feat: auto_packaging toggle via Benchling App Config settings

[QuiltSimon]

Summary

Adds a runtime auto_packaging toggle to the three-tier routing system, configured via Benchling App Configuration Items rather than AWS Secrets Manager.

What changes

• New App Config setting: ["quilt", "settings", "auto_packaging"] — when false, entry events (v2.entry.*) and canvas lifecycle events (v2.canvas.initialized, v2.canvas.created) no longer automatically enqueue packaging work. The canvas renders with the Update Package button so scientists trigger packaging per-entry.
• Defaults to true: existing behavior is preserved when the setting is absent or unrecognized.
• Fail-open on config errors: if the Benchling App Config lookup fails, packaging stays enabled so an API hiccup never silently drops work.
• Immediate toggle: the manifest now subscribes to v2-beta.app.configuration.updated, so toggling the value in the Benchling UI takes effect on the next event (no restart, no60s cache wait).
• Button-driven packaging unaffected: the Update Package button always enqueues packaging regardless of the setting.

Bugfix included

Unknown canvas button interactions now return an explicit {"status": "ignored"} response instead of falling through to the packaging path. Previously, an unrecognized buttonId would enqueue unintended packaging work (with auto_packaging true) or silently re-render the canvas (with auto_packaging false).

Files to focus your review on

File	Change
docker/src/routing_config.py	RuntimeSettings.auto_packaging: bool | None, _bool_value() parser
docker/src/config.py	Config.auto_packaging, resolve_auto_packaging() method
docker/src/app.py	_resolve_auto_packaging(), _render_canvas_without_packaging(), unknown-button early return
docker/app-manifest.yaml	Subscribe to v2-beta.app.configuration.updated
docker/scripts/app_config.py	Seed default ["quilt", "settings", "auto_packaging"] as "true"
docker/tests/test_routing_config.py	Settings parsing tests for true/false/unset/garbage
docker/tests/test_app.py	Entry skipped, canvas renders without packaging, unknown button ignored

Relationship to PR #393

This supersedes the Secrets-Manager-based auto_packaging from #393. That PR routed configuration through BenchlingSecretData and sync-secrets.ts; this PR follows the platform-config-first principle discussed in the #engineering thread: all configurable behavior lives in the platform (Benchling App Config), not in AWS console configuration. Closing #393 in favor of this PR.

Test plan

• docker/tests/test_routing_config.py: auto_packaging parses "true", "False", unset, garbage
• docker/tests/test_app.py: entry event returns skipped when auto_packaging is off
• docker/tests/test_app.py: canvas lifecycle renders without packaging when off
• docker/tests/test_app.py: unknown button returns ignored without enqueuing packaging
• Full suite: 414 passed, 37 deselected
• Deploy to bench.dev.quilttest.com, toggle auto_packaging via Benchling UI, verify entry events no longer auto-package and Update Package button still works

Made with Cursor

Greptile Summary

Adds a runtime auto_packaging toggle controlled by the ["quilt", "settings", "auto_packaging"] Benchling App Config Item, wired through the existing three-tier routing/cache system. When disabled, entry and canvas lifecycle events render the canvas without enqueueing SQS work; the Update Package button is always unaffected. Also fixes a pre-existing bug where unrecognised canvas buttonId values would fall through to the packaging path.

• routing_config.py: New _bool_value() parser and RuntimeSettings.auto_packaging: bool | None field, with clear None-as-unset semantics.
• config.py: resolve_auto_packaging() reads the TTL cache and falls back to the startup-time value; apply_global_routing_config propagates the setting at startup.
• app.py: _resolve_auto_packaging() wraps the config call with a fail-open exception handler; guards are inserted at the three relevant event paths; _render_canvas_without_packaging() handles the canvas-only render; unknown buttons now return {"status": "ignored"} instead of falling through.

Confidence Score: 4/5

Safe to merge; the only finding is a cosmetic dead-parameter in a helper function. Core logic, cache behaviour, and fail-open default are all sound.

The toggle logic is straightforward and well-isolated behind the existing TTL-cache layer. The unknown-button fix is clearly correct. The single comment is about an unused payload argument in _resolve_auto_packaging that doesn't affect runtime behaviour — removing it would improve clarity but nothing breaks with it present.

docker/src/app.py — minor cleanup of the unused parameter in _resolve_auto_packaging and its three call-sites.

Important Files Changed

Filename	Overview
docker/src/app.py	Adds _resolve_auto_packaging and _render_canvas_without_packaging helpers; inserts auto_packaging guards in /event and /canvas handlers; fixes unknown-button fall-through. The payload parameter in _resolve_auto_packaging is unused.
docker/src/config.py	Adds auto_packaging field (default True), propagates it in apply_global_routing_config, and adds resolve_auto_packaging() which reads the TTL-cached routing config and falls back to the startup-time value.
docker/src/routing_config.py	Adds auto_packaging: bool
docker/app-manifest.yaml	Subscribes to v2-beta.app.configuration.updated; Benchling routing convention for v2-beta.app.* events should deliver it to /lifecycle (already handled), but the routing relies on Benchling's prefix conventions.
docker/tests/test_app.py	Adds three new tests covering the auto_packaging disabled path for entry events, canvas lifecycle events, and the unknown-button early-return fix. Tests are clear and correctly mock resolve_auto_packaging.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A[Incoming webhook event] --> B{Endpoint}
    B -->|canvas events| C[canvas handler]
    B -->|entry events| D[event handler]
    B -->|config.updated lifecycle| E[lifecycle handler]
    E --> E1[config.invalidate_routing_config]
    C --> F{userInteracted?}
    F -->|Yes| G{Known buttonId?}
    G -->|browse, page, back, metadata| H[Handle button action]
    G -->|update-package| I[handle_update_package - enqueue]
    G -->|unknown| J[Return ignored - NEW FIX]
    F -->|No - lifecycle event| K{_resolve_auto_packaging}
    K -->|False| L[render canvas without packaging Return 202]
    K -->|True| M[send updating canvas + publish_packaging_request Return 202]
    D --> N{event_type supported?}
    N -->|No| O[Return ignored]
    N -->|Yes| P{_resolve_auto_packaging}
    P -->|False| Q[Return skipped - NEW]
    P -->|True| R[publish_packaging_request - Return ACCEPTED]
    subgraph resolve[_resolve_auto_packaging closure]
        S[get_benchling_secrets] --> T[resolve_auto_packaging via TTL cache]
        T --> U{value in cache?}
        U -->|yes| V[return cached bool]
        U -->|no| W[return config.auto_packaging startup default]
        S -->|Exception| X[return True fail open]
    end

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%%{init: {'theme': 'base', 'themeVariables': {"darkMode": true, "background": "#0d1117", "primaryColor": "#21262d", "primaryTextColor": "#e6edf3", "primaryBorderColor": "#8b949e", "lineColor": "#8b949e", "textColor": "#e6edf3", "edgeLabelBackground": "#161b22", "actorBkg": "#21262d", "actorBorder": "#8b949e", "actorTextColor": "#e6edf3", "actorLineColor": "#8b949e", "signalColor": "#8b949e", "signalTextColor": "#e6edf3", "noteBkgColor": "#373320", "noteBorderColor": "#d4a72c", "noteTextColor": "#f0e6c0", "labelBoxBkgColor": "#21262d", "labelBoxBorderColor": "#8b949e", "labelTextColor": "#e6edf3", "loopTextColor": "#e6edf3", "activationBkgColor": "#30363d", "activationBorderColor": "#8b949e"}}}%%
flowchart TD
    A[Incoming webhook event] --> B{Endpoint}
    B -->|canvas events| C[canvas handler]
    B -->|entry events| D[event handler]
    B -->|config.updated lifecycle| E[lifecycle handler]
    E --> E1[config.invalidate_routing_config]
    C --> F{userInteracted?}
    F -->|Yes| G{Known buttonId?}
    G -->|browse, page, back, metadata| H[Handle button action]
    G -->|update-package| I[handle_update_package - enqueue]
    G -->|unknown| J[Return ignored - NEW FIX]
    F -->|No - lifecycle event| K{_resolve_auto_packaging}
    K -->|False| L[render canvas without packaging Return 202]
    K -->|True| M[send updating canvas + publish_packaging_request Return 202]
    D --> N{event_type supported?}
    N -->|No| O[Return ignored]
    N -->|Yes| P{_resolve_auto_packaging}
    P -->|False| Q[Return skipped - NEW]
    P -->|True| R[publish_packaging_request - Return ACCEPTED]
    subgraph resolve[_resolve_auto_packaging closure]
        S[get_benchling_secrets] --> T[resolve_auto_packaging via TTL cache]
        T --> U{value in cache?}
        U -->|yes| V[return cached bool]
        U -->|no| W[return config.auto_packaging startup default]
        S -->|Exception| X[return True fail open]
    end

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_{Reviews (1): Last reviewed commit: "feat(app-manifest): subscribe to configu..." | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

[greptile-apps]

The payload parameter is declared but never read inside the function — all logic derives solely from config and benchling captured in the closure. Keeping a dead parameter is misleading: callers may assume the result is per-payload, and future authors may accidentally add per-payload logic while thinking the signature already supports it.

Suggested change

	def _resolve_auto_packaging(payload: Payload) -> bool:
	"""Resolve auto_packaging from Tier 1 App Config for this event.
	Defaults to True (current behavior) when unset or when config lookup
	fails, so a Benchling API hiccup never silently drops packaging work.
	"""
	assert benchling is not None and config is not None
	try:
	secrets = config.get_benchling_secrets()
	return config.resolve_auto_packaging(benchling, secrets)
	except Exception as exc:
	logger.warning(
	"Failed to resolve auto_packaging setting; defaulting to enabled",
	error=str(exc),
	error_type=type(exc).__name__,
	)
	return True
	def _resolve_auto_packaging() -> bool:
	"""Resolve auto_packaging from Tier 1 App Config for this event.
	Defaults to True (current behavior) when unset or when config lookup
	fails, so a Benchling API hiccup never silently drops packaging work.
	"""
	assert benchling is not None and config is not None
	try:
	secrets = config.get_benchling_secrets()
	return config.resolve_auto_packaging(benchling, secrets)
	except Exception as exc:
	logger.warning(
	"Failed to resolve auto_packaging setting; defaulting to enabled",
	error=str(exc),
	error_type=type(exc).__name__,
	)
	return True

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