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Web interface for network meta-analysis based on the gemtc R package
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README.md

gemtc-web

User interface for evidence synthesis based on the gemtc R package and Patavi. For more information on all components of the ADDIS project, please refer to the overall readme.

Architecture

The Gemtc-web system consists of several components:

Overview of the gemtc-web architecture

The web frontend talks to a NodeJS backend, which performs user and data management, and queues R tasks in patavi. Data are stored in a PostgreSQL database, and patavi model results are also cached there. Patavi R tasks expose a websocket URL to the frontend, which listens there for progress updates and results. Running gemtc model tasks requires at least one patagi gemtc worker.

Prerequisites for running gemtc-web

  • A PostgreSQL instance with an initialised database. You can create one in a docker container by running the setup-db.sh script. Make sure to change the passwords from the default.

If you already have a postgresql database you can use, it can be initialised as follows (change passwords as desired):

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 (shell script)

for i in changesets/create-database-changeset-*.sql; do psql -h localhost -U gemtc -d gemtc -f $i; done
  • A patavi-server instance along with a rabbitMQ service. see the patavi repository for installation and running instructions.

  • At least one gemtc patavi worker, started by executing the run-worker.sh script.

Running as Docker container

Building the image (optional)

You can build a new local image by executing the build-docker.sh script. This would be required for example if you wish to change the default SSL keys. Note that this script assumes that your keys are present in an ssl subdirectory of the main gemtc directory. Also note that, if your patavi server presents a certificate that is not trusted by default, there should be a CA certificate for the signing certificate authority of your patavi container in this directory. The default patavi server image presents a certificate signed by the Drugis self-signed certificate authority

The build-docker.sh script also lets you specify the signin method via command line arugment. The current options are Google OAuth 2.0 (GOOGLE) and username/password (LOCAL). The default signin method is Google OAuth 2.0.

For local signin, there are several further dependencies (assuming a version of NodeJS of 10.x) to generate the users and passwords:

sudo npm -g install yarn
sudo npm -g install npx
yarn

After installing these dependencies, you can add users for the LOCAL signin method by using the add-user.sh script.

Running the container

Execute the run-gemtc-docker.sh script.

If you built the container with a specific login method arugment, you should run the run-gemtc-docker.sh script with the same one.

e.g.:

./build-docker.sh LOCAL
./run-gemtc-docker.sh LOCAL

Note that you should probably change the default settings in the script (e.g. check whether the link arguments match the names of your containers, and the names of the certificate files match those in your ssl directory if you built your own image). The script also assumes that the sql database and patavi server and worker are already set up and running. The run script runs the addis/gemtc image, which will be pulled from docker hub by default. The default image comes with SSL keys which assume localhost or localdocker CNs, and which are signed by our self-signed certificate authority.

Because the default patavi-server image users a certificate signed by our certificate authority you need to add this certificate to the browser's trusted authorities for R results to be displayed.

Development

If you wish to run the application locally for development, follow these steps:

  • (Optional) Initialise 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 yarn to install the dependencies

    yarn

  • Ensure that your prerequisites are in place (see above)

  • Setup environment variables

    export GEMTC_GOOGLE_KEY=100331616436-dgi00c0mjg8tbc06psuhluf9a2lo6c3i.apps.googleusercontent.com
    export GEMTC_GOOGLE_SECRET=9ROcvzLDuRbITbqj-m-W5C0I
    export DB_HOST=<pc-name>.spice.drugis.org
    export GEMTC_DB=gemtc
    export GEMTC_DB_USERNAME=gemtc
    export GEMTC_DB_PASSWORD=develop
    export GEMTC_HOST=http://localhost:3001
    export GEMTC_AUTHENTICATION_METHOD=GOOGLE
    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

Note: this google key/secret combination expects the server to run at localhost:3001

Note: replace the path with the location of your SSL client key and certificate

Build the application

npm run build-prod

Run the application

npm start

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

Running tests

The Angular app is tested by karma:

npx karma start

The node backend is tested by mocha:

npx 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
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