A docker-compose setup to start a demo iCat system

The compose file describes three services:

• database_icat: This is a MySQL database for the icat server based on mysql:5.7 image on docker hub.
• database_topcat: This is a MySQL database for the topcat based on mysql:5.7 image on docker hub.
• webserver: This is a Payara application server based on a local build of the provided Dockerfile.

Services

Start services

Use the following script in the directory of the project.

docker-compose -f docker-compose.yaml up -d

Access logs

Use the following script in the directory of the project.

docker-compose -f docker-compose.yaml logs -f

However, this is not so useful, because application logs are not visible via docker logs.

Build the webserver

Use the following script in the directory of the project.

docker-compose -f docker-compose.yaml build webserver

Restart after only configuration change

Use the following script in the directory of the project.

docker-compose -f docker-compose.yaml restart webserver

Stop services

Use the following script in the directory of the project.

docker-compose -f docker-compose.yaml down

Access

Web admin

Payara admin access is available on: https://localhost:4848
The user is admin.
Script to obtain the password:

echo $(docker-compose -f docker-compose.yaml exec webserver cat .gfclient/pass | grep asadmin | awk '{print $2}' | base64 -d -i)

Topcat

Topcat server is available on: http://localhost:8080
Anonymous and simple authentication methods are enabled with the provided configurations. Simple user is 'usera' and the password is 'passworda'.

Ingestion

Fill up with dummy data

Run the following script in the directory of the script with using pipenv. The Pipfile and the lock files are provided as well.

pipenv sync
pipenv shell
python ingest_dummy_data.py

This script will fill up your database with some dummy data.
(1 facility, 3 investigations and 1 dataset per investigation)

TODO:

• add more dummy data
• use large data files (> 10GB)
• add parameters
• add users and permissions
• persistent volume option for the compose file