Local Test Deployment

Profile test-local-3nodes

This test profile deploys 3 MedCo nodes on a single machine for test purposes. It can be used either on your local machine, or any other machine to which you have access. The version of the docker images used are the latest released versions. This profile is for example used for the MedCo public demo.

MedCo Node Deployment (except IRCT)

First step is to get the MedCo Deployment latest release.

$ cd ~
$ wget https://github.com/lca1/medco-deployment/archive/v0.1.1c.tar.gz
$ tar xvzf v0.1.1c.tar.gz
$ mv medco-deployment-0.1.1c medco-deployment

Next step is to download and build the docker images:

$ cd ~/medco-deployment/compose-profiles/test-local-3nodes
$ docker-compose pull
$ docker-compose build

Final step is to run the nodes. They will run simultaneously, and the logs of the running containers will maintain the console captive. No configuration changes are needed in this scenario before running the nodes. To run them:

$ docker-compose up

Wait some time for the initialization of the containers to be done (up to the message: “i2b2-medco-srv… - Started x of y services (z services are lazy, passive or on-demand)”), this can take up to 10 minutes. For the subsequent runs, the startup will be faster.

IRCT Deployment and Configuration

First step is to clone the IRCT repository with the correct branch.

$ cd ~
$ git clone -b MedCo-v0.1.1 https://github.com/lca1/IRCT.git

Currently IRCT must be deployed separately, this will change in the future:

$ cd ~/IRCT/deployments
$ docker-compose -f docker-compose.medco.test-local-3nodes.yml build

Next, if running on another machine than the local host, a configuration file must be changed. If running on the local host, the default settings can be left in place. Edit the file ~/medco-deployment/compose-profiles/test-local-3nodes/.env to reflect your configuration. For example:

MEDCO_NODE_URL=https://medco-demo.epfl.ch
HTTP_SCHEME=https

MEDCO_NODE_URL should include the protocol and the fully qualified domain name of the host, HTTP_SCHEME should be http or https.

Follow HTTPS Configuration to set up the certificates needed for HTTPS. If you are deploying on another host than the local host without HTTPS take note of the following: Disabling HTTPS requirement for external connections.

In a separate terminal run the IRCT container:

$ chmod -R a+rw ../
$ docker-compose -f docker-compose.medco.test-local-3nodes.yml up

Again, the initial startup takes up a few minutes as IRCT is compiled at that point (up to the message: “irct_1… - Started x of y services (z services are lazy, passive or on-demand)”).

In order to stop the containers, simply hit Ctrl+C in all the active windows.

Keycloak Configuration

Follow the instructions from Keycloak Configuration and then you should be able to login in Glowing Bear.

Test the deployment

In order to test that the local test deployment of MedCo is working, access Glowing Bear in your web browser at http://<domain name> (or https) and use the credentials previously configured during the Keycloak Configuration. If you are new to Glowing Bear you can watch the Glowing Bear user interface walkthrough video.

By default MedCo loads a specific test data, refer to Description of the default test data for expected results to queries. To load a dataset, follow the guide Loading Data. For reference, the database address (host) to use during loading is <domain name>:5432 and the databases i2b2medcosrv0, i2b2medcosrv1 and i2b2medcosrv2.