CENtree Install and Run Guide

Use this guide to help you run a full standalone version of CENtree from the same server or computer.

For other advanced topics, including updating CENtree, please check the wiki.

Minimum Requirements

• Docker engine
• Docker compose
• Valid Scibite CENtree license
• Dockerhub user with access to CENtree dockerhub repository (access will be granted by SciBite on valid licence)

You will need docker and docker-compose installed in your server/computer. This version has being tested with docker (installing docker) 19.03.4-ce and docker compose (installing docker compose) 1.24.1. But is very likely it will work also with older/newer versions.

You also need a valid CENTree license. Please replace the example license with the one we provide you into that same location. If not, the server will refuse to start.

Your server requires a minimum of 16GB of ram. If you only have 8GB at your disposal, you may still run CENtree, but you will need to lower the available memory for CENtree on the Application configuration file

      - _JAVA_OPTIONS=-Xmx5g

You will not be able to load the biggest ontologies, but that would be all. Please refer to the CENtree user manual for minimum/recommended server requirements.

You will also need to have a dockerhub user that has access to CENtree dockerhub repository. If not, you will not be able to pull the docker containers images needed to run CENtree.

Installing and Starting CENtree

Clone or download the docker file (above) which contains the start and stop scripts, the yml config and license folder:

https://github.com/SciBiteLtd/centree-devops/tree/master/docker

Ensure you are logged into Docker:

docker login

If you have not previously saved credentials it will prompt for your username and password. Use the same account that has access to the CENtree Dockerhub which you have previously sent to SciBite.

If both requirements are satisfied (docker compose and access to CENtree dockerhub repository) you just need to run the following command:

cd docker
./start-centree.sh

Depending on your environment and how you install docker, you may need to run as sudo. The script will first pull the latest image (no action is taken if you already have the latest release image downloaded), then initiate the platform to start. If you want to pull a specific verson of CENtree and not the latest release please use a named version - see the updating CENtree wiki page

To check if everything went well, run:

./show-logs.sh

And you should get a similar output as this at the end:

15:42:46.306+0000 INFO  [main] OntologyManagerApp: Started OntologyManagerApp in 30.441 seconds (JVM running for 32.011)
15:42:46.314+0000 INFO  [main] OntologyManagerApp: 
----------------------------------------------------------
	Application 'OntologyManager' is running! Access URLs:
	Local: 		https://localhost:8443/
	External: 	https://192.168.48.2:8443/
	Profile(s): 	[prod, swagger]
----------------------------------------------------------

If you can see this output, you should be able now to access your server at https://localhost:8443/ if you are running the service locally.

(Optional) Mail configuration

If you want to make use of the email outgoing service, you will need to provide the following necessary properties editing the Application configuration file:

      - JHIPSTER_MAIL_FROM=Centree@centree.scibite.io 
      - JHIPSTER_MAIL_BASE_URL=https://centree.scibite.io
      - SPRING_MAIL_HOST=email-smtp.eu-west-1.amazonaws.com
      - SPRING_MAIL_PORT=587
      - SPRING_MAIL_USERNAME=REPLACE_WITH_USERNAME
      - SPRING_MAIL_PASSWORD=REPLACE_WITH_PASSWORD
      

In this example, amazon mail service is used, but you can use whatever smtp server you prefer. Make sure you change the base url to match a public address that a person receiving an email is able to access your Centree instance, so he can be able to open any links that gets into his email (Ex. password resets)

(Optional) SSL certificate override

You can override the default self signed certificate with your own, please uncomment the ssl properties editing the Application configuration file and it should look something like this:

      # Uncumment the next lines if you want to override the self signed certificate with your own
      - SERVER_SSL_KEY_STORE=/var/lib/app/data/ssl/ontologymanager.p12
      - SERVER_SSL_KEY_STORE_TYPE=PKCS12
      - SERVER_SSL_KEY_ALIAS=ontologymanager
      - SERVER_SSL_KEY_STORE_PASSWORD=changeme
    volumes:
      - ontologymanager-app:/var/lib/app/data/
      - ./data/license/:/var/lib/app/data/license/
      # You will need to provide a volume that stores your certificate if ssl is overriden
      - ./data/ssl/:/var/lib/app/data/ssl/
      

Here, you are overriding the ssl certificate with ontologymanager.p12. Modify the properties to meet your demands.