MedCo Technical Documentation
GithubDocker HubMedCoLDS
v2.0.1
v2.0.1
  • Home
  • Releases
  • For System Administrators
    • Requirements
    • Deployment
      • Local Test Deployment
      • Network Deployment
      • Configuration
        • Passwords
        • Keycloak
        • Setting Authorizations
        • HTTPS Configuration
        • Configuring SwitchAAI Authentication
    • Data Loading
      • Synthetic SPO Data
      • v0 (Genomic Data)
      • v1 (I2B2 Demodata)
    • Command-Line Interface (CLI)
    • Network Architecture
    • Common Problems
  • For Developers
    • Local Development Deployment
    • System Architecture
    • Description of the default test data
    • Database
    • Live Demo
    • Release a new version
  • For users
    • MedCo Live Demo Tutorial
Powered by GitBook
On this page
  • Pre-requisites
  • Generation of the deployment Profile
  • Step 1
  • Step 2
  • MedCo Stack Deployment
  • Keycloak Configuration
  • Test the deployment

Was this helpful?

Export as PDF
  1. For System Administrators
  2. Deployment

Network Deployment

Deployment of profile test-network.

This profile deploys an arbitrary set of MedCo nodes independently in different machines that together form a MedCo network. This deployment assumes each node is deployed in a single dedicated machine. All the machines have to be reachable between each other. Nodes should agree on a network name and individual indexes beforehand (to be assigned a unique ID).

The next set of steps must be fully executed individually by each node of the network.

Pre-requisites

First step is to get the MedCo Deployment latest release at each node. Adapt ${MEDCO_SETUP_DIR} to where you wish to install MedCo.

export MEDCO_SETUP_DIR=~/medco MEDCO_SETUP_VER=v2.0.1
git clone --depth 1 --branch ${MEDCO_SETUP_VER} https://github.com/ldsec/medco.git ${MEDCO_SETUP_DIR}

Generation of the deployment Profile

Next the compose and configuration profiles must be generated using a script, executed in two steps.

  • Step 1: each node generates its keys and certificates, and shares its public information with the other nodes

  • Step 2: each node collects the public keys and certificates of the all the other nodes

Step 1

For step 1, the network name ${MEDCO_SETUP_NETWORK_NAME} should be common to all the nodes. ${MEDCO_SETUP_NODE_DNS_NAME} corresponds to the machine domain name where the node is being deployed. As mentioned before the different parties should have agreed beforehand on the members of the network, and assigned an index ${MEDCO_SETUP_NODE_IDX} to each different node to construct its UID (starting from 0, to n-1, n being the total number of nodes).

export MEDCO_SETUP_NETWORK_NAME=example \
    MEDCO_SETUP_NODE_IDX=0 \
    MEDCO_SETUP_NODE_DNS_NAME=medconode0.example.com
cd "${MEDCO_SETUP_DIR}/scripts/network-profile-tool"
bash step1.sh ${MEDCO_SETUP_NETWORK_NAME} ${MEDCO_SETUP_NODE_IDX} ${MEDCO_SETUP_NODE_DNS_NAME}

This script will generate the compose profile and part of the configuration profile, including a file srv${MEDCO_SETUP_NODE_IDX}-public.tar.gz. This file should be shared with the other nodes, and all of them need to place it in their configuration profile folder (${MEDCO_SETUP_DIR}/deployments/test-network-${MEDCO_SETUP_NETWORK_NAME}-node${MEDCO_SETUP_NODE_IDX}/configuration).

Step 2

Before proceeding to this step, you need to have gathered all the files srv${MEDCO_SETUP_NODE_IDX}-public.tar.gz from the persons deploying MedCo on the other nodes.

Once all nodes have shared their srv${MEDCO_SETUP_NODE_IDX}-public.tar.gz file with all other nodes, step 2 can be executed:

cd "${MEDCO_SETUP_DIR}/scripts/network-profile-tool"
bash step2.sh ${MEDCO_SETUP_NETWORK_NAME} ${MEDCO_SETUP_NODE_IDX}

The deployment profile is now ready to be used.

MedCo Stack Deployment

Next step is to download the docker images and run the node:

cd "${MEDCO_SETUP_DIR}/deployments/test-network-${MEDCO_SETUP_NETWORK_NAME}-node${MEDCO_SETUP_NODE_IDX}"
make pull
make up

Wait some time for the initialization of the containers to be done, this can take up to 10 minutes. For the subsequent runs, the startup will be faster. You can use make stop to stop the containers and make down to delete them.

Keycloak Configuration

Test the deployment

The database is pre-loaded with some encrypted test data using a key that is pre-generated from the combination of all the participating nodes’ public keys. For the network deployment profile this data will not be correctly encrypted, since the public key of each node is generated independently, and, as such, the data must be re-loaded before being able to test the system successfully.

make load_test_data
PreviousLocal Test DeploymentNextConfiguration

Last updated 4 years ago

Was this helpful?

At this point, it is possible to edit the default configuration generated in ${MEDCO_SETUP_DIR}/deployments/test-network-${MEDCO_SETUP_NETWORK_NAME}-node${MEDCO_SETUP_NODE_IDX}/.env This is needed in order . When editing this file, be careful to change only the passwords and not the other values.

You will need to follow two sets of instruction to make Keycloak functional and be able to log in. and then:

Note that by default the certificates generated by the script are self-signed and thus, when using Glowing Bear, the browser will issue a security warning. To use your own valid certificates, see . If you wish anyway to use the self-signed certificates, you will need to visit individually the page of Glowing Bear of all nodes in your browser, and select to trust the certificate.

Run first the MedCo loader (see ) to load some data and be able to test this deployment. Or to load some test data by performing a simple data loading you can execute the following:

Then access Glowing Bear in your web browser at https://${MEDCO_SETUP_NODE_DNS_NAME} and use the default credentials specified in . If you are new to Glowing Bear you can watch the video. You can also use the to perform tests.

to modify the default passwords
HTTPS Configuration
Loading Data
Glowing Bear user interface walkthrough
CLI client
Access the Keycloak administration interface
Update the MedCo OIDC client
Update the Keycloak realm keys
Keycloak user management