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  1. IL-0506 UC Berkeley DataHub logins failed and students got empty home directories after the JupyterHub database was overwritten
    UC Berkeley2017
    Symptoms

    At about 1 AM on 9 February 2017, UC Berkeley's DataHub was reported down: users trying to log in got a proxy error. The hub pod was running, but its log was full of sqlite errors.

    Service outageData lossMisrouted requests
    Trigger

    While debugging, an operator ran `.save jupyterhub.sqlite` in sqlite3 inside the hub pod without having attached the database, which replaced the JupyterHub database file with an empty one.

    Root cause
    Operator error
    Component
    DatabasePersistent volumes and stateful setsJupyterHub
    Contributing factor
    No safeguard on destructive changeUnsafe failure behaviourHarmful manual action
    Detection

    DataHub was reported down at about 1 AM, when users got a proxy error at login. At 1:12 AM a user reported that he could log in but all his notebooks were gone.

    Remediation
    • Scaled the hub to 0 replicas
    • Rebuilt the JupyterHub sqlite database by matching Kubernetes PVC names back to user ids
    • Set cookie_id to null instead of a dummy value and attached the rebuilt database to the hub
    • Changed the cookie secret in the hub pod and restarted it to log all users out
    • Deleted all user pods to log everyone out
    • Ran a script that filled in cookie_id for all users, restarted the hub and deleted all user pods again
    • Dropped the new users with a '.' in their name and renamed the older users from '-' to '.'
    Action items
    • Report upstream that JupyterHub uses only part of the cookie secret and discards the rest
    • Report upstream that the cookie_id column of the users table should have UNIQUE and NOT NULL constraints
    • Ask KubeSpawner to support username hashes in PVC and pod names so the names stay the same when the database is deleted
    • Ask OAuthenticator to support using the id from the Google authenticator as the user id, giving stable user ids
    • Switch to Google Cloud SQL, a hosted and managed MySQL database
    • Take regular and tested backups of the database
    • Start an operational FAQ of things to do and not to do
    • Set up better monitoring and paging
    • Document escalation procedures explicitly
    View case
Check your cluster for this

This case involves Database and JupyterHub. kubegap audits a Kubernetes cluster for gaps like these, read-only, from Claude Code or Codex; its checks cite public reports like the ones in this library.

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By root cause1

Operator error1 case

Component
DatabaseJupyterHubPersistent volumes and stateful sets
Contributing factor
Harmful manual actionNo safeguard on destructive changeUnsafe failure behaviour
Organisation
UC Berkeley
  1. IL-0506 UC Berkeley DataHub logins failed and students got empty home directories after the JupyterHub database was overwritten
    UC Berkeley2017