gemtc-web

User interface for evidence synthesis based on the gemtc R package and Patavi

Setup for the stand-alone version

Init and update the scss from the drugis main project

git submodule init
git submodule update

Compile the scss to css using compass

compass compile

Use bower to install the front-end dependencies

bower install

Use npm to install the back-end dependencies

npm install

Use psql to create the db to store data

CREATE USER gemtc WITH PASSWORD 'develop';
CREATE DATABASE gemtc ENCODING 'utf-8' OWNER gemtc;

Create a .pgpass in the user home to store the database password the file should contain a line with the following format hostname:port:database:username:password

localhost:5432:gemtc:gemtc:develop

Create the schema

for i in create-database-changeset-*.sql; do psql -h localhost -U gemtc -d gemtc -f $i; done

Setup environment variables

export GEMTC_GOOGLE_KEY=100331616436-dgi00c0mjg8tbc06psuhluf9a2lo6c3i.apps.googleusercontent.com
export GEMTC_GOOGLE_SECRET=9ROcvzLDuRbITbqj-m-W5C0I
export DB_HOST=localhost
export GEMTC_DB=gemtc
export GEMTC_DB_USERNAME=gemtc
export GEMTC_DB_PASSWORD=develop
export GEMTC_HOST=http://localhost:3001
export PATAVI_HOST=localhost 
export PATAVI_PORT=3000
export PATAVI_CLIENT_KEY=path-to/app-env-key.pem
export PATAVI_CLIENT_CRT=path-to/app-env-crt.pem
export PATAVI_CA=path-to/provider-name.crt

Running the patavi worker

First, build the R base dependencies for the gemtc worker:

in the R/r-base directory

docker build --tag gemtc/r-base-amqp .

Then, build the worker itself, in the R directory:

docker build --tag patavi/worker-amqp-gemtc .

Run the worker:

docker run -d --link <rabbitmq-container-name>:rabbit --name amqp-gemtc patavi/worker-amqp-gemtc

Running for the stand-alone version

node gemtc

now visit the app at http://localhost:3001

Running a forever service that will restart on crashes

sudo npm install -g forever
forever gemtc.js

Running tests

The Angular app is tested by karma:

karma start karna-conf.js

The node backend is tested by mocha:

To install mocha globally:

npm install -g mocha

To run nodebackend unit tests:

mocha

To run nightwatch integration tests:

set env variable GEMTC_NIGHTWATCH_URL ( b.v. $GEMTC_HOST)

sudo npm install -g nightwatch
cd test/integration
wget http://selenium-release.storage.googleapis.com/2.45/selenium-server-standalone-2.45.0.jar
node gemtc &
nightwatch --config nightwatch-local.json