APHP - REDCap Helm Chart

Presentation

This repository hosts the REDCap Helm Chart developed by the Greater Paris University Hospitals (APHP in French - Assistance Publique des Hôpitaux de Paris). This Chart allows for a cloud-native and cloud-agnostic deployment of REDCap, a secure web application for building and managing online surveys and databases.

REDCap is developed by the Vanderbilt University and is not provided by this Chart or any of its dependencies. If you wish to use REDCap and are not sure where to start, you may visit the dedicated REDCap Community Site.

This Chart aims to provide with an easy way to retrieve the REDcap application from the official server (using your consortium member's credentials), and deploying it in a standard Kubernetes cluster, be it on-premise or in a managed cloud environment.

How does it works?

The architecture of the REDCap stack deployed by this Chart is as follows :

A minimal setup of this stack includes :

• The HTTPd component
• The PHP FPM Server hosting the REDCap Application
• The MySQL Database used by REDCap

On top of that, you can also choose to deploy :

• A Backup Cronjob, that can generate an archive containing a database dump, a dump of the edocs folder, and a dump of the folder containing the REDCap Application. This backup is then send to an S3-compatible storage.
• A Restore Job that can be triggered to restore a previous backup from a S3 storage.
• An audit component, that will query the Audit tables of the REDCap Database, and use Logstash to ship them to the audit stack of your choice

The documentation of the Chart can be found in its README file.

How can I test it?

In the example directory, are several subdirectories containing documented examples according to your needs.

• If you want to quickly bootstrap a local/test environment, you can start by looking at the local example
• If you want to start deploying a more stable and secure environment, you can have a look at the production example

Lifecycle management

Here are a few important notions to keep in mind to efficiently manage a REDCap installation on a day-to-day basis.

Initialisation process

If you choose to automatically install REDCap using your community credentials with this chart, an Kubernetes Job called init-job will be automatically fired during the chart's installation process:

• The StartupPrope will call the install.php or upgrade.php script (depending if you're installing REDCap from scratch or upgrading from an existing installation) with the query parameter auto=1
• The ReadinessProbe will call a MySql script allowing to configure REDCap with the following parameter, extracted from the Chart values :
  • REDCap Base URL
  • Institution Name
  • Organization Name
  • Name of REDCap Administrator
  • Email Address of REDCap Administrator
  • Contact name to display on Home page
  • Contact name email
  • Local file storage location
• The LivenessProbe will call the cron.php script every minute

Note : The auto-install feature doesn't fully configure the REDCap installation, hence you'll need to do those post-installation actions in the REDCap Control Center as soon as possible :

• Set an authentication method
• Checks that the CronJobs were called (you can manually launch one if the Kubernetes CronJob dedicated to this task hasn't run yet)
• Launch the Configuration Check

Backup Cronjob

This chart allows to backup your REDCap installation automatically. The backup process creates and uploads on an S3 bucket an archive containing the following elements :

• A dump of the edocs dir, which contains user-uploaded data
• A dump of the redcap directory, which contains the application
• A dump of the database

A dedicated Kubernetes CronJob has been created to this end, called backup-cronjob. It runs by default every 8 hours, using the following schedule : 0 */8 * * *. You can modify this scheduling pattern in the chart's parameters (see the chart's documentation).

You'll need to enable and configure the CronJob in the chart's parameters in order to use it.

If, for any reasons, you need to manually fire a instance of this CronJob, you can just use kubectl to create spawn a job manually using this command :

kubectl -n redcap create job manual-backup-job --from cronjob/redcap-backup-job

The name of your namespace as well as the name of the jobs may vary depending your installation's configuration and the name you gave to your Helm release.

Note : The backup process has not been validated by the maintainers of REDCap. Now that this chart is wildly available, we would be glad to work with them to enhance this process. Until then, keep in mind that this process is not official and may contains flaws or limitations, although it has been battle-tested on our end several times.

Restoration Job

With the backup process, a restoration job has also been set up. It does the reverse of the backup job, and retrieves the backup archive to :

• Restores the edocs dir, which contains user-uploaded data
• Restores the redcap directory, which contains the application
• Restores the database dump

In order to have a job template ready to be fired on-demand, a dedicated Kubernetes CronJob has been created to this end, called restore-cronjob. It never runs (you wouldn't want to have your data periodically erased by a restore process ;)), but it allows to run a restore process from the latest backup at any time, just with the kubectl command :

kubectl -n redcap create job manual-restore-job --from cronjob/redcap-restore-job

The name of your namespace as well as the name of the jobs may vary depending your installation's configuration and the name you gave to your Helm release.

You'll need to enable and configure the CronJob in the chart's parameters in order to use it (see the chart's documentation).

Note : The restore process has not been validated by the maintainers of REDCap. Now that this chart is wildly available, we would be glad to work with them to enhance this process. Until then, keep in mind that this process is not official and may contains flaws or limitations, although it has been battle-tested on our end several times.

General questions

• Is this installation compatible with OIDC/SAML?

  Yes, you can configure OIDC directly in REDCap settings, whilst you'll need to configure and activate SAML2 in the chart's settings see the chart's documentation. Other authentication methods like LDAP should also work, but haven't been tested properly.

• What REDCap feature can I use?

  This Chart aims to deploy REDCap in an environment that looks 'familiar' for the application, so you should be able to use any feature you'd use in a more traditional context. At the Greater Paris University Hospitals, we're using this chart in production for more than a year on several projects. It is possible though that with time, new versions of REDCap will need extra dependencies to be available on the PHP FPM server. If it's the case, the corresponding container image will be released.

• How secure is it?

  With its many parameters, and the exposition of several admin pages like cronjob or install, this installation will be as secure as its configuration. This chart offers many security feature (containerization, rootless processes, traffic isolation with network policies, read-only filesystems, etc.), so be sure to check them, and to have a comprehensive view of your installation!

• How can I update it?

  We recommend to setup your REDCap installation using the default method stated in the examples, that is to provide the chart with your REDCap Community credentials via a Kubernetes Secret, as it will ease the update process. Regarding the update process, you can follow two routes :

  • Standard Update : You can upgrade your REDCap version in the values.yaml of your Helm Release (redcap.version parameter), and then redeploy your release.
  • Easy Update : You can use REDCap's Easy Upgrade feature, which allows you to update your installation directly from the Control Center, as an admin user. This method is disabled by default, as it allows the application to modify its own files, which may be considered as a security breach. If you still wish to proceed, make sure you set the redcap.config.readOnlyAppDir parameter to false in the values.yaml file of your Helm Release.

• How can I manage backups?

  If you're going with the backup/restore feature of this Chart, every backup will contain the redcap application directory, the edocs directory, and a database dump, so you'll be able to restore everything in one go. You're of course free to use any other method!

• I can't get the REDCap application package via the community website because my admins won't whitelist the URL/whatever other reasons!

  You can override the initContainer in charge of retrieving the REDCap application, and add as many other initContainers you like to build your own retrieval logic. It might take some time to get into the logic, but you can help yourself with the few snippets presents in the example directory.

Continuous Integration / Continuous Delivery

This project contains a Github Workflow, which will :

• Lint the Chart using helm ct
• Verify the generated Kubernetes resources using kubeconform
• Scan the Chart for anti-patterns and security issues using polaris
• Validates the Chart deployment on kind using helm ct
• Package en release the chart on Github using helm-cr

How can I contribute?

You're welcome to read the contribution guidelines.

How is this project licensed?

The information about the licensing and the dependencies of this project can be found under :

• The project's license file
• The legal notice