orderly.runner

A small HTTP server for running orderly reports.

The worker and API server are intended to be run as separate containers created from the same image, using the two different entrypoints in docker/bin.

Installation

To install orderly.runner from GitHub:

remotes::install_github("mrc-ide/orderly.runner", upgrade = FALSE)

Local development

Installation

To install for local development, you can use:

devtools::install(dependencies = TRUE)

Set the SSH key environment variable

To develop (or test) functions that use private git repositories, you will need to set the environment variable TEST_PRIVATE_REPO_SSH_KEY.

  1. Create an ssh key - crucially, without setting a passphrase.
  2. Add it as a deploy key on the private test repo at this link.
  3. Then set the private key as an environment variable:
Sys.setenv(TEST_PRIVATE_REPO_SSH_KEY = paste(readLines("path/to/ssh/key"), collapse = "\n"))

Testing (outside docker) 

devtools::test()
# or to run a specific test file:
devtools::test(filter='e2e')

If redis is not running, then tests relying on redis will be skipped.

Running redis

To run a redis container, use scripts/redis start. Bring it down with scripts/redis stop.

To run the full docker setup

  1. Optionally modify docker/test/examples orderly reports. These will be used as reports in the container
  2. Run docker/test/run-test to use the docker image from GitHub Container Registry, or docker/test/run-test --local to build from your local version for development. This will produce a test-repo directory to show you what was copied into the docker containers (you can create just this directory without running the docker containers by running docker/test/setup-test-repo if you want).
  3. The server will be available at localhost:8001
  4. To view the orderly root directory in the docker container (you may want to do this after workers have run orderly reports for example), run docker/test/copy-orderly-root and this will copy the contents to docker/test/orderly-root-volume
  5. Finally to clear docker and remove test-repo and orderly-root-volume directories run docker/test/clear-test

Notes for deploying

When running the server or worker containers, you should set REDIS_URL to point to your Redis instance. You should also set the ORDERLY_RUNNER_QUEUE_ID to the same thing between server and worker containers so they connect to the same queue.

License

MIT © Imperial College of Science, Technology and Medicine