Orderly supports a centralised workflow, where a central server holds the canonical version of a report. In order to make this workflow work, we need a number of things:
To make this workflow work, we have developed some additional software.
First, we have a docker-based server system called OrderlyWeb which can be deployed onto a server. We will communicate with this server over https using a package
orderlyweb which will follow
orderly onto CRAN.
The OrderlyWeb server software provides a number of things
orderly that can run reports as needed using the
Getting OrderlyWeb installed requires a little work, and you will need access to an appropriate server running docker, our python-based deployment tool, and TLS certificates for the server that you are using. We recommend using vault for storing certificates and any secrets used in deployment.
OrderlyWeb will use GitHub for authentication, the setup for which is described here.
orderly to talk to OrderlyWeb
Once OrderlyWeb is running, we can tell
orderly about it by adding an appropriate setting to the
orderly_config.yml file. For example, if you had one testing and one production instance
$GITHUB_TOKEN is an environment variable that holds a GitHub token with “user” scope. The
testing remote is listed first, and so will be the default one used in any remote-using command.
Several commands can interact with the remote server:
orderly::orderly_run_remote will run a report on a remote server, committing it immediately. This will save the log alongside the report.
orderly::orderly_pull_archive will pull a version of a report from a remote server
orderly::orderly_pull_dependencies will pull all the dependencies of a report from the remote server (i.e., versions of reports declared in the
depends: section of a report)
We hope that this system will become easier to deploy in future. We use it internally on two projects with orderly archives that hold gigabytes of analyses, and it has evolved to meet our needs. If you think it might work for you but can’t get started, please get in touch.
We recommend using HashiCorp’s vault for storing secrets (of which several are used here), and our tooling is designed to make this easy.
You will need to set up and/or gather a few things beforehand:
vimc/orderly.server:master, for example the Dockerfile for the coronavirus response and push that to some accessible location (either docker hub or a private registry). You can initially skip this step and just use
vimc/orderly.server:master but the set of built-in packages is very limited
You need to install the
orderly-web deployment scripts from PyPi
pip3 install --user orderly-web
With all that done, running
orderly-web start .
should bring everything up!