dcc-dashboard

The Core's web dashboard including a faceted file browser

This iteration of the File Browser uses the web API from https://github.com/BD2KGenomics/dcc-dashboard-service

Set up the web API

Follow the directions on https://github.com/BD2KGenomics/dcc-dashboard-service.

Locally run the Dashboard for Testing Purposes Only

Create a local host

Follow the directions on https://github.com/BD2KGenomics/dcc-dashboard-service.

Setup the Dashboard

Virtual environment and dependencies:

virtualenv env
source env/bin/activate
pip install --upgrade pip
pip install -r ./requirements.txt

See http://bitwiser.in/2015/09/09/add-google-login-in-flask.html

Within an interactive python session:

from app import db
db.create_all()
from werkzeug.serving import make_ssl_devcert
make_ssl_devcert('./ssl', host='localhost')

Environment variables needed:

# dcc-dashboard
export GOOGLE_CLIENT_ID=<FILLMEIN>
export GOOGLE_CLIENT_SECRET=<FILLMEIN>
export REDWOOD_ADMIN=<FILLMEIN>
export REDWOOD_ADMIN_PASSWORD=<FILLMEIN>
export REDWOOD_SERVER=storage.ucsc-cgl.org
export REDWOOD_ADMIN_PORT=8443
export DCC_DASHBOARD_HOST=localhost
export DCC_DASHBOARD_PORT=5000
export DCC_DASHBOARD_PROTOCOL=https

Run it:

python run.py

Installing the Dashboard on an Apache Server for Production

Note: This assumes you have already installed the web-service and Apache. See https://github.com/BD2KGenomics/dcc-dashboard-service for instructions on how to do this. Then come back here and follow the instructions below.

Clone the repository in the root directory, by doing:

git clone https://github.com/BD2KGenomics/dcc-dashboard.git

Make the soft link:

sudo ln -sT ~/dcc-dashboard-service /var/www/html/dcc-dashboard

Go to the /etc/apache2/sites-enabled/000-default.conf file and add DocumentRoot /var/www/html/dcc-dashboard under ServerAdmin webmaster@localhost, like this:

<VirtualHost *:80>
	#Change as appropriate
        ServerName your-server-name.com 
        Header set Access-Control-Allow-Origin "*"
	#Change as appropriate
        ServerAdmin webmaster@localhost
        DocumentRoot /var/www/html/dcc-dashboard

        WSGIDaemonProcess dcc-dashboard-service threads=5
        WSGIScriptAlias /api/v1 /var/www/html/dcc-dashboard-service/dcc-dashboard-service.wsgi
        <Directory dcc-dashboard-service>
                 WSGIProcessGroup dcc-dashboard-service
                 WSGIApplicationGroup %{GLOBAL}
                 Order deny,allow
                 Allow from all
        </Directory>
        ErrorLog ${APACHE_LOG_DIR}/error.log
        CustomLog ${APACHE_LOG_DIR}/access.log combined
</VirtualHost>

Restart the apache server by doing:

sudo apachectl restart

Running tests

Right now, the test framework is minimal and underdeveloped. This will change soon!

To run tests, first set up a python2.7 virtual environment in the repository's directory

virtualenv venv -p python2.7

and activate it

source venv/bin/activate

Make sure requirements are installed:

pip install -r requirements.txt

and then test!

python -m unittest tests