Real-Time Presence, Observability Hardening, and Abby's Growing Medical Brain

A productive Sunday on the Parthenon platform — 70 commits landed today covering four distinct themes: hardening the real-time Commons presence system, fixing a persistent CSRF authentication bug, overhauling the Grafana observability stack, and significantly expanding the medical knowledge base powering Abby, our AI research assistant.

Real-Time Presence in Commons: Now Actually Working

The in-app Commons feature — Parthenon's collaborative research space — had a subtle but frustrating bug: authenticated users weren't consistently appearing as "online" to one another. The root cause was that the presence channel registration was scoped too narrowly and wasn't being initialized globally on authentication. Today's fix (1bdf9ad1) ensures the presence channel is registered at the application bootstrap level for all authenticated sessions, so the online roster in Commons reflects reality.

Alongside that, two related issues were resolved:

• React Router v7 future flag warnings were being logged noisily on every page load. These are suppressed now, and the underlying routing configuration was cleaned up to eliminate a 403 broadcasting auth error that appeared when unauthenticated users triggered WebSocket handshakes (c94a36d2, 9b758408).
• Reverb WebSocket support is now properly enabled in production builds — previously it was only wired up in local dev, meaning presence and live updates were silently broken in deployed environments.

If you're building features that depend on broadcasting or real-time state, the Reverb config in config/broadcasting.php and the frontend Echo initialization are now the canonical reference.

CSRF Fixed: The 419 That Kept Coming Back

The Echo authentication request — used to authorize private and presence channels — was failing with a 419 CSRF token mismatch error in certain session configurations. The fix (10f48a4f) adds the X-XSRF-TOKEN header explicitly to the Echo authEndpoint Axios config. This is a known Laravel + Sanctum + Echo gotcha when the CSRF cookie and session cookie lifetimes diverge: Echo's default auth request doesn't always pick up the XSRF cookie automatically. Future developers integrating additional WebSocket channels should ensure this header is always forwarded.

Grafana & Observability Stack Overhaul

Several monitoring infrastructure issues were tackled today, bringing the Grafana/Prometheus/cAdvisor stack to a more reliable baseline:

cAdvisor was upgraded to v0.51.0 (0b6a0ae5). The previous version had container name pattern mismatches that caused metric gaps in the dashboards — cAdvisor's label schema changed between releases, and our Prometheus scrape configs and Grafana panel queries were targeting the old patterns. The fix also switches Promtail from static scrape configuration to Docker service discovery, meaning new containers are picked up automatically without manual config changes. This is a meaningful operational improvement for a platform that spins up heterogeneous service containers.

Dashboard generator improvements (e5d357c0) clean up the Python-based Grafana JSON generator: stat_panel now accepts a shared datasource parameter rather than having it hardcoded per panel, and path handling is safer when generating output files. The unified dashboard spec (13e3bedd) was also documented with research backing — linking panel design decisions to observability best practices.

Combined, the monitoring stack should now provide accurate container CPU, memory, and restart metrics without the phantom gaps that were appearing in the production Grafana instance.

Abby's Medical Brain: Expanded Textbook Ingestion

Abby is Parthenon's embedded AI research assistant, backed by a ChromaDB vector store that she uses for retrieval-augmented generation over medical literature. Today's commit (9af46d19) significantly expands and corrects the medical textbook ingestion pipeline.

The work focused on improving chunking quality, fixing metadata tagging issues that caused retrieval misses, and broadening the corpus of ingested source material. For outcomes researchers, this means Abby can now draw on a richer grounding of clinical evidence when answering questions about study design, phenotyping, and drug safety — rather than falling back to pure parametric recall.

This is part of the ongoing effort to make Abby a genuinely useful research collaborator rather than a generic chatbot wrapper. The ingestion scripts live in the abby/ directory if you want to add additional textbooks or clinical guidelines to the corpus.

Production Safety: No More Fake Data Sources

A quiet but important guard (03f00b3d) was added to prevent synthetic/fake data sources from ever being instantiated in production environments. During development, placeholder sources are useful for UI testing, but there have been cases where misconfiguration allowed them to bleed into non-dev deployments. The fix adds an environment check at the data source factory level — if APP_ENV=production, fake sources throw rather than silently returning stub data. This protects the integrity of any analysis run against what researchers assume is real OMOP data.

What's Next

With the Commons presence system stable and the observability stack on solid footing, the near-term focus shifts to:

• Phase 9.10 documentation — the API reference and developer guide pages that are still in progress
• Abby retrieval quality evaluation — now that the corpus is larger, we need systematic evals to confirm retrieval precision hasn't regressed
• Dashboard generator test coverage — the refactored stat panel generator needs unit tests before we add more panel types
• Promtail Docker SD validation — confirming all service containers are being picked up correctly in the production log pipeline

The platform is in a good place heading into the week. The combination of real-time fixes, observability improvements, and AI knowledge expansion makes today's commit batch one of the more satisfying cross-cutting days in recent memory.