A web interface for the scoring of biomedical digital objects by user evaluation according to the FAIR data principles: Findability, Accessibility, Interoperability, and Reusability.
Available at http://fairshake.cloud/
- FAIRshake: The django project settings
- FAIRshakeHub: The website itself, gets all of its information from FAIRshakeAPI
- FAIRshakeAPI: The primary API facilitator, is enabled with the other API components
- extensions: Extensions to dependent libraries
Python 3 is required to run this project.
Install all dependencies into your environment.
pip install -r requirements.txt
mysqlclient is the recommended client but
pymysql can be used as a fallback.
# Run in debugging mode, show errors and host staticfiles locally export DEBUG=1 # Specify location of mysql config file for production database export MYSQL_CONFIG=$(pwd)/ssl/my.cnf
ipython is recommended:
pip install ipython
Django Live Reloading Server
In separate terminals execute these commands and then navigate to http://localhost:8000/.
./manage.py runserver ./manage.py livereload
Django keeps track of database migrations. When modifying
models it is imperative to create and apply migrations on all old databases. Migrations can be safely removed if they have been applied to all independent databases (for that reason, it's probably better to just not remove them).
./manage.py makemigrations ./manage.py migrate
Note that this will try but not always succeed to detect renamed fields and such and migrate the backend database accordingly. If it is unable to, it may require manual intervention. For more information https://docs.djangoproject.com/en/2.0/topics/migrations/.
# Run Tests ./manage.py test # Run Tests with Coverage coverage run --source='.' manage.py test && coverage report
Database Backup & Restore
# Backup data, omit django internals (which could cause loading to fail) ./manage.py dumpdata \ -e contenttypes \ -e admin \ -e auth.Permission \ --natural-foreign \ --indent=2 \ > mybackup.json
# Ensure database is initialized ./manage.py migrate # Load data from backup ./manage.py loaddata mybackup.json
For the docker-compose to work properly in production,
/ssl/ should have the following files:
my.cnf: mysql configuration file with production database credentials
- This file can be specified with
- This file can be specified with
secret.txt: Secret key for production (random private string of characters)
cert.key: SSL Private Key
cert.crt: SSL CA Signed Public Key
Errors involving mysql trying to load from /tmp/sock arrise when
MYSQL_CONFIG environment variable is being read, but the file on the other end is problematic.
- You're not using an absolute path, so django, running perhaps elsewhere, can't find it. Try:
- Verify that it's accessible at the environment variable with
- Your configuration file has loose permissions, Try:
chmod 644 ssl/my.cnfbefore trying again.
- Your configuration is malformed.
In general, if the database has changed (and there are new migration files), if you're running a local database you may need to apply new migrations with
No Cache Table
If the cache table doesn't yet exist, you can create it with
First try re-executing
pip install -r requirements.txt.
In the worst case you may need to rebuild your environment from nothing (starting from scratch, and installing dependencies again).
pyenv for managing isolated python environments.