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.
The Gemtc-web system consists of several components:
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.
- A PostgreSQL instance with an initialised database. You can create one in a docker container by running the
setup-db.shscript. 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
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A patavi-server instance along with a rabbitMQ service. see the patavi repository for installation and running instructions.
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At least one gemtc patavi worker, started by executing the
run-worker.shscript.
You can build a new local image by executing the build-docker.sh script.
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.
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). 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.
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
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Compile the scss to css using compass
compass compile
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Use yarn to install the dependencies
yarn
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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_API_KEY=someApiKey
export SECURE_TRAFFIC=false
Note: this google key/secret combination expects the server to run at localhost:3001
Build the application
yarn build-prod
Run the application
yarn start
Now visit the app at http://localhost:3001
The Angular app is tested by karma:
yarn karma start
The node backend is tested by mocha:
yarn mocha
To run nightwatch integration tests:
yarn test-end-to-end