Problem: In a BSL-2 clinical genomics wet lab preparing Whole Genome Sequencing (WGS) libraries for rare genetic disease testing, technologists wear double nitrile gloves and cannot touch a keyboard without de-gloving. However, gating a $5,000+ sequencing flow cell (FLOWCELL-WGS-07) and downstream cloud bioinformatics pipelines (Illumina Connected Analytics → DRAGEN → Emedgene) requires more than conversational memory: it requires authoritative backend state, server-side numeric bounds validation, idempotent retry safety, physical instrument locking, and policy-bound exception resolution.
Solution: Checkpoint separates conversational interaction (Alexa+ over MCP Streamable HTTP) from authoritative workflow execution. It exposes 6 MCP tools (start_inspection, get_inspection_status, record_inspection_result, resolve_inspection_exception, complete_inspection, and configure_notifications) protected by two-tier OAuth 2.1 (mcp:service and mcp:tools with PKCE S256 and headerless HTTP 401 responses).
Key Reliability Features Demonstrated:
Crash & Restart Survival (AC3, AC4): Resumes interrupted wet-lab QC runs from authoritative SQLite WAL / DynamoDB storage without relying on conversation history.
Atomic Idempotency (AC5–AC7): Canonical SHA-256 request payload fingerprinting returns immutable outcomes with duplicate: true on network retries and rejects payload mismatches with IDEMPOTENCY_CONFLICT.
Multi-Session Disambiguation & Asset Exclusivity (AC17): Prevents two operators from inspecting the same physical flow cell concurrently (ASSET_ALREADY_UNDER_INSPECTION) and disambiguates when one technologist has multiple active flow cells (AMBIGUOUS_ACTIVE_SESSION).
Policy-Whitelisted Exception Gating (AC8–AC10): Blocks out-of-range readings (such as 310.0 pM loading molarity), rejects premature completion (WORKFLOW_BLOCKED), and rejects arbitrary LLM-invented overrides (FORCE_PASS).
Transactional Live Notifications (AC18): Emits pause, revision, block, status, and completion alerts via NotificationPort (local sink or Amazon SNS).
Candor & Safety Note: All genomics flow-cell IDs (FLOWCELL-WGS-07), pump assets (PUMP-07), and readings are synthetic software reliability fixtures. Our CLI walkthrough (run_demo_walkthrough.py) explicitly labels simulated MCP runs (LOCAL_MCP_SIMULATION / REMOTE_AWS_MCP_SIMULATION).
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