FAIRDataTeam compose collection

This repository contains a collection of Docker compose files for development and testing of FAIRDataTeam applications like FAIR Data Point, FAIR Data Train, etc.

Important

These files are not intended for use in production.

Quickstart

1. cd into the directory for the desired configuration, e.g. cd fdp/ephemeral/v1 (this important because we rely on autodetection of compose.override.yml files)
2. set up: docker compose up -d
3. visit http://localhost in your browser to play around with the application
4. tear down: docker compose down (from the same directory)

Note: To remove persistent data, it is convenient to use docker compose down --volumes. Do be careful though, because this is irreversible.

Description

Re-usable Docker compose services are specified in separate directories such as fdp/components. These components are used to construct compose files for various use cases.

For example, fdp/ephemeral/v1/compose.yml defines a minimal setup, consisting of the following Docker containers:

• mongodb
• fdp v1.x
• fdp-client v1.x

This uses the FDP's default in-memory triplestore, and mongodb data is non-persistent (ephemeral), because no Docker volumes are defined. If you tear these containers down, the data are gone.

If you want persistent storage, use one of the setups from the fdp/persistent directory, which do use Docker volumes.

Similarly, if you're interested in the FDP index, run the setup from fdp/ephemeral/v1/index, for example.

Usage

Although it is possible to specify one or more Docker compose files on the command line, using the -f option, this repo relies on the default Docker compose behavior which is to automatically merge the following files:

• compose.yml
• compose.override.yml (optional)

This way, we can cd into the desired directory and then simply call docker compose commands, without having to specify files explicitly using -f. Moreover, some configurations rely on this method to override certain service attributes.

For example, compare this approach to merge compose.yml with compose.override.yml:

cd fdp/ephemeral/v1/dev/fdp
docker compose up -d

with the alternative:

docker compose -f fdp/ephemeral/v1/dev/fdp/compose.yml -f fdp/ephemeral/v1/dev/fdp/compose.override.yml up -d

To check the actual result of such a merge, we can use the compose config command:

docker compose config

If desired, specific Docker image versions can be specified using environment variables, before calling compose up. For example:

export FDP_CLIENT_VERSION=2.0.0-alpha.3

Refer to the compose files in the components directories to see the environment variable names.

If you want to persist the use of specific versions, create a .env file in the applicable directory with the desired environment variables. This file will be picked up automatically when you run docker compose. See docker environment variables for more information.

Troubleshooting

Compose up fails with "no matching manifest" on macOS

On a mac with Apple silicon (or on other computers with arm64 processor architecture), docker compose up -d may produce an error like the following:

no matching manifest for linux/arm64/v8 in the manifest list entries

This is because the fdp-client version 1.17.1 does not have Docker images for arm64 architectures, for reasons explained in FAIRDataTeam/FAIRDataPoint-client#188.

That is fixed in version 1.18.0.

If you still want to use 1.17.1, here are some workarounds:

• roll back to an older version of the client, using env variables, e.g. export FDP_CLIENT_VERSION=1.17.0
• (not tested) force emulation by specifying platform: linux/amd64 for the fdp-client service in the compose file

Check the OS/ARCH column on Docker hub to see which client versions do support linux/arm64.

Work in progress...

• Compose files for fdt need to be added (fair data train etc.)