molgenis-emx2 BETA

This is a BETA implementation of new MOLGENIS/EMX2 data service. Core differences with molgenis/molgenis include that it is simpler to setup and operate, it allows multiple data schemas and that for developers it exposes data via a self-documenting graphql api.

Demo server: https://emx2.test.molgenis.org/

How to run

You can start molgenis-emx2:

using docker compose
using java commandline + postgresql
using kubernetes

Details below:

1. Using docker compose

Install Docker compose.
Download molgenis-emx2 docker-compose.yml file
In directory with docker-compose.yml run:

docker-compose up

To update to latest release, run:

docker-compose pull

Stop by typing ctrl+c.

N.B.

because postgres starts slow, emx2 will restart 2-4 times because of 'ConnectException: Connection refused'. This is normal.
the data of postgresql will be stored in 'psql_data' folder. Remove this folder you want a clean start.
if you want particular molgenis-emx2 version then add version in docker-compose.yml file 'molgenis/molgenis-emx2:version'

2. Using java and your own postgresql

Install java (we use java 11 or higher)
Download a molgenis-emx2-version-all.jar from releases.
Download and install Postgresql (we use 11 or higher)

Create postgresql database with name 'molgenis' and with superadmin user/pass 'molgenis'. On Linux/Mac commandline:

sudo -u postgres psql
postgres=# create database molgenis;
postgres=# create user molgenis with superuser encrypted password 'molgenis';
postgres=# grant all privileges on database molgenis to molgenis;

Start molgenis-emx2; will run on 8080

java -jar molgenis-emx2-<version>-all.jar

Optionally, you can change defaults using either java properties or using env variables:

MOLGENIS_POSTGRES_URI
MOLGENIS_POSTGRES_USER
MOLGENIS_POSTGRES_PASS
MOLGENIS_HTTP_PORT

For example:

java -DMOLGENIS_POSTGRES_URI=jdbc:postgresql:mydatabase -DMOLGENIS_HTTP_PORT=9090 -jar molgenis-emx2-<version>-all.jar

3. Using Helm on Kubernetes

If you have Kubernetes server then you can install using Helm.

Add helm chart repository (once)

helm repo add emx2 https://github.com/molgenis/molgenis-ops-helm/tree/master/charts/molgenis-emx2

Run the latest release (see Helm docs)

helm install emx2/emx2

Update helm repository to get newest release

helm repo update

Alternatively, download latest helm chart

For developers