyve.nl	2017-06-23 10:32:50.0	40

README

Cookiecutter Data Portal for tranSMART

This is a simple request portal with basic support for codebooks and file sharing. It is capable of extracting requested variables from tranSMART ver 1.2. Adapting it to higher version is easily possible. Use config.env to configure which transmart instance to integrate with.

 TRANSMART_URL=https://domain.com/transmart

Log in as an admin (see flask-base docs below for details on configuration) and sync studies using Admin Dashboard/tranSMART config

flask-base

A Flask application template with the boilerplate code already done for you.

Documentation available at http://hack4impact.github.io/flask-base.

What's included?

• Blueprints
• User and permissions management
• Flask-SQLAlchemy for databases
• Flask-WTF for forms
• Flask-Assets for asset management and SCSS compilation
• Flask-Mail for sending emails
• gzip compression
• Redis Queue for handling asynchronous tasks
• ZXCVBN password strength checker
  
• CKEditor for editing pages

Demos

Home Page:

Registering User:

Admin Editing Page:

Admin Editing Users:

Setting up

Clone the repo

t clone https://github.com/hack4impact/flask-base.git
 flask-base

Initialize a virtualenv

p install virtualenv
rtualenv -p /path/to/python3.x/installation env
urce env/bin/activate

For mac users it will most likely be

p install virtualenv
rtualenv -p python3 env
urce env/bin/activate

Note: if you are using a python2.x version, point the -p value towards your python2.x path

(If you're on a mac) Make sure xcode tools are installed

ode-select --install

Add Environment Variables

Create a file called config.env that contains environment variables in the following syntax: ENVIRONMENT_VARIABLE=value. For example, the mailing environment variables can be set as the following. We recommend using Sendgrid for a mailing SMTP server. But anything else will work as well.

_USERNAME=SendgridUsername
_PASSWORD=SendgridPassword
ET_KEY=SuperRandomStringToBeUsedForEncryption

Other Key value pairs:

• ADMIN_EMAIL: set to the default email for your first admin account (default is flask-base-admin@example.com)
• ADMIN_PASSWORD: set to the default password for your first admin account (default is password)
• DATABASE_URL: set to a postgresql database url (default is data-dev.sqlite)
• REDISTOGO_URL: set to Redis To Go URL or any redis server url (default is http://localhost:6379)
• RAYGUN_APIKEY: api key for raygun (default is None)
• FLASK_CONFIG: can be development, production, default, heroku, unix, or testing. Most of the time you will use development or production.

Note: do not include the config.env file in any commits. This should remain private.

Install the dependencies

p install -r requirements.txt

Other dependencies for running locally

You need to Redis, and Sass. Chances are, these commands will work:

Sass:

m install sass

Redis:

Mac (using homebrew):

ew install redis

Linux:

do apt-get install redis-server

You will also need to install PostgresQL

Mac (using homebrew):

 install postgresql

Linux (based on this issue):

 apt-get install libpq-dev

Create the database

thon manage.py recreate_db

Other setup (e.g. creating roles in database)

thon manage.py setup_dev

Note that this will create an admin user with email and password specified by the ADMIN_EMAIL and ADMIN_PASSWORD config variables. If not specified, they are both flask-base-admin@example.com and password respectively.

[Optional] Add fake data to the database

thon manage.py add_fake_data

Running the app

urce env/bin/activate
ncho start -f Local

For Windows users having issues with binding to a redis port locally, refer to this issue.

Formatting code

Before you submit changes to flask-base, you may want to auto format your code with python manage.py format.

Contributing

Contributions are welcome! Check out our Waffle board which automatically syncs with this project's GitHub issues. Please refer to our Code of Conduct for more information.

Documentation Changes

To make changes to the documentation refer to the Mkdocs documentation for setup.

To create a new documentation page, add a file to the docs/ directory and edit mkdocs.yml to reference the file.

When the new files are merged into master and pushed to github. Run mkdocs gh-deploy to update the online documentation.

Related

https://medium.freecodecamp.com/how-we-got-a-2-year-old-repo-trending-on-github-in-just-48-hours-12151039d78b#.se9jwnfk5

License

MIT License