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README.md

gitlist — Git Browser Component for code.bioconductor.org

Description

The gitlist directory contains the Dockerized GitList web application used to browse Bioconductor package repositories.

Architecture

The service runs as two cooperating processes inside a single container:

  • nginx – A lightweight web server that:

    • Listens for HTTP requests from clients.
    • Serves static assets (CSS, JS, images) directly for speed.
    • Forwards requests that require PHP processing to php-fpm.

  • php-fpm – The PHP FastCGI Process Manager that:

    • Runs the GitList PHP code.
    • Handles dynamic requests like rendering repository views, diffs, and commit history.
    • Returns generated HTML back to nginx over a FastCGI interface.

Flow of a request:

  1. User requests a GitList page (e.g., /packages/myPackage/commit/1234).
  2. nginx checks if it’s a static file — if not, it proxies the request to php-fpm via FastCGI.
  3. php-fpm executes the GitList PHP code, which reads from the Git repositories mounted at /var/git.
  4. The generated HTML is sent back through nginx to the user’s browser.

This separation allows:

  • Static files to be served very quickly without touching PHP.
  • PHP code to run in a managed, pooled environment (improving performance and stability).

GoAccess Web Logs

The GitList service’s access logs are analysed using GoAccess, a real-time log analyzer.
The GoAccess output is published as a password-protected dashboard at: https://code.bioconductor.org/logs

GoAccess Features:

  • Tracks visitor counts, request types, most popular repositories/pages.
  • Monitors response codes, referrers, and bandwidth usage.
  • Generates a live HTML report updated every second.
  • The /logs endpoint is protected by HTTP Basic Authentication configured in nginx. Contact Mike Smith for details on the password or update the nginx-auth-secret in kubernetes.

Log Rotation & Maintenance

To prevent large log files from filling the disk:

  • logrotate is configured to:

    • Rotate nginx access and error logs on a daily schedule retaining the last 90 days.
    • Trigger GoAccess processing after rotation so that stats are up-to-date.

  • Kubernetes CronJob:

    • Runs logrotate daily to ensure log files are rotated without manual intervention.
    • Sends a kill -USR1 1 message to the pods running nginx and goaccess to ensure they start using the newly created log files.