Health Record Ingestion service

The Alvearie Health Record Ingestion service is an open source project designed to serve as a “front door”, receiving health data for cloud-based solutions. This repo contains the documentation for the project.

See the list of source code repos here: https://github.com/Alvearie?q=hri

Communication

• Please join our Slack channel for further questions: #health-record-ingestion
• Please see recent contributors or maintainers

Editing the documentation

Uses mkdocs https://www.mkdocs.org/. To add links modify mkdocs.yml.

How to render locally

• Prerequisites:

  • Building the docs requires the mkdocs, mkdocs-material, and pymdown-extensions packages.
  • Publishing the docs to GitHub Pages requires the mike package. (You can likely leave this step to the GitHub action builds, see below)
  • All of these can be installed with pip (ensure you are running python 3 at least) by running pip install -r requirements.in.

• From the base directory of the repo, run mkdocs serve.

• In your browser, go to the localhost address printed in the output of the mkdocs serve command.

How to publish to GitHub pages

We use a tool called mike to publish multiple versions of our documentation from different branches of the docs repo. The mike deploy command helps us build the docs, give that build a tag (e.g. v3.x) and publish that version of the documentation to the GitHub pages of the repo. Generally, you should not need to run this locally, as automated GitHub actions builds keep our published docs up to date. It will automatically build and deploy any changes to the main and support-* branches. If for some reason you need to, or you want to experiment in a private repo, you can see the actions for how we use mike.

Checks

The refCheck.sh script is included to detect bad references and orphaned images. Just run this script from the base directory. It will print out any images in the documentation/images/ directory that are being referenced in the markdown files and any references in the markdown files to a file or image that do not exist.

Diagrams

The diagrams are created with draw.io. You can download the app from GitHub: https://github.com/jgraph/drawio-desktop/releases/. All diagrams are png images with an embedded diagram, so they can be easily updated. To create a new one use File -> Export as -> PNG..., and select 'Include a copy of my diagram'. Save the images to documentation/images.

Contribution Guide

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.