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README.md

Description

This directory contains a docker-compose configuration for setting up instances of the METASPACE platform for personal and development use.

This configuration has not been secured for production use and should not be deployed to any server with the intent of providing public access without first considering the security implications. In particular, administrative ports for back-end services have not been closed in this configuration, and easily guessable passwords are used and stored in plain text.

Usage

Install Docker

sudo apt-get install docker-compose git
sudo snap install docker

After installation, log out and log back in to start the Docker daemon. If this step isn't done, docker will hang when trying to start containers.

Docker config file

Copy .env.example to .env and customize it if needed.

Development installation

The full metaspace repository is mounted into most containers and projects are run from your checked-out code. This makes it much easier to make live code changes.

Running setup-dev-env.sh will copy the pre-made docker config files into the projects in this repository and start the docker containers.

To avoid disruption due to changes in the docker-compose files while updating from git, changing branches, etc. it's recommended to make a copy of the docker-compose.yml file that is excluded from git:

  • Copy docker-compose.yml to docker-compose.custom.yml (this file is already .gitignored)
  • Update .env with COMPOSE_FILE=docker-compose.custom.yml

Webapp and graphql are set to auto-reload if code changes, but they'll need to be restarted if dependencies change. Api, update-daemon and annotate-daemon will need to be manually restarted for code changes to take effect.

Recommended bash aliases

Add these to your ~/.bashrc or ~/.bash_profile:

alias dc="docker-compose"
alias dclogs="dc logs -f --tail 0 api update-daemon annotate-daemon lithops-daemon graphql webapp"
dcr() {
    docker-compose kill "$@" ; docker-compose up -d --no-deps --no-recreate "$@"
}
  • To start everything: dc up -d
  • To stop everything: dc kill (note: don't use dc down as it cleans up, making the containers take longer to start later)
  • To restart one or more containers: dcr graphql webapp (kill/re-up is faster than dc restart)
  • To view logs of METASPACE containers: dclogs

Import data

docker-compose run --rm api /sm-engine/install-dbs.sh
./fetch-mol-images.sh

Configuration

Running setup-dev-env.sh should set up individual projects' config files to a working state, though some adjustments may be required if container names or credentials have changed. The most common causes of runtime errors in new development environments are mismatched credentials and incorrect service names.

Accessing METASPACE

Development tools:

  • localhost:9200 - Elasticsearch REST endpoint. Can be accessed with GUIs such as Elasticvue and dejavu
  • localhost:5432 - Postgres server. Can be used with e.g. DataGrip. Username: postgres, Password: postgres, Database: sm
  • http://localhost:15672/ - RabbitMQ management interface

Watching application logs:

  • docker-compose logs --tail 5 -f api update-daemon annotate-daemon lithops-daemon graphql webapp

Rebuilding the Elasticsearch index:

  • docker-compose run --rm api /sm-engine/rebuild-es-index.sh

Creating an admin user

  1. Register through the METASPACE web UI
  2. Use the email verification link to verify your account (can be found in the graphql logs, or your inbox if the AWS credentials are set up)
  3. Update your user type to admin in the graphql.user table in the database. If you don't have a DB UI set up yet, you can do this instead: docker-compose exec postgres psql sm postgres -c "UPDATE graphql.user SET role = 'admin' WHERE email = '<your email address>';"

Non-Linux host support

When Docker runs containers in a VM, only directory-based volumes can be mounted. This is why the nginx/elasticsearch services have custom dockerfiles that create symlinks to files in a mounted config directory, rather than mounting the files directly.

There's no cross-platform way to do the /etc/timezone mounts, but they're optional and can just be commented out on non-Linux systems.