Local Development Deployment

Profile dev-local-3nodes

This deployment profile deploys 3 MedCo nodes on a single machine for development purposes. It is meant to be used only on your local machine, i.e. localhost. The version of the docker images used are all dev, i.e. the ones built from the development version of the different source codes. They are available either through Docker Hub, or built locally.

MedCo Node Deployment (except IRCT)

First step is to clone the medco-deployment repository with the correct branch. This example gets the data in the home directory of the current user, but that can be changed.

$ cd ~
$ git clone -b dev https://github.com/lca1/medco-deployment.git

Next step is to download or build the docker images:

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

Next 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 fork/thehyve 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.dev-local-3nodes.yml build

In a separate terminal run the IRCT container:

$ chmod -R a+rw ../
$ docker-compose -f docker-compose.medco.dev-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)”).

Glowing Bear Deployment and Configuration

First step is to clone the glowing-bear repository with the correct branch.

$ cd ~
$ git clone -b picsure https://github.com/lca1/glowing-bear-medco.git

Glowing Bear is deployed separately for development, as we use its very practical development server:

$ cd ~/glowing-bear-medco/deployment
$ docker-compose build dev-server

In another separate terminal run the glowing bear development server:

$ docker-compose up dev-server

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 development deployment of MedCo is working, access Glowing Bear in your web browser at http://localhost:4200 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 localhost:5432 and the databases i2b2medcosrv0, i2b2medcosrv1 and i2b2medcosrv2.