# VigilCare Clinical API

A production-quality clinical backend built with ASP.NET Core 8, PostgreSQL, Apache Kafka, RabbitMQ, Elasticsearch, Redis, and MinIO. The domain models the observe-alert-acknowledge lifecycle at the center of any clinical monitoring system: patient encounters, continuous vital sign and lab result ingest, real-time sepsis and NEWS2 scoring, and clinician notification with automatic escalation.

**Implementation status:** Thirty-three planned phases are complete through Phase 35 (plus Phases 20–23) — from schema and CRUD through Kafka, Elasticsearch CQRS, sepsis detection, RabbitMQ paging with DLQ escalation, reconciliation jobs, Prometheus/Grafana observability, the MinIO Parquet data lake, clinical data model expansion, warning alerts and orders, the NEWS2 composite scoring engine, trend detection with alert suppression, qSOFA bedside screening, medication administration with alert correlation annotations, the console replay simulator, the **Vue 3 ward dashboard**, clinician feedback mode, **Glasgow Coma Scale (GCS) scoring**, **SOFA organ-dysfunction scoring with baseline tracking and delta sepsis alerts**, the **Sepsis-3 clinical refactor** (SIRS removed, qSOFA repositioned as screening, SOFA delta ≥ 2 triggers bundles), **frontend GCS entry and SOFA display**, **expanded simulator scenarios with clinical validation**, the **Site & Gateway Registry** with dual authentication, shared clinical sync contracts, and fleet health Prometheus gauges, the **Ward Gateway Service** (local-first clinical path with offline buffering and central sync), the **FHIR R4 Inbound Facade** for EHR integration, **Role-Based Access Control (RBAC) with clinical audit logging**, the **Dashboard Gap Analysis Fixes** (SOFA/GCS/qSOFA history charts, patient banner, encounter timeline, medication markers on vital charts), the **Enhanced Dashboard** (department overview, sepsis bundle board, critical alert notifications, shift handoff reports, vitals entry form, sortable/filterable ward table), **Degraded Operations Visibility** (gateway fleet operations panel, stale gateway auto-detection, discharge summary API, admin panels for user/threshold/audit/reconciliation management, degraded-mode banner), **Alert Quality Analytics** (server-side clinician feedback with `AlertFeedback` entity, `AlertQualityAggregatorService` background metrics, quality metrics API, Grafana alert quality dashboard), **Explainable Alerts** (immutable JSONB `explanation` on composite alerts with score contributors, trend context, structured medication context, and bedside `NarrativeSummary`; `AlertResponse` DTO on GET/list/acknowledge/resolve; dashboard `AlertReasoning.vue`; ES indexer and data lake propagation; ward gateway sync), and **MIMIC-IV Replay Scenario Generator** (offline CLI tool converting real de-identified ICU data from MIT PhysioNet into VigilCare scenario JSONs; streaming CSV parser for 668K-row chartevents; 17 chart + 8 lab item ID mappings to VigilCare observation codes; GCS text-to-numeric conversion; Fahrenheit-to-Celsius; blood pressure deduplication preferring non-invasive over arterial; 10-observation cluster limit enforcement; `mimic-list` and `mimic-generate` CLI commands with Spectre.Console output; 100 patients / 140 ICU stays available for replay through NEWS2, SOFA, GCS, qSOFA, trend detection, and alerting). Post-phase hardening includes health check endpoints, Kafka poison pill protection, outbox dead-letter with retry tracking, data lake partial-commit safety, MRN sequence-based generation, FHIR bundle transaction rollback, **FHIR R4 read/search endpoints** (Patient and Encounter), **alert threshold deletion with audit trail**, **FHIR API key rotation** (constant-time multi-key validation), **authorization failure logging** with Prometheus metrics, **JWT signing key validation** at startup, **token refresh and revocation** (short-lived access tokens with rotating refresh tokens, server-side logout, proactive frontend refresh), and **concurrency hardening** (transactional sepsis bundle creation, unique active encounter constraint). See [Implemented Phases](#implemented-phases) for the full breakdown. Guides: [dashboard-guide.md](docs/dashboard-guide.md) (technical), [clinical-testing-guide.md](docs/clinical-testing-guide.md) (doctors & nurses).

## Domain Model — How It Maps to a Real Clinical System

In a hospital, a patient presents for care and an encounter is opened. Bedside monitors and lab systems post observations continuously against that encounter — either directly via the REST API, through the FHIR R4 facade that maps HL7 FHIR resources from integration engines (Mirth Connect, Rhapsody), or via ward gateway edge nodes that buffer observations locally during connectivity loss and sync to the central API when the link recovers. The FHIR facade also exposes read and search interactions so EHR systems can query patient and encounter data back in standard FHIR R4 format. A rules engine evaluates each observation against configured thresholds and flags abnormal values as clinical alerts. Composite scoring engines (NEWS2, GCS, SOFA, qSOFA) aggregate multiple vitals and labs into acuity scores. The sepsis pathway follows Sepsis-3 consensus: qSOFA ≥ 2 creates a bedside screening alert recommending SOFA labs; when SOFA delta ≥ 2 from baseline confirms organ dysfunction, a `SOFA_SEPSIS` alert triggers the treatment bundle. Clinicians authenticate via JWT with short-lived access tokens (15 min) and rotating refresh tokens (7 days), and role-based access control (RBAC) gates every endpoint by clinical role (Nurse, Physician, Admin, Integration). Clinicians acknowledge and resolve alerts. If a critical alert goes unacknowledged for five minutes, the system escalates to the on-call backup. All clinical write actions — patient registration, alert acknowledgment, threshold changes, encounter transitions — are recorded in an append-only audit log with user identity, IP address, correlation ID, and before/after state. All events flow through Kafka so the Elasticsearch dashboard, scoring engines, and data lake writer consume the same stream independently.

```
Patient ─────────────────────────── one patient = one MRN, many lifetime encounters
 └── Encounter                       one clinical episode (inpatient, outpatient, ED)
      ├── Observation                 one measurement: vital sign, lab value, SpO₂
      │    └── OutboxEvent            written in the same transaction → relayed to Kafka
      └── ClinicalAlert              generated on threshold breach, qSOFA screen, SOFA delta, or NEWS2 composite score
           ├── OutboxEvent            → Kafka → RabbitMQ → clinician page → escalation
           └── SepsisBundle           auto-created on SOFA_SEPSIS alert → four treatment orders → compliance tracking
```

### Patient

A `Patient` is registered with demographic information and assigned a Medical Record Number (MRN) — a stable identifier that never changes across encounters. Optional clinical fields include blood type (`A+`, `O-`, etc.), known allergies, and emergency contact name/phone. Patient search supports both MRN exact match and name partial match (`ILIKE`).

### Encounter

An `Encounter` is a single clinical episode. Status follows a controlled machine: `scheduled → active → discharged` (or `cancelled` from any pre-discharged state). Optional `roomBed` and `admissionReason` fields support ward assignment and clinical context; `dischargeDiagnosis` is set on discharge. Observations, alerts, and orders belong to an encounter, not directly to a patient — this bounds queries naturally and mirrors real clinical data ownership. Discharge triggers a RabbitMQ job to generate a discharge summary.

### AlertThreshold

Alert thresholds define the numeric boundaries that trigger a clinical alert for a given observation code. Each threshold has four optional bounds: `criticalLow`, `warningLow`, `warningHigh`, `criticalHigh`. Thresholds are pre-loaded into Redis on startup and invalidated on write — they are read on every observation ingest and must not add database latency to the hot path.

### Observation

An `Observation` is a single recorded measurement: a vital sign, lab value, or pulse oximetry reading. Observations are append-only — never updated or deleted. Each observation is evaluated against the Redis-cached threshold immediately on ingest. A `CRITICAL` breach synchronously creates a `ClinicalAlert` within the same transaction before the API returns. A `WARNING` breach is deferred to the Kafka consumer. This split is a deliberate patient safety decision.

An `idempotencyKey` (partial unique index) prevents duplicate observations when medical devices retry on network failure.

### ClinicalAlert

A `ClinicalAlert` is generated when an observation breaches a threshold, when the qSOFA engine detects two or more organ-dysfunction criteria (screening), when SOFA delta ≥ 2 from baseline confirms sepsis, or when the NEWS2 engine computes a medium/high-risk composite score (or a single-parameter score of 3). Lifecycle: `open → acknowledged → resolved` (or `escalated` after a five-minute NACK cycle through the RabbitMQ dead-letter queue). Alerts carry an audit trail: who acknowledged, when, and with what note. Composite alerts from NEWS2, SOFA, GCS, and trend detection also carry an immutable JSONB `explanation` snapshot — score contributors, trend context, medication context, and a bedside narrative — frozen at alert creation time. The human-readable `details` string remains for backward compatibility. Only `SOFA_SEPSIS` alerts trigger automatic sepsis bundle creation.

### SepsisBundle

A `SepsisBundle` is created automatically when the SOFA scoring engine detects a delta ≥ 2 from baseline (`SOFA_SEPSIS` alert). Each bundle contains four mandatory treatment elements (blood cultures, serum lactate, broad-spectrum antibiotics, IV fluid resuscitation) mapped to clinical orders that are created simultaneously. A one-hour compliance deadline is set from the recognition time. As linked orders are resulted, bundle elements transition to `COMPLETED`; when all four are done, the bundle is marked `COMPLIANT` (within deadline) or `NON_COMPLIANT` (past deadline). Only one in-progress bundle can exist per encounter at a time.

### OutboxEvent

An `OutboxEvent` is written in the same transaction as any observation or alert, then relayed to Kafka by a background worker. This decouples Kafka availability from the ingest transaction — observations commit to PostgreSQL while Kafka is down, and the relay catches up on recovery.

---

## Features

- **Patient Registration** — register patients with MRN generation; optional blood type, allergies, and emergency contact; paginated list with name (`ILIKE`) and MRN (exact) search; patient detail with active encounter summary
- **Encounter Management** — open encounters against a patient with optional room/bed and admission reason; encounter status state machine (`scheduled → active → discharged / cancelled`) with 409 on illegal transitions; unique active encounter per type per patient enforced by partial unique index (concurrent duplicate attempts return 409); optional discharge diagnosis on discharge; encounter timeline as a merged chronological view across status changes, observation summaries, and alerts
- **Alert Threshold Management** — configure per-observation-code numeric bounds (`criticalLow`, `warningLow`, `warningHigh`, `criticalHigh`) for 12 observation codes; thresholds pre-loaded into Redis on startup; write-through cache invalidation on update and delete; `DELETE /alert-thresholds/{id}` removes a threshold with `THRESHOLD_DELETED` audit trail and Redis cache invalidation
- **Observation Ingest** — `POST /encounters/:id/observations` accepts single or small batch (up to 10); idempotency via `Idempotency-Key` header (partial unique index); plausibility validation per observation code; synchronous critical alert creation within the ingest transaction; warning-range breaches evaluated asynchronously by `WarningAlertService` (Kafka consumer group `warning-evaluator`); outbox event written in the same commit; cursor-paginated history on `(encounter_id, observation_code, recorded_at DESC)`
- **Warning Threshold Alerts** — `WarningEvaluator` reads thresholds from Redis; creates `WARNING`-severity alerts for values above `warningHigh` or below `warningLow` that are not also critical breaches; idempotent `INSERT WHERE NOT EXISTS` per encounter and alert type while status is `OPEN` or `ACKNOWLEDGED`; warning alerts are indexed in Elasticsearch but not published to the RabbitMQ paging queue
- **Clinical Order Management** — `POST /encounters/:id/orders` create; `GET /encounters/:id/orders` list with optional status filter; `GET /orders/:id` detail; `PATCH /orders/:id/status` status transitions; `PATCH /orders/:id/result` record result and transition to `Resulted`; status machine enforces `Pending → InProgress → Resulted` and terminal `Cancelled`
- **Clinical Alert Lifecycle** — paginated alert list per encounter and globally; acknowledge with clinician ID and optional note; resolve (must be acknowledged first); global list filterable by status, severity, and department
- **Outbox Relay** — `IHostedService` polling every 500ms; reads unprocessed outbox rows with `FOR UPDATE SKIP LOCKED` (safe for concurrent instances), publishes to Kafka via idempotent producer (`EnableIdempotence = true`), marks processed; per-event retry tracking (`RetryCount`, `LastError`); events exceeding `OutboxMaxRetries` (default 10) are marked permanently failed (`FailedAt`) and excluded from future polls; partitioned by `encounterId` for per-encounter ordering
- **Kafka Pipeline** — core topics (`observation.recorded`, `alert.generated`, `encounter.status.changed`, `gcs.scored`, sepsis bundle topics) with six partitions each; configurable `ReplicationFactor` (default 3); KRaft mode, no Zookeeper; `KAFKA_AUTO_CREATE_TOPICS_ENABLE=false` — topics are provisioned explicitly by `KafkaTopicProvisioner` (including `gcs.scored` for SOFA CNS re-scoring and `sofa.scored` for downstream consumers); all consumers protected by `PoisonPillGuard` (permanent errors skipped, transient errors retried up to `MaxPoisonRetries`)
- **Elasticsearch CQRS Projection** — `EsIndexerService` consumer group upserts `patient_encounters` documents, appends to the `observations` index, increments `openAlertCount` on alert events, stamps `news2Score` / `news2RiskLevel` when a NEWS2 alert is generated, and projects `sepsisBundleStatus` / `sepsisBundleElementsCompleted` / `sepsisBundleDeadlineAt` from SOFA-triggered sepsis bundle events; patient/encounter search; per-encounter observation trend (hourly avg/min/max); alert volume summary by department and severity; population query (numeric range aggregation across all patients)
- **Sepsis Screening Engine** — `SepsisEngineService` Kafka consumer evaluates qSOFA criteria per encounter using Redis keys with a 30-minute TTL sliding window; qSOFA evaluates respiratory rate ≥ 22, systolic BP ≤ 100, and altered mentation (GCS < 15 or AVPU ≥ 1); on ≥ 2 active criteria and no open screening alert, inserts a `QSOFA_SCREEN` (WARNING-level) alert idempotently (`INSERT WHERE NOT EXISTS`); every evaluation is persisted to `qsofa_evaluations` with criteria values and screen-alert-fired flag; `GET /encounters/:id/qsofa/history` provides cursor-paginated evaluation history; qSOFA screening recommends ordering SOFA labs — definitive sepsis detection and bundle triggering are handled by `SofaScoringService` via SOFA delta ≥ 2
- **Sepsis Bundle Compliance** — `SepsisBundleService` creates a four-element treatment bundle (blood cultures, serum lactate, broad-spectrum antibiotics, IV fluid resuscitation) when a `SOFA_SEPSIS` alert fires (delta ≥ 2 from baseline); each element maps to an auto-created clinical order (`orderedBy: sepsis-bundle-engine`); one-hour compliance deadline from recognition; `OrderService.RecordResult` calls back to `OnOrderResultedAsync` to mark elements complete; final element completion sets bundle to `COMPLIANT` or `NON_COMPLIANT`; `SepsisBundleMonitorService` scans every 5 minutes for overdue in-progress bundles past their deadline and marks them `NON_COMPLIANT`; idempotent — only one in-progress bundle per encounter; `GET /encounters/:id/sepsis-bundle/current` and `GET /sepsis-bundles/:id` expose bundle state; Kafka topics `sepsis.bundle.created` / `sepsis.bundle.updated`; Prometheus `qsofa_detections_total` and `sepsis_bundle_compliance_total`
- **NEWS2 Composite Scoring Engine** — `News2ScoringService` Kafka consumer (`news2-scoring`) evaluates seven vital parameters per encounter (`RESP_RATE`, `SPO2`, `SYSTOLIC_BP`, `HEART_RATE`, `AVPU`, `TEMP_C`, `SUPPLEMENTAL_O2`) using Redis keys with a 4-hour TTL; when all seven are present, computes the official NEWS2 aggregate score, persists to `news2_scores`, and creates `NEWS2_WARNING` (score 5–6 or single param = 3) or `NEWS2_EMERGENCY` (score ≥ 7) alerts idempotently; consciousness resolves GCS-first with AVPU fallback; `GET /encounters/:id/news2/current` and `/history` expose score history; Prometheus `news2_scores_total` and `news2_scoring_duration_seconds`
- **Glasgow Coma Scale (GCS) Scoring** — `GcsScoringService` Kafka consumer (`gcs-scoring`) tracks three components (`GCS_EYE`, `GCS_VERBAL`, `GCS_MOTOR`) in Redis; when all three are present, computes total score and classification (`MILD` / `MODERATE` / `SEVERE`), persists to `gcs_scores`, creates `GCS_CRITICAL` (total ≤ 8) or `GCS_WARNING` (9–12) alerts idempotently, and publishes `gcs.scored` via outbox for downstream SOFA CNS re-scoring; feeds NEWS2 consciousness and qSOFA altered mentation; `GET /encounters/:id/gcs` exposes the latest score; `GET /encounters/:id/gcs/history` provides cursor-paginated score history with component breakdown; Prometheus `gcs_scores_total`
- **SOFA Organ-Dysfunction Scoring** — `SofaScoringService` Kafka consumer (`sofa-scoring`) subscribes to `observation.recorded` and `gcs.scored`; scores six organ systems (respiratory, coagulation, liver, cardiovascular, CNS, renal) from Redis lab cache with carry-forward staleness, MAP derivation, SpO₂/FiO₂ fallback, and vasopressor detection from `MedicationAdministration`; persists to `sofa_scores` with baseline tracking (≥ 4 populated organ systems) and delta-from-baseline; delta ≥ 2 creates `SOFA_SEPSIS` (CRITICAL), delta = 1 creates `SOFA_WARNING`; skips stale Kafka events when the encounter row no longer exists; `GET /encounters/:id/sofa` and `/sofa/history` expose scores; Prometheus `sofa_scores_total` and `sofa_scoring_duration_seconds`
- **Trend Detection Engine** — `TrendAnalyzerService` Kafka consumer (`trend-analyzer`) tracks rate-of-change for five vital parameters (`HEART_RATE`, `RESP_RATE`, `SYSTOLIC_BP`, `TEMP_C`, `SPO2`) using Redis sliding-window history; when velocity exceeds configured thresholds (e.g. 72→95 bpm in 30 min), creates a `RAPID_DETERIORATION` alert even if the current value is below warning thresholds; Prometheus `trend_alerts_total` and `trend_analysis_duration_seconds`
- **Alert Suppression Windows** — acknowledging a suppressible alert (`WARNING_*`, `NEWS2_WARNING`) sets a Redis key `suppress:{encounterId}:{alertType}` with a configurable TTL (default 30 min from `AlertSuppression` config; optional per-code override via `alert_thresholds.suppression_window_minutes`); `WarningEvaluator` and `News2Detector` check suppression before creating new warning alerts; critical alerts (`CRITICAL_*`, `NEWS2_EMERGENCY`, `SEPSIS_WARNING`, `RAPID_DETERIORATION`) are never suppressed; observations and NEWS2 scores continue to persist during suppression; Prometheus `alert_suppressions_total`
- **Medication Administration** — `POST /encounters/:id/medications` records drug administrations (name, dose, route, timestamp, administered-by); `GET /encounters/:id/medications` lists with optional `since` filter; `GET /medications/:id` detail; active-encounter guard; FluentValidation on request DTOs
- **Medication Correlation Annotations** — `MedicationCorrelationHelper` appends medication context to warning alert `details` when a mapped drug was administered within the correlation window (default 90 min); explainable alerts (NEWS2, SOFA, GCS, rapid deterioration) receive structured `MedicationContext` in the JSONB `explanation` via `TryGetContextAsync()`; drug-to-vital mappings in `MedicationCorrelation` config (`appsettings.json`); annotates rather than suppresses — alerts still fire; sepsis, trend, and critical sync-path alerts are never annotated; design rationale in `docs/decisions/medication-correlation-design.md`
- **Ward Dashboard APIs** — `GET /encounters` returns paginated `WardEncounterSummary` rows (patient name/MRN, room/bed, department, status, latest NEWS2 score, live qSOFA criteria count from Redis, sepsis bundle status, open alert count, SOFA score/delta, GCS score/classification, attending physician, admitted-at, last observation time); filterable by `status` and `department`; `GET /encounters/:id/qsofa/current` exposes Redis-backed qSOFA state; `GET /sepsis-bundles` lists bundles hospital-wide with optional `status` filter (returns `SepsisBundleSummary` with patient demographics, elements, and deadlines); CORS policy `Dashboard` allows configured origins (default `http://localhost:5173`)
- **Ward Dashboard Frontend** — Vue 3 SPA (`vigilcare-dashboard/`) with virtual ward table (multi-column sortable, patient search, quick-filters for critical/alerts/sepsis), patient detail (vitals, scores, alerts, orders, sepsis bundle, GCS entry form, SOFA score panel, patient banner with demographics/allergies/emergency contact, encounter timeline, vitals entry form for manual observation recording, discharge summary panel), alert center (global acknowledge/resolve with role-aware modal and acknowledgment note preview), department overview (unit-level snapshot cards with acuity bars, patient/alert/bundle counts per department), sepsis bundle board (real-time countdown timers, on-track/at-risk/overdue urgency sorting), critical alert banner with browser notifications and audible tone, shift handoff report generator (SBAR format with ward summary, exportable via print/PDF), vital sign trend charts with medication administration markers and local replay scrubbing, NEWS2 history chart, SOFA history chart with organ-system breakdown, GCS history chart with component tracking, qSOFA evaluation history, structured alert reasoning (`AlertReasoning.vue` — score contributors, trend context, medication context, narrative summary from `explanation`), clinician feedback on every alert, admin panels (threshold management, user management, audit log viewer, reconciliation viewer), gateway operations dashboard with degraded-mode banner, and alert quality analytics with quality charts; role-aware sidebar navigation; polls API every 5–10 s; guides in `docs/dashboard-guide.md` and `docs/clinical-testing-guide.md`
- **FHIR R4 Inbound Facade** — `POST /fhir/R4/{Patient,Encounter,Observation,MedicationAdministration}` accepts FHIR R4 JSON resources (`application/fhir+json`); `POST /fhir/R4` processes transaction Bundles (Patient → Encounter → Observation in dependency order); `GET /fhir/R4/metadata` returns a CapabilityStatement; LOINC-to-internal code mapping (19 observation codes + SNOMED CT fallbacks); Fahrenheit-to-Celsius unit conversion; `ExternalResourceIdentifier` table links hospital MRNs and visit numbers to internal UUIDs for idempotent upserts; `FhirApiKeyOrJwtMiddleware` authenticates via JWT bearer or `X-Api-Key` header (supports multiple keys via `Fhir:ApiKeys` array for zero-downtime rotation; constant-time comparison via `CryptographicOperations.FixedTimeEquals`); `FhirExceptionFilter` returns FHIR `OperationOutcome` on errors; configurable identifier systems, department codes, and encounter class mappings via `Fhir` config section; Prometheus `fhir_ingest_total` and `fhir_mapping_errors_total`; integration guide for Mirth Connect HL7v2→FHIR channels in `docs/integration/mirth-fhir-channels.md`
- **FHIR R4 Read/Search** — `GET /fhir/R4/Patient/{id}` reads a Patient by internal ID; `GET /fhir/R4/Patient` searches by `identifier` (system|value) or lists all patients; `GET /fhir/R4/Encounter/{id}` reads an Encounter by internal ID; `GET /fhir/R4/Encounter` searches by `patient` (UUID) and/or `status` (`in-progress`, `finished`, `cancelled`); all return FHIR R4 JSON (`application/fhir+json`); search endpoints return `Bundle.type=searchset`; requires `fhir:read` permission (Admin and Integration roles); internal resources mapped back to FHIR via `PatientFhirMapper.ToFhirResponse` / `EncounterFhirMapper.ToFhirResponse` with hospital identifier resolution; Prometheus `fhir_read_total` counter with `resource_type`, `interaction`, `outcome` labels
- **Role-Based Access Control (RBAC)** — JWT bearer authentication (`POST /auth/login`); four clinical roles (`Nurse`, `Physician`, `Admin`, `Integration`) with 18 granular permissions (`patients:read`, `alerts:acknowledge`, `alerts:feedback`, `thresholds:write`, `fhir:ingest`, `fhir:read`, `audit:read`, etc.); `AuthorizePermission` attribute on every controller action; `PermissionAuthorizationHandler` resolves role → permission at runtime from `ClinicalRolePermissionMap` and logs authorization failures with structured details (user, role, permission, endpoint) plus `authorization_failures_total` Prometheus counter; `CurrentUserService` exposes authenticated identity (user ID, display name, role, IP address) to services; nurses and physicians get clinical read/write permissions; admins additionally get `thresholds:write`, `fhir:read`, `audit:read`, and `users:admin`; integration accounts get FHIR ingest and read access; FHIR endpoints accept both JWT and `X-Api-Key` authentication via `FhirApiKeyOrJwtMiddleware`; alert `acknowledgedBy` is set from the authenticated user identity, not the request body; startup validates JWT signing key is at least 256 bits (HMAC-SHA256 minimum); **token refresh and revocation** — short-lived access tokens (15 min) paired with rotating opaque refresh tokens (7 days) stored in the `refresh_tokens` table; `POST /auth/refresh` exchanges a valid refresh token for a new access + refresh token pair (rotation on every use revokes the previous token); `POST /auth/logout` revokes the refresh token server-side with `USER_LOGOUT` audit log; frontend auto-refreshes 1 minute before expiry, retries on 401, and redirects to login when the refresh token is exhausted; logout button in header, sidebar, and mobile nav; four seeded demo users (`nurse.demo`, `physician.demo`, `admin.demo`, `integration.mirth`)
- **Clinical Audit Logging** — append-only `clinical_audit_logs` table records clinical write actions with user identity, entity type/ID, before/after state (JSONB), reason, IP address, and correlation ID; twelve audit actions (`THRESHOLD_CREATED`, `THRESHOLD_UPDATED`, `THRESHOLD_DELETED`, `ALERT_ACKNOWLEDGED`, `ALERT_RESOLVED`, `ENCOUNTER_STATUS_CHANGED`, `PATIENT_REGISTERED`, `SUPPRESSION_WINDOW_SET`, `USER_LOGIN`, `AUTHORIZATION_DENIED`, `USER_LOGOUT`, `TOKEN_REFRESHED`); `AuditService` writes log entries inline with domain operations; `GET /audit-logs` admin-only query endpoint with filters by entity type, entity ID, user ID, action, and time range; indexed on entity type, entity ID, user ID, and timestamp
- **Site & Gateway Registry** — `ClinicalSite` and `WardGateway` domain entities model ward edge nodes that buffer clinical data during connectivity loss; `POST /sites` creates clinical sites; `POST /sites/{siteId}/gateways` registers gateways under a site; `PATCH /gateways/{gatewayId}/heartbeat` (gateway API key auth) updates status (`ONLINE`, `DEGRADED`, `OFFLINE`) and reported buffer depth; `GET /sites/{siteId}/gateways` lists gateways with optional `?department=` filter; dual authentication — JWT + RBAC (`users:admin`) for admin CRUD, `GatewayApiKeyAuthenticationHandler` (`X-Api-Key` + `X-Gateway-Id`) for gateway heartbeat and future sync upload; constant-time key comparison via `CryptographicOperations.FixedTimeEquals`; `VigilCare.ClinicalContracts` shared class library with sync DTOs (`ClinicalSyncBatchRequest`, `SyncedObservation`, `SyncedAlertEvent`, `GatewayHeartbeatRequest`) consumed by both central API and ward gateway projects; Prometheus `ward_gateways_offline_gauge` and `ward_gateway_buffer_depth` via `WardGatewayMetricsCollector` (60s periodic); `GatewayRegistrySeeder` provides demo site and gateway for Docker Compose and tests; FluentValidation on all request DTOs; `GatewayRegistryTests` and `ClinicalContractsTests` integration tests
- **Ward Gateway Service** — `VigilCare.WardGateway` (`http://localhost:5081`) is a standalone ASP.NET Core 8 deployable with its own PostgreSQL, Redis, and RabbitMQ; ingests observations locally via `POST /encounters/:id/observations` with plausibility validation, Redis-cached threshold evaluation, and synchronous critical alert creation; `LocalWarningEvaluator` creates warning-range alerts; `BufferedSyncWriter` writes all clinical events to `buffered_sync_items` for central upload; `EncounterReplicaSyncService` pulls patient/encounter data from central API; `ThresholdCacheLoader` fetches thresholds from central into local Redis; `CentralReachabilityService` tracks central API connectivity; `GatewayHeartbeatService` reports status and buffer depth; `SyncUploaderService` batches and uploads buffered items when online; local RabbitMQ paging and escalation queues; `GET /encounters` ward list and `GET /encounters/:id` detail; `GET /health/live` and `GET /health/ready` (Redis, RabbitMQ, encounter replica readiness); Docker Compose `ward-gateway` profile
- **Health Check Endpoints** — `GET /health/live` (liveness — always returns 200 if the process is running) and `GET /health/ready` (readiness — checks PostgreSQL, Redis, Kafka, RabbitMQ, and Elasticsearch connectivity); both return structured JSON with per-check status and duration; anonymous access; suitable for Kubernetes probes and load balancer health checks
- **Kafka Poison Pill Protection** — `PoisonPillGuard` prevents a single un-processable message from blocking a consumer partition forever; permanent errors (malformed JSON, bad format) are skipped immediately; transient errors are retried up to `MaxPoisonRetries` (default 5) before the offset is committed and the message is abandoned; all eight Kafka consumers use the guard; skipped messages are logged at CRITICAL with full payload and tracked by Prometheus `kafka_poison_pills_skipped_total` (labeled by consumer group and topic)
- **Outbox Dead-Letter with Retry Tracking** — `OutboxRelayService` tracks `RetryCount`, `LastError`, and `FailedAt` per event; events that fail `OutboxMaxRetries` (default 10) Kafka produce attempts are marked permanently failed (`FailedAt` set) and excluded from future relay polls; uses `FOR UPDATE SKIP LOCKED` for safe concurrent relay instances; idempotent Kafka producer (`EnableIdempotence = true`) prevents duplicate messages from network-level retries
- **Data Lake Partial-Commit Safety** — `DataLakeWriterService` commits Kafka offsets only for topic-partitions where all MinIO uploads succeeded; failed partition buffers are retained in memory and retried on the next flush cycle; prevents data loss from partial upload failures
- **ThresholdCacheLoader Resilience** — retries Redis connection up to 3 times with exponential backoff (2s, 4s, 8s); if Redis remains unavailable, the application starts without the cache and observation ingest falls back to PostgreSQL queries for threshold lookups
- **MRN Sequence Generation** — MRN numbers are generated via a PostgreSQL sequence (`mrn_seq`) instead of MAX+1 queries; eliminates race conditions under concurrent patient registration; configurable prefix and digit count via `PatientOptions`
- **FHIR Bundle Transaction Rollback** — `FhirBundleProcessor` wraps all bundle entry processing in a database transaction; on any entry failure, the transaction is rolled back and the response includes the `OperationOutcome` for the failed entry; prevents partial state from orphaned Patient/Encounter records
- **Clinician Feedback Mode** — six quick ratings per alert (useful, too early, too late, false positive, missing context, would act); optional notes; server-side `AlertFeedback` entity persisted per user per alert (`POST /alerts/{id}/feedback`); `alerts:feedback` permission for Nurse, Physician, and Admin roles; Feedback Summary with aggregate stats and JSON/CSV export; client-side persistence for product research
- **Alert Quality Analytics** — `AlertQualityAggregatorService` periodically computes per-alert-type quality metrics (acknowledgement rate, false positive rate, useful rate, would-act rate, avg seconds to acknowledge/resolve) into `alert_quality_metrics` table; `AlertQualityMetricsController` exposes `GET /alerts/quality-metrics` (time-range filterable, optional alert type) and `GET /alerts/quality-metrics/summary`; Grafana alert quality dashboard (`infra/grafana/dashboards/alert-quality-dashboard.json`); frontend `AlertQualityAnalytics.vue` with `AlertQualityChart.vue`; Prometheus `alert_quality_useful_rate` and `alert_quality_false_positive_rate` gauges
- **Explainable Alerts** — `AlertExplanation` value object (`ScoreContributor`, `TrendContext`, `MedicationContext`, `NarrativeSummary`) serialized as JSONB on `ClinicalAlert.Explanation` at creation time; `AlertExplanationBuilder` and contributor builders (NEWS2, SOFA, GCS, trend) assemble explanation from scoring outputs; `ClinicalAlertFactory` idempotent INSERT with explanation; NEWS2, SOFA, GCS, and `TrendDetector` wire explanation and include `explanation` in `alert.generated` outbox payloads; `AlertResponse` DTO exposes optional `Explanation` on GET/list/acknowledge/resolve; Elasticsearch indexes `NarrativeSummary`; data lake Parquet includes `explanation_json`; ward gateway `LocalClinicalAlert.ExplanationJson` synced via `ClinicalSyncBatchProcessor`; dashboard `AlertReasoning.vue` + `alertExplanation.js` composable render structured reasoning; simulator `ExpectedOutcomeValidator` supports `narrativeContains` on key scenarios; `ExplainableAlertsTests` (10 tests) + `run-phase34-verification.sh`
- **Degraded Operations Visibility** — `GatewayStaleDetectorService` auto-marks gateways OFFLINE when heartbeat exceeds configurable `StaleThresholdMinutes`; `OperationsController` (`GET /operations/gateways`, `GET /operations/gateways/{id}`, `GET /operations/sites/{siteId}/summary`) provides fleet management API; `DischargeSummaryService` with `GET /encounters/{id}/discharge-summary` (info) and `GET /encounters/{id}/discharge-summary/content` (MinIO PDF download); `DischargeSummaryPanel.vue` on patient detail; `DegradedModeBanner.vue` warns when gateways are offline; `GatewayOperations.vue` operations dashboard
- **User Management** — `UsersController` (`GET /users`, `POST /users`, `PATCH /users/{id}`) for admin user account CRUD; `UserService` with BCrypt password hashing; `UserManagementView.vue` with `UserFormModal.vue` (create/edit users, role assignment, active toggle)
- **Admin Dashboard Panels** — `ThresholdManagementView.vue` with `ThresholdFormModal.vue` (create/edit alert thresholds); `AuditLogView.vue` (filterable audit log viewer with action/entity/user/date filters); `ReconciliationView.vue` (safety finding viewer); sidebar navigation with role-aware admin section; `CollapsibleSection.vue` and `SeverityBadge.vue` UI components
- **Console Replay Simulator** — standalone `VigilCare.Simulator` .NET console app replays JSON scenario files against the live API with configurable speed (`--speed 0` instant, `60` = 60× faster); commands: `replay`, `replay-all`, `validate`, `dry-run`, `mimic-list`, `mimic-generate`; optional `--poll` shows alerts, NEWS2, GCS, SOFA, and sepsis bundle state during replay; `--gateway` targets the ward gateway (`http://localhost:5081`) with `--encounter-id`, `--skip-setup`, and `--gateway-token`; `alert_ack` events poll for open alerts on central before acknowledging (handles async alert pipeline at `--speed 0`); `ExpectedOutcomeValidator` validates alert `narrativeContains` on key scenarios; twelve sample scenarios in `VigilCare.Simulator/Scenarios/List/` (including ward outage reconnect, GCS neurological decline, SOFA sepsis progression, and SpO₂/FiO₂ fallback); MIMIC-IV scenario generation from real ICU data; user guide in `docs/simulator-guide.md`
- **MIMIC-IV Scenario Generator** — offline CLI tool that reads MIMIC-IV CSV files (`docs/MIMIC-IV/`, 100 patients, 140 ICU stays, 668K chart events, 107K lab events) and generates VigilCare scenario JSONs; `mimic-list <dir>` displays a Spectre.Console table of available stays with demographics, care unit, LOS, and outcome; `mimic-generate <dir> --stay-id <id>` produces a scenario with options for `--max-hours`, `--no-medications`, `--no-labs`, `--validate`; streaming CSV parser (`MimicCsvReader`) filters 668K-row chartevents by stay_id and item ID set at the string level before allocating records; `MimicItemMap` maps 17 chart event items (vitals, GCS, FiO₂, PaO₂, labs) and 8 lab event items to VigilCare observation codes; GCS text labels ("Obeys Commands" → 6, "To Speech" → 3) resolved from `valuenum` with text-to-numeric fallback dictionary; Fahrenheit temperature converted to Celsius; blood pressure deduplication prefers non-invasive (NBP) over arterial (ABP); 10-observation-per-cluster limit enforced by priority-based splitting (vitals first, labs spill to next offset); medications from prescriptions with dose parsing; generated scenarios pass `ScenarioValidator` and replay through the standard `replay` command
- **RabbitMQ Notification Workers** — `NotificationPublisherService` reads `alert.generated` from Kafka and publishes paging jobs to `alerts.paging.queue`; `PagingWorkerService` sends the page and waits for acknowledgment; if no ack arrives before timeout it NACKs to `alerts.paging.dlq` with `x-message-ttl = 300000ms`; if the host is stopping, in-flight paging messages are NACKed with `requeue=true` so they are retried after restart and do not false-escalate; `EscalationWorkerService` pages the on-call backup and sets alert status to `escalated`; `DischargeSummaryWorkerService` reads `encounter.status.changed`, generates a discharge summary, and stores it in MinIO under `/discharge-summaries/{encounterId}/summary.pdf`
- **Data Lake Writer** — `DataLakeWriterService` (consumer group `data-lake-writer`) buffers `observation.recorded`, `alert.generated`, and `encounter.status.changed` events, flushes date-partitioned Parquet files to MinIO (`/observations/`, `/alerts/`, `/encounters/`), and commits Kafka offsets only for topic-partitions where all uploads succeeded; failed partition buffers are retained in memory and retried on the next flush cycle (prevents data loss from partial upload failures); shutdown flush uses an uncanceled token so MinIO writes complete on Ctrl+C; `kafka_partition` and `kafka_offset` columns provide audit lineage
- **Reconciliation Jobs** — three scheduled checks: (1) unacknowledged CRITICAL alerts older than 30 minutes, (2) pending orders without results after 4 hours, (3) active inpatients with no observation in 2 hours; each finding creates a `reconciliation_alerts` row and publishes to RabbitMQ
- **Standard Envelope** — all responses use a consistent `{ success, statusCode, data, error }` wrapper; validation errors use the same shape; `ApiBehaviorOptions` overridden so model validation also produces the standard envelope with field-level `details`
- **Input Validation** — FluentValidation validators on all request DTOs (patient registration, encounter open, observation ingest, alert acknowledge, alert thresholds, orders); invalid requests return 400 before reaching the service layer
- **Observability** — Serilog structured logging enriched with `correlationId`, `encounterId`, `patientId` on alert paths; Seq sink (`http://localhost:5345`); Prometheus (`http://localhost:9101`) scrapes `GET /metrics`; application metric families via `ClinicalMetrics` (including GCS and SOFA scoring) and three background collectors (`AlertsUnacknowledgedCollector`, `OutboxPendingCollector`, `KafkaConsumerLagCollector`); Grafana clinical dashboard (`http://localhost:3101`, admin/admin) with `alerts_unacknowledged_gauge` as the primary safety panel; per-request correlation IDs in request logs and `X-Correlation-Id` response headers
- **Swagger UI** — OpenAPI spec via Swashbuckle (Development only)

---

## Architecture

```
HTTP request
  → FhirApiKeyOrJwtMiddleware (X-Api-Key or JWT bearer for /fhir/* routes)
  → CorrelationIdMiddleware
  → ExceptionHandlerMiddleware
  → JWT Authentication + RBAC (PermissionAuthorizationHandler) / GatewayApiKeyAuthenticationHandler (X-Api-Key for gateway routes)
  → Controllers (REST API + FHIR R4 ingest + Site/Gateway registry)
  → Services
      ├── CurrentUserService (authenticated user identity from JWT claims)
      ├── AuthService (login, refresh token rotation, logout with revocation)
      ├── AuditService (append-only clinical_audit_logs on write actions)
      ├── PostgreSQL (EF Core — writes, keyed reads)
      ├── Redis (threshold cache, qSOFA state, NEWS2 parameter state, GCS state, SOFA lab cache, trend history, alert suppression keys)
      └── OutboxEvent (same transaction as domain write)

IHostedServices (background):
  ThresholdCacheLoader   → pre-loads Redis on startup
  KafkaTopicProvisioner  → creates topics with correct partition count
  RabbitMqTopologyProvisioner → declares exchange, queues, DLQ bindings
  ElasticIndexProvisioner → creates index mappings
  OutboxRelayService     → PostgreSQL outbox → Kafka (every 500ms)
  EsIndexerService       → Kafka → Elasticsearch (consumer group: es-indexer)
  SepsisEngineService    → Kafka → Redis qSOFA state → PostgreSQL QSOFA_SCREEN alert (consumer group: sepsis-engine)
  WarningAlertService    → Kafka → WarningEvaluator (+ MedicationCorrelationHelper) → PostgreSQL WARNING alert (consumer group: warning-evaluator)
  News2ScoringService    → Kafka → News2Detector (+ MedicationCorrelationHelper) → Redis NEWS2 state → PostgreSQL score + alert (consumer group: news2-scoring)
  GcsScoringService      → Kafka → GcsDetector → Redis GCS components → PostgreSQL gcs_scores + gcs.scored outbox (consumer group: gcs-scoring)
  SofaScoringService     → Kafka (observation.recorded + gcs.scored) → SofaDetector → Redis SOFA lab cache → PostgreSQL sofa_scores + delta alerts → SepsisAlertHandler → SepsisBundleService on SOFA_SEPSIS (consumer group: sofa-scoring)
  TrendAnalyzerService   → Kafka → TrendDetector → Redis trend history → PostgreSQL RAPID_DETERIORATION alert (consumer group: trend-analyzer)
  AlertSuppressionService → Redis suppress:{enc}:{type} keys set on acknowledge; read by WarningEvaluator, News2Detector, QsofaDetector
  NotificationPublisherService → Kafka → RabbitMQ paging.queue (consumer group: notification-publisher)
  PagingWorkerService    → RabbitMQ paging.queue → log page → NACK on timeout (or requeue on shutdown)
  EscalationWorkerService → RabbitMQ escalation.queue → update alert status
  DischargeSummaryWorkerService → RabbitMQ discharge.queue → MinIO PDF
  DataLakeWriterService  → Kafka (data-lake-writer) → Parquet files in MinIO
  ReconciliationScheduler → three scheduled safety checks → reconciliation_alerts + RabbitMQ
  SepsisBundleMonitorService → polls overdue bundles every 5 min → marks NON_COMPLIANT
  PoisonPillGuard (per consumer) → skips permanently malformed messages after MaxPoisonRetries
  AlertsUnacknowledgedCollector → polls PostgreSQL every 30s → alerts_unacknowledged_gauge
  OutboxPendingCollector     → polls outbox every 30s → outbox_pending_events
  KafkaConsumerLagCollector  → polls four consumer groups every 30s → kafka_consumer_lag
  WardGatewayMetricsCollector → polls gateway status/buffer depth every 60s → ward_gateways_offline_gauge, ward_gateway_buffer_depth
  GatewayStaleDetectorService → polls gateways on interval → marks OFFLINE when heartbeat exceeds StaleThresholdMinutes
  AlertQualityAggregatorService → periodically computes per-alert-type quality metrics → alert_quality_metrics table + Prometheus gauges
  ClinicalMetrics (singleton) → inline counters/histogram from ingest, qSOFA, NEWS2, GCS, SOFA, trend, suppression, bundle compliance, escalation paths, alert quality

Ward Gateway (VigilCare.WardGateway — separate deployable on port 5081):
  HTTP request → ExceptionHandlerMiddleware → Controllers (Observations, Alerts, Encounters, CentralRequired)
  Services:
    LocalObservationService → PostgreSQL (ward) + Redis (ward) threshold cache → critical alert + outbox
    LocalWarningEvaluator   → Redis threshold lookup → WARNING alert creation
    LocalAlertService       → Acknowledge/resolve local alerts
    BufferedSyncWriter      → Writes sync items to buffered_sync_items table
    EncounterReadService    → Ward encounter list and detail views
  BackgroundServices:
    EncounterReplicaSyncService → pulls patient/encounter data from central API
    ThresholdCacheLoader        → fetches thresholds from central → local Redis
    CentralReachabilityService  → polls central /health/ready every 30s
    GatewayHeartbeatService     → reports status + buffer depth to central registry
    SyncUploaderService         → batches buffered_sync_items → central API upload
    LocalPagingWorkerService    → local RabbitMQ paging queue → clinician page
    LocalEscalationWorkerService → local RabbitMQ escalation queue → on-call backup
```

**Why Kafka and RabbitMQ coexist:** Kafka is an append-only log — the same observation event reaches the Elasticsearch indexer, the sepsis engine, and the data lake independently without coordination. Each consumer holds its own offset and can replay from the beginning. RabbitMQ handles the action side: one message, one worker, one page. A duplicate page at 3am is a patient safety concern, not a minor inconvenience — RabbitMQ's acknowledgment-then-delete model is correct here. The DLQ TTL-based escalation has no equivalent in Kafka.

---

## Tech Stack

| Layer | Technology |
|---|---|
| Server | ASP.NET Core 8 (.NET 8.0) |
| Database | PostgreSQL 16 with EF Core 8 (code-first migrations) |
| Cache / scoring state | Redis 7 |
| Message log | Apache Kafka 3.7 (KRaft, 6 partitions per topic) |
| Task queue | RabbitMQ 3.13 (direct exchange, DLQ escalation) |
| Search / analytics | Elasticsearch 8.13 (CQRS read projection) |
| Data lake | MinIO (Parquet, S3-compatible) |
| Logging | Serilog + Seq sink |
| Metrics | prometheus-net.AspNetCore (`GET /metrics`) |
| Dashboards | Prometheus 2.52 + Grafana 10.4 |
| Data lake format | Parquet.Net 4.x |
| Authentication | JWT Bearer (Microsoft.AspNetCore.Authentication.JwtBearer) |
| Password hashing | BCrypt.Net-Next |
| FHIR | Hl7.Fhir.R4 (Firely SDK — parsing, serialization, model) |
| Docs | Swagger / OpenAPI (Swashbuckle) |
| Validation | FluentValidation.AspNetCore |
| Testing | xUnit + Testcontainers + WebApplicationFactory |
| Ward dashboard | Vue 3 + Vite + Pinia + Tailwind CSS v4 + Chart.js (`vigilcare-dashboard/`) |

---

## Project Structure

```
VigilCareClinicalAPI/
├── Program.cs                                  # Service registration, middleware, seed on startup
├── appsettings.json                            # Connection strings, Kafka, Elasticsearch, RabbitMQ, MinIO, Serilog, ReconciliationJobs
├── Controllers/
│   ├── AuthController.cs                       # JWT login, token refresh, logout, authenticated user profile
│   ├── AuditLogsController.cs                  # Clinical audit log query (Admin only)
│   ├── PatientsController.cs                   # Patient CRUD, search by name/MRN
│   ├── EncountersController.cs                 # Encounter list (ward summary), get, status PATCH, timeline
│   ├── MedicationsController.cs                # Medication administration create, list, get
│   ├── QsofaController.cs                      # Current qSOFA criteria count (Redis-backed) + cursor-paginated evaluation history
│   ├── ObservationsController.cs               # Ingest POST, cursor-paginated GET
│   ├── AlertThresholdsController.cs            # Threshold CRUD + cache invalidation
│   ├── AlertsController.cs                     # Alert list (global + per-encounter), get by ID, acknowledge, resolve → AlertResponse
│   ├── OrdersController.cs                     # Order create, list, get, status transition, record result
│   ├── News2Controller.cs                      # Current NEWS2 score and cursor-paginated history
│   ├── GcsController.cs                        # Latest GCS score and cursor-paginated history per encounter
│   ├── SofaController.cs                       # Current SOFA score and cursor-paginated history
│   ├── SepsisBundlesController.cs              # Current bundle per encounter, bundle detail by ID
│   ├── SitesController.cs                      # Clinical site CRUD (create, list, get)
│   ├── GatewaysController.cs                   # Gateway register, list, get, heartbeat (dual auth: JWT + API key)
│   ├── OperationsController.cs                 # Gateway fleet operations: fleet list, gateway detail, site summary (Admin only)
│   ├── UsersController.cs                      # Clinical user account management: list, create, update (Admin only)
│   ├── AlertQualityMetricsController.cs        # Alert quality metric snapshots and aggregate summary
│   ├── FhirIngestController.cs                 # FHIR R4 ingest: Patient, Encounter, Observation, MedicationAdministration, Bundle
│   ├── FhirReadController.cs                   # FHIR R4 read/search: GET Patient/{id}, GET Patient, GET Encounter/{id}, GET Encounter
│   ├── FhirMetadataController.cs               # FHIR R4 CapabilityStatement (GET /fhir/R4/metadata)
│   └── AnalyticsController.cs                  # Elasticsearch-backed patient search, trend, alert summary, population
├── Domains/
│   ├── Entities/
│   │   ├── Patient.cs
│   │   ├── Encounter.cs                        # Status machine; SetStatus() enforces transition matrix
│   │   ├── AlertThreshold.cs
│   │   ├── Observation.cs                      # Append-only; IdempotencyKey; partial unique index
│   │   ├── ClinicalAlert.cs                    # open → acknowledged → resolved / escalated; JSONB Explanation snapshot
│   │   ├── Order.cs
│   │   ├── News2Score.cs                       # Composite score with seven component scores + risk level
│   │   ├── GcsScore.cs                         # Eye/verbal/motor components, total, classification
│   │   ├── SofaScore.cs                        # Six organ-system scores, baseline flag, delta, staleness JSON
│   │   ├── QsofaEvaluation.cs                  # Per-evaluation qSOFA record: criteria count, values, screen alert fired
│   │   ├── OutboxEvent.cs                      # topic + payload JSONB + processed_at
│   │   ├── ReconciliationAlert.cs
│   │   ├── SepsisBundle.cs                     # Four-element treatment bundle with 1-hour compliance deadline
│   │   ├── SepsisBundleElement.cs              # Individual bundle element linked to a clinical order
│   │   ├── MedicationAdministration.cs         # Drug administration record per encounter
│   │   ├── ExternalResourceIdentifier.cs       # Links external system identifiers (MRN, visit#) to internal UUIDs
│   │   ├── ClinicalSite.cs                     # Hospital site with site code, name, address
│   │   ├── WardGateway.cs                      # Ward edge node with status, buffer depth, heartbeat, sync timestamps
│   │   ├── ClinicalUser.cs                     # Username, BCrypt password hash, display name, role, active flag
│   │   ├── RefreshToken.cs                     # Opaque refresh token with user FK, expiry, revocation timestamp
│   │   ├── ClinicalAuditLog.cs                 # Append-only audit trail: action, entity, user, before/after JSONB, IP, correlation ID
│   │   ├── AlertFeedback.cs                    # Clinician feedback per alert (one per user per alert)
│   │   └── AlertQualityMetric.cs               # Per-alert-type quality metric snapshots (acknowledgement/false-positive/useful rates)
│   ├── ValueObjects/
│   │   └── AlertExplanation.cs                 # ScoreContributor, TrendContext, MedicationContext, NarrativeSummary
│   └── Enums/
│       ├── EncounterStatus.cs                  # Scheduled, Active, Discharged, Cancelled
│       ├── ClinicalRole.cs                     # Nurse, Physician, Admin, Integration
│       ├── AuditAction.cs                      # ThresholdCreated/Updated/Deleted, AlertAcknowledged/Resolved, EncounterStatusChanged, PatientRegistered, SuppressionWindowSet, UserLogin, AuthorizationDenied, UserLogout, TokenRefreshed
│       ├── EncounterType.cs                    # Inpatient, Outpatient, Emergency
│       ├── AlertSeverity.cs                    # Warning, Critical
│       ├── AlertStatus.cs                      # Open, Acknowledged, Resolved, Escalated
│       ├── AlertType.cs                        # Threshold breach, QSOFA_SCREEN, SOFA_SEPSIS, warning*, NEWS2_*, GCS_*, …
│       ├── AlertFeedbackType.cs                 # Useful, TooEarly, TooLate, FalsePositive, MissingContext, WouldAct
│       ├── GatewayStatus.cs                    # Online, Degraded, Offline with ToDbString/FromDbString
│       ├── BloodType.cs                        # A+, O-, AB-, … with ToDbString/FromDbString
│       ├── ObservationSource.cs                # Device, Manual, Lab
│       ├── SepsisBundleComplianceStatus.cs     # InProgress, Compliant, NonCompliant
│       ├── SepsisBundleElementStatus.cs        # Pending, Completed
│       ├── SepsisBundleElementType.cs          # BloodCultures, SerumLactate, BroadSpectrumAntibiotics, IvFluidResuscitation
│       ├── ExternalResourceType.cs              # Patient, Encounter — for external identifier linking
│       └── OrderType.cs / ReconciliationCheckType.cs / Department.cs / OrderStatus.cs
│   └── Json/
│       ├── ObservationSourceJsonConverter.cs
│       ├── DepartmentJsonConverter.cs
│       └── BloodTypeJsonConverter.cs           # Clinical notation (A+, AB-) in JSON API
├── Fhir/
│   ├── Codes/
│   │   ├── LoincCodeMapper.cs                  # LOINC → internal observation code (19 codes + SNOMED CT fallbacks)
│   │   ├── LoincMapping.cs                     # Code mapping record (InternalCode, ExpectedUnit, AllowFahrenheit)
│   │   └── FhirUnitConverter.cs                # Fahrenheit→Celsius conversion for temperature observations
│   ├── Mapping/
│   │   ├── PatientFhirMapper.cs                # FHIR Patient ↔ internal Patient upsert
│   │   ├── EncounterFhirMapper.cs              # FHIR Encounter ↔ internal Encounter upsert (ACT class, department, status)
│   │   ├── ObservationFhirMapper.cs            # FHIR Observation → IngestObservationRequest (single + component)
│   │   ├── MedicationAdministrationFhirMapper.cs # FHIR MedicationAdministration → CreateMedicationAdministrationRequest
│   │   ├── FhirReferenceResolver.cs            # Resolves FHIR references (identifier or UUID) to internal IDs
│   │   └── FhirMappingHelpers.cs               # DateTimeOffset extraction, reference parsing utilities
│   ├── FhirBundleProcessor.cs                  # Transaction Bundle processing in dependency order (Patient→Encounter→Obs)
│   ├── FhirExceptionFilter.cs                  # Converts exceptions to FHIR OperationOutcome responses
│   ├── FhirMappingException.cs                 # Typed exception for FHIR mapping failures
│   └── FhirOperationOutcomeBuilder.cs          # Builds FHIR OperationOutcome from exceptions and error codes
├── Authorization/
│   ├── AuthorizePermissionAttribute.cs         # [AuthorizePermission("patients:read")] attribute
│   ├── ClinicalPermissions.cs                  # 17 permission constants (patients:read, thresholds:write, fhir:read, audit:read, …)
│   ├── ClinicalRolePermissionMap.cs            # Role → permission set (Nurse, Physician, Admin, Integration)
│   ├── PermissionAuthorizationHandler.cs       # ASP.NET Core authorization handler resolving role claims
│   ├── PermissionPolicyProvider.cs             # Dynamic policy provider for perm:* policies
│   └── PermissionRequirement.cs                # IAuthorizationRequirement for a single permission string
├── Authentication/
│   └── GatewayApiKeyAuthenticationHandler.cs   # X-Api-Key + X-Gateway-Id auth for gateway heartbeat/sync routes
├── Services/
│   ├── Interfaces/                             # IPatientService, IEncounterService, IAuditService, IAuthService, ICurrentUserService, ISiteService, IGatewayRegistryService, …
│   ├── AuthService.cs                          # Login (BCrypt verify), JWT generation, refresh token rotation, logout revocation, audit logging
│   ├── AuditService.cs                         # Append-only clinical audit log writer (user, entity, before/after, IP, correlation ID)
│   ├── CurrentUserService.cs                   # Extracts authenticated user identity from JWT claims (HttpContext)
│   ├── PatientService.cs
│   ├── EncounterService.cs                     # Status state machine + ConflictException on invalid transitions
│   ├── AlertThresholdService.cs                # CRUD + Redis write-through invalidation
│   ├── ObservationService.cs                   # Ingest transaction: idempotency → plausibility → threshold → alert → outbox; emits Prometheus counters
│   ├── ObservationQueryService.cs              # Cursor-paginated history
│   ├── AlertService.cs                         # Acknowledge (sets suppression), resolve, list → AlertResponse with optional Explanation
│   ├── AlertSuppressionService.cs              # Redis suppress:{enc}:{type} TTL keys
│   ├── OrderService.cs                         # Order lifecycle; status machine; calls SepsisBundleService.OnOrderResultedAsync on result
│   ├── News2Service.cs                         # Current score + cursor-paginated history from PostgreSQL
│   ├── GcsService.cs                           # Latest GCS score from PostgreSQL
│   ├── SofaService.cs                          # Current, baseline, and history SOFA scores
│   ├── SepsisBundleService.cs                  # Bundle creation, element completion, compliance evaluation
│   ├── MedicationService.cs                    # Medication CRUD; GetRecentForEncounterAsync for correlation
│   ├── QsofaService.cs                         # Redis-backed qSOFA criteria count for API/dashboard
│   ├── ExternalIdentifierService.cs            # Links/resolves external system identifiers to internal UUIDs
│   ├── SiteService.cs                          # Clinical site CRUD
│   ├── GatewayRegistryService.cs               # Gateway register, list, heartbeat, mark offline
│   ├── OperationsService.cs                    # Gateway fleet queries, gateway detail, site summary aggregation
│   ├── UserService.cs                          # Clinical user account CRUD with BCrypt password hashing
│   ├── DischargeSummaryService.cs              # Discharge summary info and MinIO PDF content retrieval
│   ├── AlertQualityMetricsService.cs           # Alert quality metric listing and summary computation
│   ├── WarningEvaluator.cs                     # Warning-range evaluation; suppression + medication annotation; idempotent INSERT
│   ├── AnalyticsService.cs                     # Elasticsearch query wrappers
│   └── PlausibilityValidator.cs                # Per-code numeric range guard
├── Alerts/
│   ├── ClinicalAlertFactory.cs                 # Idempotent alert INSERT with explanation JSON; outbox payload serialization
│   └── AlertExplanationBuilder.cs              # Assembles explanation from contributors, trend, medication context
├── Trend/
│   ├── TrendCalculator.cs                      # Pure static rate-of-change logic
│   └── TrendDetector.cs                        # Redis history + RAPID_DETERIORATION alert creation
├── Medication/
│   └── MedicationCorrelationHelper.cs          # String annotation on warning details; structured MedicationContext for explanations
├── Validators/                                 # FluentValidation — RegisterPatient, OpenEncounter, IngestObservation, CreateMedicationAdministration, CreateSiteRequest, RegisterGatewayRequest, GatewayHeartbeatRequest, …
├── Observability/
│   └── Metrics/
│       └── ClinicalMetrics.cs                  # Prometheus metric families (counters, histograms, gauges); includes FHIR read and authorization failure metrics
├── BackgroundServices/
│   ├── ThresholdCacheLoader.cs                 # Pre-loads all thresholds into Redis on startup
│   ├── KafkaTopicProvisioner.cs                # Creates topics with NumPartitions from config
│   ├── OutboxRelayService.cs                   # Polls outbox every 500ms; publishes to Kafka; marks processed
│   ├── Metrics/
│   │   ├── AlertsUnacknowledgedCollector.cs    # Polls open CRITICAL alerts > 5 min → alerts_unacknowledged_gauge
│   │   ├── OutboxPendingCollector.cs           # Polls unprocessed outbox rows → outbox_pending_events
│   │   ├── KafkaConsumerLagCollector.cs        # Lag for es-indexer, sepsis-engine, notification-publisher, data-lake-writer
│   │   └── WardGatewayMetricsCollector.cs      # Polls gateway status/buffer depth every 60s → offline gauge, buffer depth
│   ├── GatewayStaleDetectorService.cs          # Periodic stale gateway detection → auto-marks OFFLINE
│   ├── AlertQualityAggregatorService.cs        # Periodic alert quality metric computation → alert_quality_metrics table
│   ├── ElasticsSearch/
│   │   ├── ElasticIndexProvisioner.cs          # Creates patient_encounters, observations, clinical_alerts indices
│   │   └── EsIndexerService.cs                 # consumer group: es-indexer; upserts Elasticsearch documents
│   ├── SepsisEngineService.cs                  # consumer group: sepsis-engine; qSOFA screening via Redis TTL keys
│   ├── WarningAlertService.cs                  # consumer group: warning-evaluator; observation.recorded → WARNING alerts
│   ├── News2ScoringService.cs                  # consumer group: news2-scoring; observation.recorded → NEWS2 score + alert
│   ├── GcsScoringService.cs                    # consumer group: gcs-scoring; observation.recorded → GCS score + alert
│   ├── SofaScoringService.cs                   # consumer group: sofa-scoring; observation.recorded + gcs.scored → SOFA score + delta alerts
│   ├── TrendAnalyzerService.cs                 # consumer group: trend-analyzer; observation.recorded → RAPID_DETERIORATION alert
│   ├── SepsisBundleMonitorService.cs           # Polls every 5 min; marks overdue in-progress bundles NON_COMPLIANT
│   ├── Notifications/
│   │   ├── NotificationPublisherService.cs     # consumer group: notification-publisher; alert.generated → RabbitMQ paging.queue
│   │   ├── PagingWorkerService.cs              # RabbitMQ consumer; logs page; NACK on ack timeout → DLQ, requeue on graceful shutdown
│   │   ├── EscalationWorkerService.cs          # RabbitMQ escalation.queue; logs escalation; sets alert.status = escalated
│   │   └── DischargeSummaryWorkerService.cs    # RabbitMQ discharge.queue; generates summary PDF; uploads to MinIO
│   └── Reconciliation/
│       ├── ReconciliationScheduler.cs          # Runs three safety checks on a configurable interval
│       ├── UnacknowledgedAlertsCheck.cs        # CRITICAL alerts unacknowledged > 30 min
│       ├── PendingOrdersCheck.cs               # Pending orders without results > 4 hours
│       ├── DisconnectedMonitorsCheck.cs      # Active inpatients with no observation > 2 hours
│       └── ReconciliationPublisher.cs          # Publishes findings to notifications.reconciliation.queue
├── Infrastructure/
│   ├── PoisonPillGuard.cs                      # Kafka consumer protection — skips permanent errors, retries transient up to MaxPoisonRetries
│   ├── ElasticsearchHealthCheck.cs             # Readiness check for Elasticsearch connectivity
│   ├── HealthCheckResponseWriter.cs            # Structured JSON response for /health/* endpoints
│   ├── KafkaHealthCheck.cs                     # Readiness check for Kafka broker connectivity
│   ├── RabbitMqHealthCheck.cs                  # Readiness check for RabbitMQ connectivity
│   └── RedisHealthCheck.cs                     # Readiness check for Redis connectivity
├── Configuration/
│   ├── KafkaOptions.cs / KafkaTopicOptions.cs  # Includes ReplicationFactor, OutboxMaxRetries, MaxPoisonRetries
│   ├── RabbitMqOptions.cs / MinioOptions.cs
│   ├── ReconciliationJobOptions.cs
│   ├── MedicationCorrelationOptions.cs         # Drug-vital mappings + correlation window
│   ├── PatientOptions.cs                       # MRN prefix + digit count for sequence-based generation
│   ├── FhirOptions.cs                          # API key (single + rotation array), identifier systems, department/class maps, defaults
│   ├── JwtOptions.cs                           # Issuer, audience, signing key, access token expiration (15 min), refresh token expiration (7 days)
│   ├── DashboardOptions.cs                     # CORS origins for ward dashboard frontend
│   ├── GatewayMonitoringOptions.cs             # Stale gateway detection interval and threshold
│   └── AlertQualityOptions.cs                  # Alert quality aggregation interval
├── Sepsis/
│   ├── AlertCreationGuard.cs                   # Prevents creation of deprecated alert types (SEPSIS_WARNING)
│   ├── QsofaCalculator.cs                      # Pure static qSOFA scoring (3 criteria, no I/O)
│   ├── QsofaDetector.cs                        # Redis qSOFA state, QSOFA_SCREEN alert creation, evaluation persistence to qsofa_evaluations
│   └── SepsisAlertHandler.cs                   # Bridges SOFA_SEPSIS alert → SepsisBundleService
├── News2/
│   ├── News2Calculator.cs                      # Pure static NEWS2 scoring tables (no I/O)
│   └── News2Detector.cs                        # Redis parameter state, score persistence, alert creation
├── Gcs/
│   ├── GcsCalculator.cs                        # GCS total, classification, NEWS2/qSOFA/SOFA mappings
│   └── GcsDetector.cs                          # Redis component state, score persistence, gcs.scored outbox
├── Sofa/
│   ├── SofaCalculator.cs                       # Six organ-system SOFA scoring (0–4 each)
│   ├── SofaDetector.cs                         # Lab cache compose, baseline/delta, alert creation
│   ├── SofaLabCache.cs                         # Redis carry-forward with staleness classification
│   └── SofaVasopressorResolver.cs              # Vasopressor dose from MedicationAdministration + Redis cache
├── Services/MapCalculator.cs                   # MAP from systolic + diastolic BP
├── Elasticsearch/Documents/
│   ├── PatientEncounterDocument.cs
│   ├── ObservationDocument.cs
│   └── ClinicalAlertDocument.cs
├── Notifications/
│   └── RabbitMqTopologyProvisioner.cs          # Declares exchange, queues, DLQ bindings on startup
├── Storage/
│   └── MinioClientFactory.cs
├── DataLake/
│   ├── DataLakeOptions.cs                      # Flush thresholds and bucket settings
│   ├── DataLakeWriterService.cs                # consumer group: data-lake-writer; Kafka → Parquet → MinIO; graceful shutdown flush
│   └── ParquetFileBuilder.cs                   # Topic row models → Parquet byte arrays
├── Models/Records/
│   ├── Observation/ObservationRow.cs           # Parquet row contract for observation events
│   ├── Alert/AlertRow.cs                       # Parquet row contract for alert events
│   ├── Encounter/EncounterStatusRow.cs         # Parquet row contract for encounter status events
│   ├── Encounter/WardEncounterSummary.cs       # Denormalized row for ward encounter list
│   ├── Medication/CreateMedicationAdministrationRequest.cs
│   ├── Qsofa/QsofaCurrentResponse.cs
│   └── Sepsis/QsofaResult.cs, QsofaOutcome.cs  # qSOFA detector result and screening outcome enum
├── Data/
│   ├── AppDbContext.cs                         # EF Core context — entity configs, indexes, constraints
│   ├── Configurations/                         # IEntityTypeConfiguration per entity; ClinicalUserConfiguration, RefreshTokenConfiguration, ClinicalAuditLogConfiguration, ClinicalSiteConfiguration, WardGatewayConfiguration, QsofaEvaluationConfiguration, AlertFeedbackConfiguration, AlertQualityMetricConfiguration; ElasticsearchOptions, ElasticIndexOptions
│   └── Seed/
│       ├── DataSeeder.cs                       # Seeds patients, encounters, thresholds, observations
│       ├── GatewayRegistrySeeder.cs            # Seeds demo site (SITE-DEMO) and gateway (GW-ICU-3B) with fixed GUIDs
│       └── UserSeeder.cs                       # Seeds four demo users (nurse, physician, admin, integration)
├── Common/
│   ├── ApiResponse.cs                          # { success, statusCode, data, error } envelope
│   ├── PagedResult.cs / CursorPage.cs
│   └── Exceptions/
│       ├── NotFoundException.cs
│       ├── ConflictException.cs                # Thrown by encounter status machine
│       ├── DomainException.cs
│       └── ValidationException.cs
├── Middlewares/
│   ├── FhirApiKeyOrJwtMiddleware.cs            # Dual auth for /fhir/* routes: JWT bearer or X-Api-Key (multi-key rotation, constant-time compare) → Integration identity
│   ├── CorrelationIdMiddleware.cs
│   └── ExceptionHandlerMiddleware.cs
└── Migrations/

infra/
├── prometheus/
│   └── prometheus.yml                          # Scrape config for vigilcare_api /metrics
└── grafana/
    ├── provisioning/                           # Datasource + dashboard provider config
    └── dashboards/                             # vigilcare.json clinical dashboard, alert-quality-dashboard.json

tests/
└── VigilCareClinicalAPI.Tests/
    ├── ObservationIngestTests.cs               # Ingest happy path, critical alert creation, discharged encounter rejection, idempotency
    ├── AlertLifecycleTests.cs                  # Acknowledge, resolve, escalation guard
    ├── NotificationPipelineTests.cs            # RabbitMQ topology, DLQ routing
    ├── ReconciliationTests.cs                  # Three reconciliation checks, deduplication, RabbitMQ publish
    ├── ObservabilityPhase8Tests.cs             # /metrics families and correlation header behavior
    ├── DataLakePhase9Tests.cs                  # Kafka → MinIO Parquet flow and schema checks
    ├── ClinicalDemographicsAndObservationTests.cs  # Patient/encounter enrichment, expanded observation alerts
    ├── WarningAlertTests.cs                    # WarningEvaluator — warning created, normal/critical skipped, idempotent
    ├── OrderLifecycleTests.cs                  # Orders API — create, list, record result, illegal transition 409
    ├── ValidationTests.cs                      # FluentValidation — empty fields, threshold ordering, order description
    ├── News2CalculatorTests.cs                 # Boundary tests for all seven NEWS2 scoring tables
    ├── News2DetectorTests.cs                   # NEWS2 detector — score tiers, alerts, idempotency, incomplete set
    ├── TrendCalculatorTests.cs                 # Pure unit tests — rate-of-change, threshold direction, describe
    ├── TrendDetectorTests.cs                   # Trend detector — rapid climb, stable, idempotent, non-trend code
    ├── AlertSuppressionTests.cs                # Suppression on acknowledge, read-side skip, TTL expiry
    ├── QsofaCalculatorTests.cs                 # Boundary tests for three qSOFA criteria
    ├── QsofaDetectorTests.cs                   # qSOFA detector — two-criteria QSOFA_SCREEN alert, normalization, idempotency
    ├── SepsisBundleTests.cs                    # Bundle creation from SOFA_SEPSIS, element completion, compliance outcomes
    ├── SepsisRefactorTests.cs                  # Sepsis-3 refactor — SIRS removal, qSOFA screen workflow, SOFA bundle trigger
    ├── AlertCreationGuardTests.cs              # Guard prevents deprecated SEPSIS_WARNING creation
    ├── ClinicalRefactorEndToEndTests.cs        # End-to-end scenario replay: qSOFA screen → SOFA labs → bundle
    ├── MedicationServiceTests.cs               # Medication CRUD, discharged encounter rejection, pagination
    ├── MedicationCorrelationTests.cs           # End-to-end warning/NEWS2 annotation with medication context
    ├── MedicationValidationTests.cs            # FluentValidation 400 on invalid medication requests
    ├── EncountersListTests.cs                  # Ward encounter list filters and summary fields
    ├── QsofaCurrentTests.cs                    # qSOFA current API — Redis state, criteria breakdown
    ├── GcsScoringTests.cs                      # GCS component scoring, alerts, NEWS2/qSOFA integration paths
    ├── SofaScoringTests.cs                     # SOFA organ scores, baseline, delta alerts, carry-forward, vasopressors
    ├── BackgroundServiceTests.cs                # Outbox relay, Kafka consumer, sepsis bundle monitor, reconciliation
    ├── ConcurrencyTests.cs                      # Parallel patient MRN, sepsis bundle, observation idempotency, encounter open
    ├── GapAnalysisFixTests.cs                  # Phase 22 — GCS history, qSOFA evaluation persistence/history, encounter timeline
    ├── GatewayRegistryTests.cs                 # Gateway register, heartbeat, API key auth, department filter
    ├── OperationsApiTests.cs                   # Operations fleet listing, gateway detail, site summary
    ├── Helpers/GatewayAuthHelper.cs             # WithGatewayApiKey extension method for test clients
    ├── Alerts/
    │   ├── AlertQualityAnalyticsTests.cs       # Alert feedback submission, quality aggregation, metrics API
    │   └── ExplainableAlertsTests.cs           # Explanation JSONB, AlertResponse mapping, medication context, legacy null
    ├── Auth/
    │   └── RbacTests.cs                        # RBAC — unauthenticated 401, nurse 403 on threshold write, admin audit log creation
    └── Fhir/
        └── FhirIngestTests.cs                  # FHIR R4 patient upsert idempotency, observation LOINC mapping, unknown code 422, transaction bundle

VigilCare.ClinicalContracts/                      # Phase 20 — shared sync DTOs (no ASP.NET dependency)
├── VigilCare.ClinicalContracts.csproj            # net8.0 class library, no NuGet packages
└── Sync/
    ├── ClinicalSyncBatchRequest.cs               # Batch upload envelope (batchReference, gatewayId, siteId, items)
    ├── SyncedObservation.cs                      # Per-observation sync item with idempotency key
    ├── SyncedAlertEvent.cs                       # Client-generated alert event
    ├── SyncedAlertAcknowledgment.cs              # Alert acknowledgment from ward
    ├── SyncedAlertResolution.cs                  # Alert resolution from ward
    └── GatewayHeartbeatRequest.cs                # Status + buffer depth + timestamp

VigilCare.ClinicalContracts.Tests/                # Contracts round-trip serialization tests
└── ClinicalContractsTests.cs

VigilCare.WardGateway/                            # Phase 21 — local-first ward edge API (separate DB/Redis/RabbitMQ)
├── Dockerfile
├── Program.cs
├── Common/                                        # ApiResponse envelope, CursorPage, PagedResult, domain exceptions
├── Data/
│   ├── GatewayDbContext.cs
│   └── Configurations/                           # snake_case mappings mirroring central API patterns
├── Domain/
│   ├── Entities/                                 # ReplicaPatient, ReplicaEncounter, LocalObservation, LocalClinicalAlert, BufferedSyncItem, SyncOutboxEntry, GatewaySyncState, ReplicaAlertThreshold
│   └── Enums/                                    # AlertType, AlertSeverity, AlertStatus, EncounterStatus, EncounterType, BufferedSyncItemType, SyncOutboxStatus, ObservationSource, Department
├── Models/Records/ThresholdCacheEntry.cs
├── Models/Records/Observation/IngestObservationRequest.cs
├── Models/Records/Alert/AcknowledgeAlertRequest.cs
├── Models/Records/Encounter/                      # EncounterDetail, WardEncounterSummary
├── Models/Records/LocalIngestResult.cs
├── Models/Central/CentralSyncDtos.cs              # DTOs for central API sync responses
├── Models/Central/CentralApiJson.cs
├── Validators/IngestObservationRequestValidator.cs
├── Validators/AcknowledgeAlertRequestValidator.cs
├── Services/
│   ├── PlausibilityValidator.cs
│   ├── LocalObservationService.cs
│   ├── LocalWarningEvaluator.cs
│   ├── LocalAlertService.cs
│   ├── LocalPagingPublisher.cs
│   ├── ObservationQueryService.cs
│   ├── EncounterReadService.cs
│   └── BufferedSyncWriter.cs
├── Controllers/
│   ├── ObservationsController.cs
│   ├── AlertsController.cs
│   ├── EncountersController.cs
│   └── CentralRequiredController.cs
├── Notifications/RabbitMqTopologyProvisioner.cs
├── Middlewares/ExceptionHandlerMiddleware.cs
├── BackgroundService/
│   ├── EncounterReplicaSyncService.cs             # Syncs patient/encounter data from central API on startup
│   ├── ThresholdCacheLoader.cs                    # Pre-loads alert thresholds from central API into Redis
│   ├── CentralReachabilityService.cs              # Periodic central API health check (sets online/offline state)
│   ├── GatewayHeartbeatService.cs                 # Reports gateway status and buffer depth to central API
│   ├── SyncUploaderService.cs                     # Uploads buffered observations/alerts to central API when online
│   ├── LocalPagingWorkerService.cs
│   └── LocalEscalationWorkerService.cs
├── Configurations/                               # GatewayOptions, CentralApiOptions, RabbitMqOptions, SuppressionOptions
├── Infrastructure/                               # Health checks (Redis, RabbitMQ, encounter replica ready)
└── Migrations/                                   # InitialGatewaySchema

VigilCare.WardGateway.Tests/                       # Phase 21 — ward gateway integration tests
├── VigilCare.WardGateway.Tests.csproj
├── Fixtures/
│   ├── GatewayApiFixture.cs                       # WebApplicationFactory with Testcontainers (PostgreSQL, Redis, RabbitMQ)
│   └── GatewayIntegrationCollection.cs
├── Helpers/
│   ├── GatewayDbResetHelper.cs                    # Database reset between tests
│   └── GatewayTestSeeder.cs                       # Seeds test patients, encounters, thresholds
├── WardGatewayLocalPathTests.cs                   # Local observation ingest, warning alerts, buffered sync items
└── WardGatewayPartitionTests.cs                   # Network partition simulation — offline buffering and sync upload

VigilCare.Simulator/                              # Phase 16, 29, 34, 35 — console replay simulator (HTTP-only, no direct DB/Kafka)
├── Program.cs                                    # CLI: replay, replay-all, validate, dry-run, mimic-list, mimic-generate
├── Commands/                                     # System.CommandLine command handlers
├── Client/
│   ├── VigilCareApiClient.cs                   # Typed HTTP client for all API endpoints (incl. GCS, SOFA)
│   └── Models/AlertExplanation.cs              # Explanation DTO for poll/validation
├── Engine/ReplayEngine.cs                        # Scenario replay with speed multiplier + event logging
├── Output/SimulatorConsole.cs                    # Colored output with GCS/SOFA score + explanation display
├── Polling/ApiPoller.cs                          # Optional post-event alert/score/bundle/GCS/SOFA polling
├── Mimic/                                        # Phase 35 — MIMIC-IV scenario generator
│   ├── MimicCsvReader.cs                       # Streaming CSV parser with header-index lookup and filter predicate
│   ├── MimicItemMap.cs                         # MIMIC item ID → VigilCare observation code mappings (17 chart + 8 lab)
│   ├── MimicCareUnitMap.cs                     # ICU care unit → department + tag mapping
│   ├── MimicDataLoader.cs                      # Data access layer with streaming filters for chartevents/labevents
│   ├── MimicScenarioBuilder.cs                 # Core algorithm: BP dedup, cluster limits, offset conversion
│   ├── MimicListCommand.cs                     # CLI: mimic-list — Spectre.Console table of available stays
│   └── MimicGenerateCommand.cs                 # CLI: mimic-generate — produces scenario JSON from a stay ID
├── Scenarios/                                    # schema.json, ScenarioLoader, ScenarioValidator, ExpectedOutcomeValidator
└── Scenarios/List/                             # Twelve sample scenarios + MIMIC-generated scenarios

vigilcare-dashboard/                              # Phases 17–19, 22, 23, 27–28, 31, 33–34 — Vue 3 ward dashboard SPA
├── src/
│   ├── api/                                      # HTTP client (auto Bearer header, 401 auto-refresh), encounters, clinical (GCS, SOFA, qSOFA history), alerts, analytics, sepsis, thresholds, users, audit, reconciliation, operations, alertQuality, normalize
│   ├── components/
│   │   ├── admin/                                # ThresholdFormModal, UserFormModal (admin CRUD modals)
│   │   ├── alerts/                               # AlertCard, AlertReasoning (structured explanation), AcknowledgeModal (role-aware), CriticalAlertBanner (browser notifications + audible tone)
│   │   ├── charts/                               # SofaHistory, GcsHistory, QsofaHistory, VitalChart with medication markers, AlertQualityChart
│   │   ├── departments/                          # DepartmentCard, AcuityBar (unit-level snapshot)
│   │   ├── feedback/                             # FeedbackButtons, FeedbackSummary
│   │   ├── layout/                               # AppShell, AppHeader (user + logout), AppSidebar (user + logout + role-aware admin), MobileNav (logout)
│   │   ├── patient/                              # GcsEntryForm, SofaScorePanel, PatientBanner, EncounterTimeline, VitalsEntryForm, VitalsPanel, AlertsList, DischargeSummaryPanel
│   │   ├── replay/                               # ReplayControls
│   │   ├── sepsis/                               # SepsisBundleTable, SepsisBundleRow, SepsisBundleCard (countdown timer)
│   │   ├── ward/                                 # WardTable (sortable headers), PatientRow, PatientCard, WardToolbar, SortableHeader, HandoffReport (SBAR + print)
│   │   └── ui/                                   # Button, Card, Badge, Skeleton, EmptyState, Modal, CollapsibleSection, SeverityBadge, DegradedModeBanner
│   ├── composables/                              # useChartData, useReplayControls, usePolling, useFeedback, useGcs, useSofa, useApiMode, useChartTheme, useFocusTrap, chartFormat, patientFormat, timelineFormat, chartMedications, wardSort, wardFilter, departmentFormat, sepsisFormat, alertAcknowledge, alertExplanation, criticalAlertDetect, useAlertNotification, useCriticalAlertPolling, handoffReport, vitalsForm, roleAccess, auditFormat, reconciliationFormat, thresholdForm, userForm
│   ├── plugins/                                  # medicationMarkerPlugin (Chart.js plugin for medication administration markers on vital charts)
│   ├── stores/                                   # Pinia — ward (sort + filter + search), alerts (banner + polling), settings (sort prefs + sound mute), feedback, scoring, auth (login + refresh token rotation + logout + expiry redirect), departments, sepsis, operationsStore, alertQuality
│   ├── views/                                    # LoginView, WardDashboard, PatientDetail, AlertCenter, FeedbackSummary, DepartmentOverviewView, SepsisBoardView, ThresholdManagementView, UserManagementView, AuditLogView, ReconciliationView, GatewayOperations, AlertQualityAnalytics
│   └── __tests__/                                # Vitest — tests (store, feedback, replay, charts, alerts, ward, GCS, SOFA, qSOFA, PatientBanner, EncounterTimeline, patientFormat, timelineFormat, chartMedications, wardSort, wardFilter, departmentFormat, sepsisFormat, alertAcknowledge, criticalAlertDetect, HandoffReport, handoffReport, VitalsEntryForm, vitalsForm, useAlertStore, useWardStore, DepartmentOverviewView, SepsisBoardView, AcknowledgeModal, CriticalAlertBanner, roleAccess, ThresholdManagementView, thresholdForm, DischargeSummaryPanel, GatewayOperations, alertQuality)
├── vite.config.js
└── README.md                                     # Dev quick start → docs/dashboard-guide.md

scripts/
├── run-api-redis-tests.sh                      # Phase 1 — patient/encounter/threshold + Redis cache
├── run-kafka-outbox-tests.sh                   # Phase 3 — outbox relay and Kafka topics
├── run-elasticsearch-analytics-tests.sh        # Phase 4 — Elasticsearch CQRS projection
├── run-sepsis-sirs-tests.sh                    # Phase 5 — legacy SIRS tests (now qSOFA-only)
├── run-notification-pipeline-tests.sh            # Phase 6 — RabbitMQ paging, DLQ, discharge summary
├── run-reconciliation-tests.sh                 # Phase 7 — reconciliation scheduler checks
├── run-phase8-verification.sh                  # Phase 8 — Prometheus metrics, alerts_unacknowledged_gauge, correlation headers
├── run-phase9-verification.sh                  # Phase 9 — data lake tests, Kafka offsets, MinIO Parquet, DuckDB schema
├── run-phase10-verification.sh                 # Phase 10 — 12 Redis thresholds, clinical enrichment, ES pipeline, integration tests
├── run-phase11-verification.sh                 # Phase 11 — warning alerts, orders API, validation, integration tests
├── run-phase12-verification.sh                 # Phase 12 — NEWS2 end-to-end pipeline, API, ES, Prometheus, integration tests
├── run-phase13-verification.sh                 # Phase 13 — trend detection, alert suppression, consumer lag, integration tests
├── run-phase14-verification.sh                 # Phase 14 — qSOFA, sepsis bundle compliance, integration tests
├── run-phase15-verification.sh                 # Phase 15 — medication administration + correlation annotations
├── run-phase25-verification.sh                 # Phase 25 — GCS scoring integration tests + manual API checks
├── run-phase26-verification.sh                 # Phase 26 — SOFA scoring integration tests + baseline/delta API checks
├── run-phase27-verification.sh                 # Phase 27 — Sepsis-3 refactor: SIRS removal, QSOFA_SCREEN, SOFA bundle trigger
├── run-phase28-verification.sh                 # Phase 28 — Frontend GCS entry + SOFA display + sepsis UI refactor
├── run-phase20-verification.sh                 # Phase 20 — Gateway registry tests + site/gateway/heartbeat curl checks
├── run-phase21-verification.sh                 # Phase 21 — Ward gateway local-first path, partition tests, sync upload
├── run-phase22-verification.sh                 # Phase 22 — Dashboard gap analysis fixes (SOFA/GCS/qSOFA history, patient banner, timeline, medication markers)
├── run-phase24-verification.sh                 # Phase 24 — Ward outage reconnect scenario (central + gateway replay, ack sync)
├── run-phase29-verification.sh                 # Phase 29 — Simulator scenario expansion + clinical validation
├── run-phase30-verification.sh                 # Phase 30 — FHIR R4 ingest integration tests + manual bundle/metadata checks
├── run-phase31-verification.sh                 # Phase 31 — RBAC integration tests + JWT login + audit log query
├── run-phase23-verification.sh                 # Phase 23 — Degraded operations visibility + gateway fleet + admin panels
├── run-phase33-verification.sh                 # Phase 33 — Alert quality analytics integration tests
├── run-phase34-verification.sh                 # Phase 34 — Explainable alerts integration tests
├── demo-network-partition.sh                   # Gateway network partition demo script
└── mint-gateway-jwt.sh                         # JWT minting helper for gateway testing

docs/
├── plans/                                      # Phase implementation and verification guides
├── clinical-testing-guide.md                   # Doctor/nurse guide — alert review & feedback sessions
├── dashboard-guide.md                          # VigilCare Dashboard user guide (ward, patient detail, charts)
├── dashboard-gap-analysis.md                   # Comprehensive gap analysis — P0–P5 clinical usefulness assessment
├── patient-encounter-api-lifecycle.md          # Full API walkthrough: registration → active stay → discharge
├── simulator-guide.md                          # VigilCare.Simulator user guide
├── integration/
│   └── mirth-fhir-channels.md                  # Mirth Connect HL7v2→FHIR channel mapping (ADT A01/A03/A08, ORU R01)
├── decisions/
│   ├── data-lake-design.md                     # Parquet vs JSON, partitioning, replay rationale
│   ├── sepsis-engine-design.md                 # Sepsis-3 qSOFA screening and idempotent alert design
│   ├── medication-correlation-design.md        # Drug-vital mapping and annotation rationale
│   └── clinical-refactor-sofa-gcs.md           # Interview Q&A: why SIRS→SOFA, carry-forward, GCS dependency chain
├── docker-compose-usage-and-troubleshooting.md
└── vigilcare-clinical-api-prd.md               # Product requirements and phase roadmap
```

---

## Architecture Decisions

### Synchronous vs Asynchronous Alert Detection — The Split

Critical threshold breaches are detected synchronously within the ingest transaction. A critical potassium of 2.1 mEq/L is immediately life-threatening. If the API returns `201 Created` before generating the alert and the Kafka consumer lags by 30 seconds, a patient could deteriorate during that window. The synchronous check costs one additional Redis read per observation on the hot path — acceptable for correctness.

A warning heart rate of 95 bpm warrants attention but is not an emergency. The additional latency of Kafka consumer processing is clinically acceptable for a warning.

This is the architectural decision that separates thinking about healthcare systems from thinking about financial systems. The tradeoff is latency for correctness, and the correctness definition is clinical, not technical.

### Encounter as the Aggregate Root (Not Patient)

Observations, alerts, and orders belong to an encounter, not directly to a patient. A patient's blood pressure taken during a 2022 admission belongs to that admission. This bounds queries naturally: "show me all observations for this encounter" is a bounded query. "Show me all observations ever recorded for this patient" is a cross-encounter aggregation that belongs in the data lake.

### Redis for Seven Distinct Purposes

Redis serves seven independent roles with different semantics:

1. **Threshold cache:** write-through invalidation on every threshold update. Staleness here has clinical consequences — a stale threshold could suppress a critical alert. TTL expiry is not sufficient; invalidation must be immediate on write.

2. **qSOFA sliding window:** `SET qsofa:{encounterId}:{code} EX 1800`. The 30-minute TTL is a clinical parameter — a respiratory rate that was abnormal 31 minutes ago stops contributing to the qSOFA count without any cleanup job. When a value normalizes, the key is explicitly deleted rather than waiting for TTL — a systolic BP that recovers from 90 to 120 should immediately reduce the qSOFA count.

3. **NEWS2 parameter state:** `SET news2:{encounterId}:{code}` with a 4-hour TTL. Each of the seven NEWS2 parameters is scored individually and stored in Redis; `MGET` across all seven keys determines completeness. An incomplete set (fewer than seven present keys) does not produce a score — expired parameters must be re-recorded before the aggregate is computed.

4. **GCS component state:** `SET gcs:{encounterId}:{component}` tracking Eye, Verbal, and Motor components. All three must be present before a total score is computed. Completion triggers `gcs.scored` for SOFA CNS re-scoring.

5. **SOFA lab cache:** `SET sofa:{encounterId}:{code}` with carry-forward semantics (configurable 24-hour TTL). Labs are classified as CURRENT (< 12h), STALE (12–24h), or EXPIRED (> 24h). Stale values are still used for scoring but flagged in staleness metadata. This enables SOFA scoring on wards where labs are drawn every 6–12 hours, not continuously.

6. **Trend history:** sliding-window observation history for rate-of-change detection. Five vital parameters tracked for velocity thresholds.

7. **Alert suppression windows:** `SET suppress:{encounterId}:{alertType}` with a configurable TTL (default 30 min). Set on acknowledge of suppressible alerts; checked by `WarningEvaluator` and `News2Detector` before creating new warning alerts. Critical alerts are never suppressed.

### Outbox Pattern

Observation and alert writes use the transactional outbox: the `outbox_events` row is inserted in the same transaction as the domain record. The relay publishes to Kafka asynchronously using an idempotent producer (`EnableIdempotence = true`) — the broker deduplicates in-flight retries using producer ID and sequence number. This prevents message loss when Kafka is temporarily unavailable and prevents phantom messages when the transaction rolls back. Events that repeatedly fail Kafka delivery (network partition, broker-level rejection) are retried up to `OutboxMaxRetries` (default 10) before being marked permanently failed — acting as a dead-letter mechanism that prevents a single poisoned event from blocking the entire relay. The relay uses `FOR UPDATE SKIP LOCKED` so multiple instances can run concurrently without contention.

### Kafka Partition Key: `encounterId`

All events for the same encounter land on the same partition. The sepsis engine requires this: if observations from the same patient arrive on different partitions, they may be consumed out of order and simultaneous qSOFA criteria could be missed. Six partitions balance parallelism against per-encounter ordering guarantees.

### Elasticsearch as a CQRS Read Projection

PostgreSQL is always the write side and the source of truth. Elasticsearch is a denormalized, queryable projection optimized for the queries clinicians actually run. The `population` endpoint — "how many active patients have a heart rate above 100 in the last hour" — is a numeric range aggregation across potentially millions of observation rows. Running this against PostgreSQL on the operational database would compete with ingest writes. Elasticsearch's aggregation engine is purpose-built for this pattern.

**The replay:** stop `EsIndexerService` → delete both indices → reset consumer group offset to 0 → restart → wait for rebuild → verify document count matches PostgreSQL row count. This is the proof that Elasticsearch is a projection and not a source of truth, and the clearest demonstration of why Kafka retains events after consumption.

### DLQ as a Clinical Escalation Protocol

The five-minute escalation is not a retry — it is a clinical workflow. When an alert is created, the paging worker sends a page to the attending physician. If no acknowledgment arrives within five minutes, the message NACKs to `alerts.paging.dlq` with `x-message-ttl = 300000ms`. After TTL expires, the DLQ re-routes to `alerts.escalation.queue` and the on-call backup is paged. During graceful shutdown, cancellation of the in-flight wait loop is treated as non-failure and the message is NACKed with `requeue=true`, preventing false escalation during deploy/restart windows. This pattern has no equivalent in Kafka — Kafka has no concept of per-message TTL or conditional re-routing based on consumer acknowledgment.

### Why Not a Time-Series Database for Observations?

A medium hospital with 200 concurrent inpatients at five observations per patient per minute produces approximately 17 observations per second at steady state. PostgreSQL with the composite index `(encounter_id, observation_code, recorded_at DESC)` handles this volume with headroom. TimescaleDB would be the correct next step at 10,000+ observations/second — it is PostgreSQL with automatic time partitioning, meaning the query layer would not change. The Parquet data lake handles the analytics workload that would otherwise stress the operational database over a 10-year horizon.

### Two-Tier Sepsis Detection (Sepsis-3: qSOFA Screen → SOFA Confirmation)

The sepsis pathway follows the Sepsis-3 consensus (2016), replacing the older SIRS-based approach:

1. **Screening (qSOFA):** `SepsisEngineService` evaluates three bedside criteria (respiratory rate ≥ 22, systolic BP ≤ 100, altered mentation via GCS < 15). When ≥ 2 are active, a `QSOFA_SCREEN` (WARNING-level) alert is created, recommending SOFA lab orders.

2. **Confirmation (SOFA):** `SofaScoringService` scores six organ systems from labs and vitals. When SOFA delta ≥ 2 from baseline, a `SOFA_SEPSIS` (CRITICAL) alert fires and triggers the sepsis bundle via `SepsisAlertHandler`.

This two-tier design prevents false-positive bundle activations — SIRS criteria (temperature, heart rate, respiratory rate, WBC) were too non-specific, triggering bundles for post-surgical inflammation, anxiety, and viral infections. SOFA measures actual organ dysfunction, making the bundle trigger clinically meaningful. The legacy `SEPSIS_WARNING` and `QSOFA_WARNING` alert types are retained (marked `[Obsolete]`) for historical queries but can no longer be created.

---

## Getting Started

### Prerequisites

- .NET 8 SDK
- Docker and Docker Compose

### Start Infrastructure

**Central stack only** (default — no Compose profile):

```bash
docker compose up -d
```

**Ward gateway stack** (separate PostgreSQL, Redis, RabbitMQ, and gateway API on port 5081):

```bash
docker compose --profile ward-gateway up -d
```

**Everything** (central + ward):

```bash
docker compose --profile full up -d
```

Ward services use Compose profiles and do **not** start with a plain `docker compose up`. See `docs/docker-compose-usage-and-troubleshooting.md` §10.

All services join the `vigilcare_net` bridge network so containers can reach each other by service name (e.g. Grafana → `http://prometheus:9090`). Connection strings in `appsettings.json` use **host** ports when running `dotnet run` on your machine.

| Service | Host Port | Notes |
|---|---|---|
| PostgreSQL 16 | 5436 | Database: `vigilcare`, user: `postgres`, password: `password` |
| Redis 7 | 6382 | No auth |
| Seq | 5345 | UI at `http://localhost:5345` — login: `admin` / `admin` |
| Kafka 3.7 | 9092 | KRaft mode, no Zookeeper |
| Elasticsearch 8.13 | 9200 | Security disabled for development |
| RabbitMQ 3.13 | 5674 (AMQP), 15674 (UI) | login: `guest` / `guest` |
| MinIO | 9005 (S3 API), 9006 (console) | login: `minioadmin` / `minioadmin` |
| Prometheus 2.52 | 9101 | UI at `http://localhost:9101` — scrapes `GET /metrics` on the API |
| Grafana 10.4 | 3101 | UI at `http://localhost:3101` — login: `admin` / `admin` |

**Ward gateway stack** (`--profile ward-gateway` or `full`):

| Service | Host Port | Notes |
|---|---|---|
| Ward PostgreSQL 16 | 5437 | Database: `vigilcare_ward`, user: `postgres`, password: `password` |
| Ward Redis 7 | 6383 | No auth |
| Ward RabbitMQ 3.13 | 5675 (AMQP), 15675 (UI) | login: `guest` / `guest` |
| Ward Gateway API | 5081 | `VigilCare.WardGateway` — local-first clinical path (Phase 21) |

**Seq first-run:** `SEQ_FIRSTRUN_ADMINPASSWORD=admin` is set in `docker-compose.yml`. This password is only applied on the very first container start (when the `/data` volume is empty). After initialization, the password is stored in the volume and this env var is ignored.

### Docker notes for Linux

Prometheus scrapes the API using `host.docker.internal:5270`. On Linux, two things are required:

1. In `docker-compose.yml` under `prometheus`:
   ```yaml
   extra_hosts:
     - "host.docker.internal:host-gateway"
   ```
2. Run the API bound to all interfaces (not only loopback), so containers can reach it:
   - Use `http://0.0.0.0:5270` (or `ASPNETCORE_URLS=http://0.0.0.0:5270`)

Without this, Prometheus may show target errors like:
- `lookup host.docker.internal ... no such host` (DNS mapping missing), or
- `dial tcp 172.17.0.1:5270: connect: connection refused` (API bound only to `127.0.0.1`)

For full Docker troubleshooting and recovery steps, see:
- `docs/docker-compose-usage-and-troubleshooting.md`

### Install and Run

```bash
cd VigilCareClinicalAPI
dotnet restore
dotnet run
```

On startup the application:
1. Runs EF Core migrations
2. Seeds two patients (with blood type, allergies, emergency contact), one active inpatient encounter each (with room/bed and admission reason), twelve alert thresholds, sample observations, and four clinical users (nurse, physician, admin, integration)
3. Pre-loads all thresholds into Redis
4. Provisions Kafka topics and Elasticsearch indices
5. Declares the RabbitMQ exchange and queue topology
6. Starts all background consumers (outbox relay, ES indexer, sepsis engine with qSOFA screening, warning evaluator, NEWS2 scoring, GCS scoring, SOFA scoring, trend analyzer, notification workers, data lake writer, reconciliation scheduler, sepsis bundle monitor)
7. Starts Prometheus metric collectors (unacknowledged alerts, outbox pending, Kafka consumer lag, ward gateway fleet health)

Swagger UI is available at `http://localhost:5270/swagger` in Development (API binds to `0.0.0.0:5270` per `launchSettings.json`).

Health checks (anonymous, no JWT required):
- `GET /health/live` — liveness probe (always 200 if process is running)
- `GET /health/ready` — readiness probe (checks PostgreSQL, Redis, Kafka, RabbitMQ, Elasticsearch)

### Run the Simulator

With the API running, replay a scenario from the repository root:

```bash
dotnet run --project VigilCare.Simulator -- replay \
  VigilCare.Simulator/Scenarios/List/uti-sepsis-elderly-01.json \
  --speed 60 --poll
```

Other commands: `validate <file>`, `dry-run <file>`, `replay-all <directory>`. See `docs/simulator-guide.md` for the full user guide.

**MIMIC-IV real patient data (Phase 35):** generate and replay scenarios from de-identified ICU records:

```bash
# List 140 available ICU stays across 100 patients
dotnet run --project VigilCare.Simulator -- mimic-list docs/MIMIC-IV/

# Generate a 24-hour scenario from a CVICU patient
dotnet run --project VigilCare.Simulator -- mimic-generate docs/MIMIC-IV/ \
  --stay-id 32604416 --max-hours 24 --validate

# Replay the generated scenario
dotnet run --project VigilCare.Simulator -- replay \
  VigilCare.Simulator/Scenarios/List/mimic-s32604416.json --speed 0 --poll
```

**Ward outage reconnect (Phase 24):** scenario `ward-outage-reconnect-01.json` exercises critical hyperkalemia alerting and nurse acknowledgment during a central outage, then sync back to central when connectivity returns. Manual procedure in `docs/simulator-guide.md` §10; automated end-to-end check:

```bash
./scripts/run-phase24-verification.sh
```

Requires Docker Compose (central API, ward gateway stack) and a running central API on `http://localhost:5270`. Use `SKIP_DOCKER=1` when the stack is already up. Notes from verification runs: `docs/resilience/phase-24-verification-notes.md`.

### Run the Dashboard

With the API running, start the Vue frontend:

```bash
cd vigilcare-dashboard
npm install
npm run dev
```

Open `http://localhost:5173` — log in with a demo account (e.g. `nurse.demo` / `DemoNurse1!`). **Virtual Ward** lists active patients sorted by NEWS2 score. Click a row for patient detail (vitals, alerts, charts, replay scrubbing, alert reasoning). Use **Alert Center** for hospital-wide triage. After reviewing alerts, rate them with the six feedback buttons and export results from **Feedback Summary** (`/feedback`).

Replay a simulator scenario in another terminal to watch charts and alerts populate in real time. Run dashboard tests with `cd vigilcare-dashboard && npm test`. See `docs/dashboard-guide.md` for technical documentation and `docs/clinical-testing-guide.md` for structured clinician evaluation sessions.

### Run Tests

```bash
dotnet test
```

Integration tests use `WebApplicationFactory` with a `Testing` environment and Testcontainers where needed (PostgreSQL, Redis, Kafka, RabbitMQ, Elasticsearch, MinIO). No manual infrastructure setup is required for `dotnet test`.

| Test class | Phase | Coverage |
|---|---|---|
| `ObservationIngestTests` | 2 | Ingest happy path, critical alert creation, discharged encounter rejection, idempotency |
| `AlertLifecycleTests` | 2 | Acknowledge, resolve, escalation guard |
| `SepsisRefactorTests` | 27 | Sepsis-3 refactor — SIRS removed, qSOFA creates QSOFA_SCREEN, SOFA delta triggers bundle |
| `AlertCreationGuardTests` | 27 | Guard prevents creation of deprecated SEPSIS_WARNING alerts |
| `ClinicalRefactorEndToEndTests` | 29 | End-to-end scenario replay: qSOFA screen → SOFA labs → SOFA_SEPSIS → bundle |
| `NotificationPipelineTests` | 6 | RabbitMQ topology, DLQ routing, paging |
| `ReconciliationTests` | 7 | Three reconciliation checks, deduplication, RabbitMQ publish |
| `ObservabilityPhase8Tests` | 8 | All ten `/metrics` families, correlation headers, ingest counter increment |
| `DataLakePhase9Tests` | 9 | Kafka → MinIO Parquet flow and schema checks |
| `ClinicalDemographicsAndObservationTests` | 10 | Patient clinical fields, encounter enrichment, expanded observation codes, critical glucose alert |
| `WarningAlertTests` | 11 | WarningEvaluator — warning HR alert, normal/critical skipped, duplicate idempotent |
| `OrderLifecycleTests` | 11 | Orders API create, list, record result, cancel-resulted 409 |
| `ValidationTests` | 11 | FluentValidation 400 on empty first name, invalid threshold order, empty order description |
| `News2CalculatorTests` | 12 | Boundary tests for all seven NEWS2 scoring tables and risk-level determination |
| `News2DetectorTests` | 12 | NEWS2 detector — score tiers, alert creation, incomplete parameters, idempotency |
| `TrendCalculatorTests` | 13 | Pure unit tests — delta/time rate, SPO2/BP decline direction, describe formatting |
| `TrendDetectorTests` | 13 | Trend detector — rapid HR climb alert, stable high HR, idempotency, non-trend code |
| `AlertSuppressionTests` | 13 | Acknowledge sets Redis key, suppressed warning skipped, critical/NEWS2 emergency never suppressed, TTL expiry |
| `QsofaCalculatorTests` | 14 | Boundary tests for three qSOFA criteria (RESP_RATE, SYSTOLIC_BP, AVPU) |
| `QsofaDetectorTests` | 14 | qSOFA detector — two-criteria QSOFA_SCREEN alert, normalization key delete, idempotent duplicate, non-qSOFA code ignored |
| `SepsisBundleTests` | 14 | Bundle creation from SOFA_SEPSIS, four auto-orders, element completion, compliant/non-compliant outcomes, monitor marks overdue bundles, idempotency |
| `MedicationServiceTests` | 15 | Medication create/list on active encounter, discharged encounter 409, pagination, `since` filter |
| `MedicationCorrelationTests` | 15 | Warning and NEWS2 alert details annotated when correlated drug administered |
| `MedicationValidationTests` | 15 | FluentValidation 400 on empty drug name, zero dose, future `administeredAt` |
| `EncountersListTests` | — | Ward encounter list — status/department filters, summary fields |
| `QsofaCurrentTests` | — | `GET /qsofa/current` — criteria count and breakdown from Redis |
| `GcsScoringTests` | 25 | GCS component scoring, classification, alerts, CNS integration with SOFA |
| `SofaScoringTests` | 26 | SOFA organ scores, baseline eligibility, delta alerts, carry-forward, vasopressors |
| `OperationsApiTests` | 23 | Operations fleet listing, gateway detail, site gateway summary |
| `AlertQualityAnalyticsTests` | 33 | Alert feedback submission, quality aggregation, metrics API |
| `GatewayRegistryTests` | 20 | Gateway register, heartbeat status/buffer, API key auth 401, degraded status, department filter |
| `ClinicalContractsTests` | 20 | ClinicalSyncBatchRequest JSON round-trip serialization |
| `FhirIngestTests` | 30 | FHIR R4 patient upsert idempotency, LOINC observation mapping, unknown code 422, transaction bundle |
| `RbacTests` | 31 | Unauthenticated 401, nurse 403 on threshold write, admin threshold update with audit log creation, alert acknowledge uses authenticated user |
| `BackgroundServiceTests` | — | Outbox relay, Kafka consumer, sepsis bundle monitor, reconciliation |
| `ConcurrencyTests` | — | Parallel patient registration unique MRNs, parallel sepsis alerts single bundle, parallel observation idempotency, parallel encounter open duplicate rejection |
| `GapAnalysisFixTests` | 22 | GCS history API, qSOFA evaluation persistence and history API, encounter timeline with patient data |
| `WardGatewayLocalPathTests` | 21 | Local observation ingest, critical/warning alert creation, buffered sync item generation |
| `WardGatewayPartitionTests` | 21 | Network partition simulation — offline buffering, sync upload to central API, encounter replica sync |

### Verification Scripts

With the API running (`dotnet run`) and Docker Compose up:

```bash
./scripts/run-phase22-verification.sh  # Dashboard gap analysis fixes — SOFA/GCS/qSOFA history, patient banner, timeline
./scripts/run-phase21-verification.sh  # Ward gateway local-first path, partition tests, sync upload verification
./scripts/run-phase24-verification.sh  # Ward outage reconnect — gateway replay, local ack, central sync after restart
./scripts/run-phase20-verification.sh  # Gateway registry tests, site/gateway/heartbeat API verification
./scripts/run-phase8-verification.sh   # Prometheus target UP, ten metrics, alerts_unacknowledged_gauge live update
./scripts/run-phase9-verification.sh   # DataLakePhase9Tests, Kafka consumer group, MinIO Parquet, DuckDB schema
./scripts/run-phase10-verification.sh  # 12 Redis thresholds, clinical enrichment, ES pipeline, Phase 10 integration tests
./scripts/run-phase11-verification.sh  # Warning alert pipeline, orders API, FluentValidation, Phase 11 integration tests
./scripts/run-phase12-verification.sh  # NEWS2 end-to-end pipeline, API, Elasticsearch, Prometheus, Phase 12 integration tests
./scripts/run-phase13-verification.sh  # Trend detection, alert suppression, consumer lag, Phase 13 integration tests
./scripts/run-phase14-verification.sh  # qSOFA, sepsis bundle compliance, Phase 14 integration tests
./scripts/run-phase15-verification.sh  # Medication administration + correlation annotation pipeline
./scripts/run-phase27-verification.sh  # Sepsis-3 refactor: SIRS removal, QSOFA_SCREEN, SOFA bundle trigger
./scripts/run-phase30-verification.sh  # FHIR R4 ingest integration tests + manual bundle/metadata checks
./scripts/run-phase31-verification.sh  # RBAC integration tests + JWT login + audit log query
./scripts/run-phase23-verification.sh  # Degraded operations visibility + gateway fleet + admin panels
./scripts/run-phase33-verification.sh  # Alert quality analytics integration tests
./scripts/run-phase34-verification.sh  # Explainable alerts integration tests
```

Phase 25 — GCS scoring (requires running API + Docker Compose; set an active encounter UUID):

```bash
export ENCOUNTER_ID=$(docker compose exec -T postgres psql -U postgres -d vigilcare -t -A \
  -c "SELECT id FROM encounters WHERE status = 'ACTIVE' LIMIT 1;")
./scripts/run-phase25-verification.sh
```

Phase 26 — SOFA scoring (same prerequisites; script polls for async Kafka scoring):

```bash
export ENCOUNTER_ID=$(docker compose exec -T postgres psql -U postgres -d vigilcare -t -A \
  -c "SELECT id FROM encounters WHERE status = 'ACTIVE' LIMIT 1;")
./scripts/run-phase26-verification.sh
```

Phase 13 unit/integration tests only:

```bash
dotnet test --filter "FullyQualifiedName~Trend|FullyQualifiedName~Suppression"
```

Phase 15 unit/integration tests only:

```bash
dotnet test --filter "FullyQualifiedName~Medication"
```

Phase 21 ward gateway tests only:

```bash
dotnet test --filter "FullyQualifiedName~WardGateway"
```

Phase 20 gateway tests only:

```bash
dotnet test --filter "FullyQualifiedName~GatewayRegistry|FullyQualifiedName~ClinicalContracts"
```

Phase 31 RBAC tests only:

```bash
dotnet test --filter "FullyQualifiedName~Rbac"
```

Phase 22 dashboard gap analysis tests only:

```bash
dotnet test --filter "FullyQualifiedName~GapAnalysisFix"
```

Phase 23 operations tests only:

```bash
dotnet test --filter "FullyQualifiedName~OperationsApi"
```

Phase 33 alert quality analytics tests only:

```bash
dotnet test --filter "FullyQualifiedName~AlertQuality"
```

Phase 34 explainable alerts tests only:

```bash
dotnet test --filter "FullyQualifiedName~ExplainableAlerts"
```

Per-phase test runners (subset of `dotnet test`):

```bash
./scripts/run-api-redis-tests.sh
./scripts/run-kafka-outbox-tests.sh
./scripts/run-elasticsearch-analytics-tests.sh
./scripts/run-sepsis-sirs-tests.sh
./scripts/run-notification-pipeline-tests.sh
./scripts/run-reconciliation-tests.sh
```

Phase 9 optional tools (install without sudo):

```bash
# MinIO client — object listing and download
mkdir -p ~/.local/bin
curl -fsSL https://dl.min.io/client/mc/release/linux-amd64/mc -o ~/.local/bin/mc
chmod +x ~/.local/bin/mc

# DuckDB — query Parquet files locally
curl https://install.duckdb.org | sh
export PATH="$HOME/.duckdb/cli/latest:$HOME/.local/bin:$PATH"
```

See `docs/plans/phase-8-plan.md` through `docs/plans/phase-12-plan.md` for manual Grafana, Seq, Kafka replay, and DuckDB query examples.

---

## Prometheus Metrics

`GET /metrics` exposes application metric families registered in `ClinicalMetrics`. Three background collectors poll PostgreSQL and Kafka every 30 seconds; counters and histograms are updated inline during request handling and background processing.

| Metric | Type | Labels | Source |
|---|---|---|---|
| `observations_ingested_total` | Counter | `observation_code`, `source` | `ObservationService` on each committed observation |
| `observation_ingest_duration_seconds` | Histogram | — | `ObservationService` — full ingest transaction to COMMIT |
| `clinical_alerts_total` | Counter | `alert_type`, `severity` | `ObservationService`, `QsofaDetector`, `News2Detector`, `TrendDetector`, `SofaDetector`, `WarningEvaluator` |
| `qsofa_detections_total` | Counter | — | `QsofaDetector` — only on successful idempotent QSOFA_SCREEN insert |
| `sepsis_bundle_compliance_total` | Counter | `status` | `SepsisBundleService` — on bundle completion (`COMPLIANT`, `NON_COMPLIANT`) |
| `news2_scores_total` | Counter | `risk_level` | `News2Detector` — on each persisted score (`LOW`, `MEDIUM`, `HIGH`, …) |
| `news2_scoring_duration_seconds` | Histogram | — | `News2Detector` — Redis update through score persistence |
| `gcs_scores_total` | Counter | `classification` | `GcsDetector` — on each persisted score (`MILD`, `MODERATE`, `SEVERE`) |
| `sofa_scores_total` | Counter | `has_delta_alert` | `SofaDetector` — on each persisted score (`true` / `false`) |
| `sofa_scoring_duration_seconds` | Histogram | — | `SofaDetector` — full SOFA compose + persist |
| `trend_alerts_total` | Counter | `observation_code` | `TrendDetector` — on each `RAPID_DETERIORATION` alert created |
| `trend_analysis_duration_seconds` | Histogram | — | `TrendDetector` — per-observation trend evaluation |
| `alert_suppressions_total` | Counter | `alert_type` | `AlertSuppressionService` — on each suppression window set after acknowledge |
| `escalations_total` | Counter | — | `EscalationWorkerService` on DLQ escalation |
| `alerts_unacknowledged_gauge` | Gauge | — | `AlertsUnacknowledgedCollector` — open CRITICAL alerts older than 5 minutes |
| `outbox_pending_events` | Gauge | — | `OutboxPendingCollector` — unprocessed outbox rows |
| `kafka_consumer_lag` | Gauge | `consumer_group` | `KafkaConsumerLagCollector` — `es-indexer`, `sepsis-engine`, `notification-publisher`, `data-lake-writer` |
| `fhir_ingest_total` | Counter | `resource_type`, `outcome` | `FhirIngestController` — per resource type (`Patient`, `Encounter`, `Observation`, `MedicationAdministration`, `Bundle`) with `success` / `error` outcome |
| `fhir_read_total` | Counter | `resource_type`, `interaction`, `outcome` | `FhirReadController` — per resource type (`Patient`, `Encounter`) with interaction (`read`, `search`) and `success` outcome |
| `authorization_failures_total` | Counter | `permission`, `role` | `PermissionAuthorizationHandler` — authorization denials by required permission and user role |
| `fhir_mapping_errors_total` | Counter | `resource_type` | `FhirExceptionFilter` — mapping/validation failures by resource type |
| `ward_gateways_offline_gauge` | Gauge | `site_code` | `WardGatewayMetricsCollector` — count of gateways with status OFFLINE or DEGRADED per site |
| `ward_gateway_buffer_depth` | Gauge | `gateway_code`, `department` | `WardGatewayMetricsCollector` — reported unsynced event count per gateway |
| `kafka_poison_pills_skipped_total` | Counter | `consumer_group`, `topic` | `PoisonPillGuard` — messages skipped as permanently un-processable (malformed JSON, format errors, or transient failures exceeding MaxPoisonRetries) |
| `alert_quality_useful_rate` | Gauge | `alert_type` | `AlertQualityAggregatorService` — proportion of feedback rated "useful" per alert type |
| `alert_quality_false_positive_rate` | Gauge | `alert_type` | `AlertQualityAggregatorService` — proportion of feedback rated "false positive" per alert type |
| `alert_feedback_total` | Counter | `feedback_type` | `AlertService` — feedback submissions by type |

Prometheus scrapes the API via `infra/prometheus/prometheus.yml` (`job: vigilcare_api` → `host.docker.internal:5270`). Grafana loads the clinical dashboard from `infra/grafana/dashboards/vigilcare.json`.

---

## API Reference

All endpoints are prefixed `/api/v1`. Responses follow the standard envelope:

```json
{ "success": true, "statusCode": 200, "data": {}, "error": null }
```

Error response:

```json
{
  "success": false,
  "statusCode": 422,
  "data": null,
  "error": {
    "message": "Observation value exceeds plausible range for this code.",
    "code": "OBSERVATION_OUT_OF_PLAUSIBLE_RANGE"
  }
}
```

### Patients

| Method | Path | Description |
|---|---|---|
| POST | `/patients` | Register a patient; generates MRN |
| GET | `/patients` | Paginated list; optional `q` search by name (`ILIKE`) or MRN (exact) |
| GET | `/patients/{id}` | Patient detail with active encounter summary |

**POST body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `firstName` | string | yes | |
| `lastName` | string | yes | |
| `dateOfBirth` | date | yes | |
| `gender` | string | yes | |
| `bloodType` | string | no | Clinical notation: `A+`, `O-`, `AB-`, etc. |
| `allergies` | string | no | Free-text allergy list |
| `emergencyContactName` | string | no | |
| `emergencyContactPhone` | string | no | |

### Encounters

| Method | Path | Description |
|---|---|---|
| GET | `/encounters` | Paginated ward list with clinical summaries; optional `status`, `department` filters |
| POST | `/patients/{id}/encounters` | Open an encounter |
| GET | `/encounters/{id}` | Encounter detail with recent observations and open alerts |
| PATCH | `/encounters/{id}/status` | Advance encounter status |
| GET | `/encounters/{id}/timeline` | Merged chronological view: status changes, observations, alerts |
| GET | `/encounters/{id}/discharge-summary` | Discharge summary info (status, availability) |
| GET | `/encounters/{id}/discharge-summary/content` | Download discharge summary PDF from MinIO |
| GET | `/encounters/{id}/qsofa/current` | Current qSOFA active criteria count (0–3) from Redis |
| GET | `/encounters/{id}/qsofa/history` | Cursor-paginated qSOFA evaluation history |

**GET `/encounters` query params:** `status` (DB literal, e.g. `ACTIVE`), `department` (DB literal, e.g. `ICU`), `page`, `pageSize`

**Ward summary fields:** `encounterId`, `patientId`, `mrn`, `firstName`, `lastName`, `roomBed`, `department`, `status`, `news2Score`, `news2RiskLevel`, `qsofaScore`, `sepsisActive`, `sepsisBundleStatus`, `openAlertCount`, `sofaScore`, `sofaDelta`, `gcsScore`, `gcsClassification`, `lastObservationAt`, `attendingPhysician`, `admittedAt`

**Encounter status machine:**

```
scheduled → active → discharged
          → cancelled
```

`PATCH /encounters/{id}/status` returns **409** on illegal transitions.

**POST body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `encounterType` | string | yes | `INPATIENT`, `OUTPATIENT`, `EMERGENCY` |
| `department` | string | yes | |
| `attendingPhysician` | string | yes | |
| `roomBed` | string | no | Ward and bed assignment (e.g. `ICU-1A`) |
| `admissionReason` | string | no | Clinical reason for admission |

**PATCH `/encounters/{id}/status` body** — optional `dischargeDiagnosis` when transitioning to `DISCHARGED`.

### Alert Thresholds

| Method | Path | Description |
|---|---|---|
| POST | `/alert-thresholds` | Create a threshold |
| GET | `/alert-thresholds` | List all thresholds (paginated) |
| GET | `/alert-thresholds/{id}` | Get a threshold by ID |
| PUT | `/alert-thresholds/{id}` | Update a threshold; invalidates Redis cache |
| DELETE | `/alert-thresholds/{id}` | Delete a threshold; invalidates Redis cache; audit logged |

**Body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `observationCode` | string | yes | e.g. `HEART_RATE`, `SYSTOLIC_BP`, `AVPU`, `GLUCOSE_MG_DL` |
| `displayName` | string | yes | Human-readable label |
| `unit` | string | yes | e.g. `bpm`, `°C`, `mEq/L` |
| `criticalLow` | decimal | no | |
| `warningLow` | decimal | no | |
| `warningHigh` | decimal | no | |
| `criticalHigh` | decimal | no | |

Seeded thresholds (12 codes):

| Code | Display | Unit | Critical Low | Warning Low | Warning High | Critical High |
|---|---|---|---|---|---|---|
| `HEART_RATE` | Heart Rate | bpm | 30 | 50 | 100 | 150 |
| `TEMP_C` | Temperature | °C | 35.0 | 36.0 | 38.3 | 40.0 |
| `POTASSIUM_MEQ_L` | Serum Potassium | mEq/L | 2.5 | 3.5 | 5.0 | 6.5 |
| `SPO2` | Oxygen Saturation | % | 88 | 92 | — | — |
| `RESP_RATE` | Respiratory Rate | breaths/min | — | 12 | 20 | 30 |
| `WBC_K_UL` | White Blood Cell Count | k/µL | 2.0 | 4.0 | 12.0 | 20.0 |
| `SYSTOLIC_BP` | Systolic Blood Pressure | mmHg | 70 | 90 | 160 | 180 |
| `DIASTOLIC_BP` | Diastolic Blood Pressure | mmHg | 40 | 60 | 90 | 110 |
| `LACTATE_MMOL_L` | Serum Lactate | mmol/L | — | — | 2.0 | 4.0 |
| `AVPU` | AVPU Consciousness | score | — | — | — | 2 |
| `SUPPLEMENTAL_O2` | Supplemental Oxygen | flag | — | — | — | — |
| `GLUCOSE_MG_DL` | Blood Glucose | mg/dL | 40 | 70 | 180 | 400 |

### Observations

| Method | Path | Description |
|---|---|---|
| POST | `/encounters/{id}/observations` | Ingest one or more observations (max 10 per call) |
| GET | `/encounters/{id}/observations` | Cursor-paginated observation history |

**POST body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `observations` | array | yes | One to ten observation objects |

**Observation object:**

| Field | Type | Required | Description |
|---|---|---|---|
| `observationCode` | string | yes | Must match a configured alert threshold |
| `value` | decimal | yes | Numeric measurement |
| `unit` | string | yes | Unit of measure |
| `source` | string | no | `DEVICE` (default), `MANUAL`, `LAB` |
| `recordedAt` | DateTimeOffset | yes | When the measurement was taken |

**Idempotency:** Pass an `Idempotency-Key` header. Same key → original `201` response, no duplicate row.

**Ingest transaction sequence:**

1. Validate encounter is `active`
2. Check idempotency key
3. Validate observation value within plausible range
4. Insert observation row
5. Load alert threshold from Redis cache (→ PostgreSQL on miss)
6. If value breaches `CRITICAL` threshold: insert `clinical_alert` + `outbox_event` (topic: `alert.generated`)
7. Insert `outbox_event` (topic: `observation.recorded`)
8. COMMIT

**Status codes:**

| Code | Meaning |
|---|---|
| 201 | Observation(s) recorded |
| 200 | `Idempotency-Key` matched existing observation |
| 404 | Encounter not found |
| 409 | Encounter is not active (discharged or cancelled) |
| 422 | Value outside plausible range or body invalid |

**GET query params:**

| Param | Description |
|---|---|
| `code` | Filter by observation code |
| `from` | Inclusive start (DateTimeOffset) |
| `to` | Inclusive end (DateTimeOffset) |
| `limit` | Page size (default 20) |
| `cursor` | Opaque cursor from previous response for next page |

Uses cursor pagination on `(recorded_at DESC, id DESC)` — offset pagination would shift results as new observations arrive in a continuously growing table.

### Clinical Alerts

| Method | Path | Description |
|---|---|---|
| GET | `/encounters/{id}/alerts` | Paginated alert list for an encounter |
| GET | `/alerts` | Global alert list; optional `status`, `severity`, `department` filter |
| GET | `/alerts/{id}` | Alert detail (`AlertResponse` with optional `explanation`) |
| POST | `/alerts/{id}/acknowledge` | Acknowledge with clinician ID and optional note; returns `AlertResponse` |
| POST | `/alerts/{id}/resolve` | Resolve (must be acknowledged first); returns `AlertResponse` |
| POST | `/alerts/{id}/feedback` | Submit clinician feedback (one per user per alert); requires `alerts:feedback` |

**Alert response shape:** list, get, acknowledge, and resolve endpoints return `AlertResponse` — alert fields plus optional `explanation` (`scoreContributors`, `trend`, `medicationContext`, `narrativeSummary`). Omitted on legacy and threshold-only alerts.

**Alert lifecycle:**

```
open → acknowledged → resolved
     → escalated (RabbitMQ DLQ after 5 min unacknowledged)
```

**POST `/alerts/{id}/acknowledge` body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `clinicianId` | string | yes | Clinician identifier |
| `note` | string | no | Optional acknowledgment note |

### Orders

| Method | Path | Description |
|---|---|---|
| POST | `/encounters/{id}/orders` | Create a clinical order for an active encounter |
| GET | `/encounters/{id}/orders` | List orders for an encounter; optional `status`, `page`, `pageSize` |
| GET | `/orders/{id}` | Order detail with encounter |
| PATCH | `/orders/{id}/status` | Transition order status |
| PATCH | `/orders/{id}/result` | Record a result; transitions to `Resulted` |

**Order status machine:**

```
pending → in_progress → resulted
        → cancelled
```

`PATCH /orders/{id}/status` and `PATCH /orders/{id}/result` return **409** on illegal transitions (e.g. cancelling a resulted order).

**POST body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `orderType` | string | yes | `Lab`, `Imaging`, `Medication`, `Procedure` |
| `description` | string | yes | Order description |
| `orderedBy` | string | yes | Ordering clinician |

**PATCH `/orders/{id}/result` body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `resultSummary` | string | no | Free-text result summary |

### Analytics (Elasticsearch)

| Method | Path | Description |
|---|---|---|
| GET | `/analytics/patients` | Patient/encounter search across MRN, name, department |
| GET | `/analytics/observations/trend` | Time-series aggregation (hourly avg/min/max) for a specific observation code per encounter |
| GET | `/analytics/alerts/summary` | Alert volume by department and severity over a time window |
| GET | `/analytics/population` | Count of patients with a value above or below a threshold in a time window |

**GET `/analytics/patients` query params:** `q` (free text), `department`, `status`

**GET `/analytics/observations/trend` query params:** `encounterId` (required), `code` (required), `from`, `to`

**GET `/analytics/alerts/summary` query params:** `severity`, `from`, `to`, `department`

**GET `/analytics/population` query params:** `code` (required), `threshold` (required), `from`, `to`

The `population` query uses Elasticsearch's numeric range aggregation engine — no full-text search. Running this against PostgreSQL on the operational database would compete with ingest writes under load.

### NEWS2 (National Early Warning Score 2)

| Method | Path | Description |
|---|---|---|
| GET | `/encounters/{id}/news2/current` | Latest NEWS2 score for an encounter (404 if none computed) |
| GET | `/encounters/{id}/news2/history` | Cursor-paginated score history |

**`GET /news2/current` response** includes `totalScore`, `riskLevel` (`LOW`, `LOW_MEDIUM`, `MEDIUM`, `HIGH`), all seven component scores (`respRateScore`, `spo2Score`, …), `hasSingleParamThree`, and `calculatedAt`.

**`GET /news2/history` query params:** `limit` (default 20), `cursor` (opaque token from previous response).

Scores are computed asynchronously by `News2ScoringService` after observations are ingested — allow a few seconds for the Kafka consumer to process all seven parameters before querying.

### GCS (Glasgow Coma Scale)

| Method | Path | Description |
|---|---|---|
| GET | `/encounters/{id}/gcs` | Latest GCS score for an encounter (null data if none computed) |
| GET | `/encounters/{id}/gcs/history` | Cursor-paginated GCS score history |

**`GET /gcs` response** includes `eyeScore`, `verbalScore`, `motorScore`, `totalScore` (3–15), `classification` (`MILD`, `MODERATE`, `SEVERE`), and `calculatedAt`.

**`GET /gcs/history` query params:** `limit` (default 20), `cursor` (opaque token from previous response).

All three components (`GCS_EYE`, `GCS_VERBAL`, `GCS_MOTOR`) must be recorded before a score is computed. Scores are asynchronous via `GcsScoringService`. A completed GCS score publishes `gcs.scored` to Kafka (via outbox) for SOFA CNS re-scoring.

### SOFA (Sequential Organ Failure Assessment)

| Method | Path | Description |
|---|---|---|
| GET | `/encounters/{id}/sofa` | Latest SOFA score for an encounter (404 if none computed) |
| GET | `/encounters/{id}/sofa/history` | Cursor-paginated score history |

**Response** includes `totalScore`, six component scores (`respiratoryScore` … `renalScore`), `isBaseline`, `deltaFromBaseline`, optional `staleness` metadata, and `calculatedAt`.

SOFA scores are computed asynchronously by `SofaScoringService` from SOFA-related observation codes (`PAO2_MMHG`, `FIO2_PCT`, `PLATELET_K_UL`, `BILIRUBIN_MG_DL`, `CREATININE_MG_DL`, `URINE_OUTPUT_ML_H`, vitals, `SPO2`, vasopressors) and from `gcs.scored` events (CNS organ system). Baseline is established when ≥ 4 of 6 organ systems have available data. Delta ≥ 2 from baseline creates a `SOFA_SEPSIS` alert; delta = 1 creates `SOFA_WARNING`. Poll `/sofa/history` to confirm baseline — the latest score may have `isBaseline: false` after subsequent observations.

### Sepsis Bundles

| Method | Path | Description |
|---|---|---|
| GET | `/sepsis-bundles` | Paginated list of bundles hospital-wide; optional `status` filter (`IN_PROGRESS`, `COMPLIANT`, `NON_COMPLIANT`); returns `SepsisBundleSummary` with patient demographics, elements, and deadlines |
| GET | `/encounters/{id}/sepsis-bundle/current` | Current (most recent) sepsis bundle for an encounter (404 if none) |
| GET | `/sepsis-bundles/{id}` | Bundle detail with all elements and linked orders |

**`GET /sepsis-bundle/current` response** includes `encounterId`, `triggeringAlertId`, `triggeringAlertType` (`SOFA_SEPSIS`), `recognizedAt`, `deadlineAt`, `complianceStatus` (`IN_PROGRESS`, `COMPLIANT`, `NON_COMPLIANT`), `completedAt`, and `elements[]` — each with `elementType`, `status`, `orderId`, and `completedAt`.

Bundles are created automatically by `SepsisAlertHandler` when a `SOFA_SEPSIS` alert fires (delta ≥ 2 from baseline). Four clinical orders (blood cultures, serum lactate, broad-spectrum antibiotics, IV fluid resuscitation) are auto-created with `orderedBy: sepsis-bundle-engine`. As orders are resulted via `PATCH /orders/{id}/result`, the corresponding bundle element is marked complete. When all four elements are done, the bundle transitions to `COMPLIANT` (within the 1-hour deadline) or `NON_COMPLIANT`.

### Medications

| Method | Path | Description |
|---|---|---|
| POST | `/encounters/{id}/medications` | Record a medication administration for an active encounter |
| GET | `/encounters/{id}/medications` | List administrations; optional `since` ISO 8601 filter; paginated |
| GET | `/medications/{id}` | Medication administration detail |

**POST body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `drugName` | string | yes | Drug name (case-insensitive for correlation lookups) |
| `dose` | decimal | yes | Must be > 0 |
| `doseUnit` | string | yes | e.g. `mg`, `g`, `mcg` |
| `route` | string | yes | e.g. `PO`, `IV` |
| `administeredAt` | DateTimeOffset | no | Defaults to server time if omitted |
| `administeredBy` | string | yes | Clinician or nurse identifier |

When a correlated drug was given within the `MedicationCorrelation.CorrelationWindowMinutes` window (default 90), subsequent warning and NEWS2 alerts for affected vitals include an annotation in `details` — e.g. `— note: metoprolol 25mg (PO) administered 45 min ago`. See `docs/decisions/medication-correlation-design.md`.

### Sites

| Method | Path | Auth | Description |
|---|---|---|---|
| POST | `/sites` | JWT + `users:admin` | Create a clinical site |
| GET | `/sites` | JWT + `users:admin` | List all sites |
| GET | `/sites/{siteId}` | JWT + `users:admin` | Site detail |

**POST body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `siteCode` | string | yes | Uppercase alphanumeric with hyphens (max 32) |
| `name` | string | yes | Hospital/site name (max 200) |
| `address` | string | no | Site address (max 500) |

### Gateways

| Method | Path | Auth | Description |
|---|---|---|---|
| POST | `/sites/{siteId}/gateways` | JWT + `users:admin` | Register a gateway under a site |
| GET | `/sites/{siteId}/gateways` | JWT + `users:admin` | List gateways; optional `?department=` filter |
| GET | `/gateways/{gatewayId}` | JWT + `users:admin` | Gateway detail |
| PATCH | `/gateways/{gatewayId}/heartbeat` | Gateway API key | Update status and buffer depth |

**POST `/sites/{siteId}/gateways` body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `gatewayCode` | string | yes | Unique per site (max 64) |
| `department` | string | yes | Department assignment (max 100) |

**PATCH `/gateways/{gatewayId}/heartbeat` body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `status` | string | yes | `ONLINE`, `DEGRADED`, or `OFFLINE` |
| `bufferDepth` | int | yes | Unsynced event count (≥ 0) |
| `reportedAtUtc` | DateTimeOffset | yes | Gateway-reported timestamp |

**Gateway API key auth:** Set `X-Api-Key` header (configured in `ApiKey:Gateway`) and `X-Gateway-Id` header. The handler validates the key with constant-time comparison and confirms the gateway ID in the URL matches the header.

### Authentication

| Method | Path | Auth | Description |
|---|---|---|---|
| POST | `/auth/login` | Anonymous | Authenticate with username/password; returns access + refresh tokens |
| POST | `/auth/refresh` | Anonymous | Exchange a valid refresh token for a new access + refresh token pair |
| POST | `/auth/logout` | JWT | Revoke the refresh token and end the session |
| GET | `/auth/me` | JWT | Returns the authenticated user's profile (user ID, username, display name, role) |

**POST `/auth/login` body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `username` | string | yes | Username |
| `password` | string | yes | Password |

**Login response:**

| Field | Type | Description |
|---|---|---|
| `accessToken` | string | JWT bearer token (default 15 min) |
| `refreshToken` | string | Opaque refresh token (default 7 days) |
| `expiresAt` | DateTimeOffset | Access token expiration |
| `userId` | Guid | User ID |
| `username` | string | Username |
| `displayName` | string | Display name |
| `role` | string | `NURSE`, `PHYSICIAN`, `ADMIN`, `INTEGRATION` |

**POST `/auth/refresh` body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `refreshToken` | string | yes | The current refresh token |

**Refresh response:**

| Field | Type | Description |
|---|---|---|
| `accessToken` | string | New JWT bearer token |
| `refreshToken` | string | New refresh token (previous one is revoked) |
| `expiresAt` | DateTimeOffset | New access token expiration |

Refresh tokens rotate on every use — each call revokes the previous refresh token and issues a new one. If the refresh token is expired, revoked, or the user account is deactivated, the endpoint returns 422 and the client must re-authenticate via login.

**POST `/auth/logout` body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `refreshToken` | string | yes | The refresh token to revoke |

Returns `204 No Content`. Revokes the refresh token server-side and creates a `USER_LOGOUT` audit log entry. The access token remains valid until its natural expiration (15 min max).

**Seeded demo users:**

| Username | Password | Role |
|---|---|---|
| `nurse.demo` | `DemoNurse1!` | Nurse |
| `physician.demo` | `DemoPhysician1!` | Physician |
| `admin.demo` | `DemoAdmin1!` | Admin |
| `integration.mirth` | `MirthIntegration1!` | Integration |

**RBAC permission matrix:**

| Permission | Nurse | Physician | Admin | Integration |
|---|---|---|---|---|
| `patients:read` | yes | yes | yes | — |
| `patients:write` | yes | yes | yes | yes |
| `encounters:read` | yes | yes | yes | — |
| `encounters:write` | yes | yes | yes | yes |
| `observations:ingest` | yes | yes | yes | yes |
| `alerts:read` | yes | yes | yes | — |
| `alerts:acknowledge` | yes | yes | yes | — |
| `alerts:resolve` | yes | yes | yes | — |
| `alerts:feedback` | yes | yes | yes | — |
| `thresholds:read` | yes | yes | yes | — |
| `thresholds:write` | — | — | yes | — |
| `analytics:read` | yes | yes | yes | — |
| `orders:write` | yes | yes | yes | — |
| `medications:write` | yes | yes | yes | yes |
| `fhir:ingest` | — | — | yes | yes |
| `fhir:read` | — | — | yes | yes |
| `audit:read` | — | — | yes | — |
| `users:admin` | — | — | yes | — |

All endpoints except `POST /auth/login` and `GET /fhir/R4/metadata` require authentication. Unauthenticated requests receive `401`. Authenticated requests without the required permission receive `403`.

### Audit Logs

| Method | Path | Description |
|---|---|---|
| GET | `/audit-logs` | Query clinical audit logs (Admin only — requires `audit:read` permission) |

**GET `/audit-logs` query params:** `entityType`, `entityId`, `userId`, `action`, `from`, `to`, `page`, `pageSize`

**Audit actions:** `THRESHOLD_CREATED`, `THRESHOLD_UPDATED`, `THRESHOLD_DELETED`, `ALERT_ACKNOWLEDGED`, `ALERT_RESOLVED`, `ENCOUNTER_STATUS_CHANGED`, `PATIENT_REGISTERED`, `SUPPRESSION_WINDOW_SET`, `USER_LOGIN`, `AUTHORIZATION_DENIED`, `USER_LOGOUT`, `TOKEN_REFRESHED`

Each audit log entry includes `action`, `entityType`, `entityId`, `userId`, `userDisplayName`, `previousValueJson` (JSONB), `newValueJson` (JSONB), `reason`, `ipAddress`, `correlationId`, and `createdAt`.

### Users

| Method | Path | Auth | Description |
|---|---|---|---|
| GET | `/users` | JWT + `users:admin` | List all clinical user accounts |
| POST | `/users` | JWT + `users:admin` | Create a new clinical user account |
| PATCH | `/users/{id}` | JWT + `users:admin` | Update role, display name, or active status |

**POST body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `username` | string | yes | Unique username (max 100) |
| `password` | string | yes | Password (BCrypt hashed) |
| `displayName` | string | yes | Display name (max 200) |
| `role` | string | yes | `NURSE`, `PHYSICIAN`, `ADMIN`, `INTEGRATION` |

**PATCH body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `displayName` | string | no | Updated display name |
| `role` | string | no | Updated role |
| `isActive` | bool | no | Enable/disable account |

### Operations

| Method | Path | Auth | Description |
|---|---|---|---|
| GET | `/operations/gateways` | JWT + `users:admin` | List registered gateways; optional `status` and `siteId` filters |
| GET | `/operations/gateways/{gatewayId}` | JWT + `users:admin` | Gateway detail with buffer depth, heartbeat metadata, sync history |
| GET | `/operations/sites/{siteId}/summary` | JWT + `users:admin` | Aggregate gateway summary for a site |

### Discharge Summary

| Method | Path | Description |
|---|---|---|
| GET | `/encounters/{id}/discharge-summary` | Discharge summary info (status, availability) |
| GET | `/encounters/{id}/discharge-summary/content` | Download discharge summary PDF from MinIO |

### Alert Quality Metrics

| Method | Path | Description |
|---|---|---|
| GET | `/alerts/quality-metrics` | Per-alert-type quality metric snapshots; optional `alertType`, `from`, `to` filters |
| GET | `/alerts/quality-metrics/summary` | Aggregate alert quality rates across all alert types; optional `from`, `to` |

### Alert Feedback

| Method | Path | Description |
|---|---|---|
| POST | `/alerts/{id}/feedback` | Submit clinician feedback for an acknowledged/resolved alert; one per user per alert |

**POST body:**

| Field | Type | Required | Description |
|---|---|---|---|
| `feedbackType` | string | yes | `USEFUL`, `TOO_EARLY`, `TOO_LATE`, `FALSE_POSITIVE`, `MISSING_CONTEXT`, `WOULD_ACT` |
| `comment` | string | no | Optional free-text comment |

### FHIR R4 Ingest

All FHIR endpoints are under `/fhir/R4`, accept `application/fhir+json`, and return FHIR R4 JSON responses. Authentication is via JWT bearer token or `X-Api-Key` header (configured in `Fhir:ApiKey` or the `Fhir:ApiKeys` array for zero-downtime key rotation; disabled when blank). API key validation uses `CryptographicOperations.FixedTimeEquals` to prevent timing attacks. When a valid JWT is present, the API key check is skipped — this allows both integration engines (API key) and authenticated admin users (JWT) to access FHIR resources. Write endpoints (`POST`) require `fhir:ingest` permission; read endpoints (`GET`) require `fhir:read` permission. Errors return a FHIR `OperationOutcome` with appropriate issue codes.

| Method | Path | Description |
|---|---|---|
| GET | `/fhir/R4/metadata` | CapabilityStatement — supported resource types and interactions |
| POST | `/fhir/R4/Patient` | Upsert a Patient by hospital identifier (MRN); idempotent |
| GET | `/fhir/R4/Patient/{id}` | Read a Patient by internal ID; returns FHIR R4 Patient resource |
| GET | `/fhir/R4/Patient` | Search Patients by `identifier` (system\|value) or list all; returns Bundle (searchset) |
| POST | `/fhir/R4/Encounter` | Upsert an Encounter by visit identifier; resolves patient by identifier |
| GET | `/fhir/R4/Encounter/{id}` | Read an Encounter by internal ID; returns FHIR R4 Encounter resource |
| GET | `/fhir/R4/Encounter` | Search Encounters by `patient` (UUID), `status` (`in-progress`/`finished`/`cancelled`); returns Bundle (searchset) |
| POST | `/fhir/R4/Observation` | Ingest an Observation; maps LOINC/SNOMED codes to internal codes; supports component observations |
| POST | `/fhir/R4/MedicationAdministration` | Record a medication administration; resolves encounter by identifier |
| POST | `/fhir/R4` | Process a transaction Bundle (Patient → Encounter → Observation/MedicationAdministration in dependency order) |

**CapabilityStatement:** `GET /fhir/R4/metadata` advertises `create`, `read`, and `searchType` interactions for Patient and Encounter; `create` only for Observation and MedicationAdministration; and Bundle transaction support.

**Identifier resolution:** FHIR resources reference each other by hospital identifiers (e.g. MRN in `Patient.identifier`, visit number in `Encounter.identifier`). The `ExternalResourceIdentifier` table maps these to internal UUIDs. On first ingest, a new internal record is created and the identifier is linked. Subsequent requests with the same identifier update the existing record (idempotent upsert).

**LOINC code mapping:** 19 LOINC codes and 3 SNOMED CT fallback codes map to internal observation codes (see `LoincCodeMapper`). Unsupported codes return `422` with an `OperationOutcome`. Temperature observations in Fahrenheit (`[degF]`) are automatically converted to Celsius.

**Transaction Bundles:** `POST /fhir/R4` accepts `Bundle.type=transaction`. Entries are processed in dependency order (Patient first, then Encounter, then Observation/MedicationAdministration). On first failure, processing stops (transaction semantics) and the response includes the `OperationOutcome`.

**Read interactions:** `GET /fhir/R4/Patient/{id}` and `GET /fhir/R4/Encounter/{id}` return the internal resource mapped back to a FHIR R4 resource with hospital identifiers resolved from `ExternalResourceIdentifier`. Returns `404` with an `OperationOutcome` if the resource is not found.

**Search interactions:** `GET /fhir/R4/Patient?identifier=system|value` searches by external identifier; omitting `identifier` lists all patients (up to `_count`, default 20). `GET /fhir/R4/Encounter?patient={uuid}&status=in-progress` filters encounters by patient and/or FHIR status (`in-progress`, `finished`, `cancelled`). Both return a `Bundle` with `type=searchset`.

**Integration with Mirth Connect:** HL7v2 ADT messages (A01 admit, A03 discharge, A08 update) and ORU R01 lab results can be mapped to FHIR Bundles via Mirth channels. See `docs/integration/mirth-fhir-channels.md`.

---

## Data Models

### Patient

```
id                    Guid    PK
mrn                   string  required, unique — auto-generated on registration (e.g. MRN-000001)
firstName             string  required (max 100)
lastName              string  required (max 100)
dateOfBirth           Date    required
gender                string  required (max 10)
bloodType             string? A+ | A- | B+ | B- | AB+ | AB- | O+ | O-
allergies             string? free text
emergencyContactName  string? (max 200)
emergencyContactPhone string? (max 30)
status                string  active | inactive  (default: active)
createdAt             DateTimeOffset
```

### Encounter

```
id                  Guid    PK
patientId           Guid    FK → Patient
encounterType       string  INPATIENT | OUTPATIENT | EMERGENCY
status              string  scheduled | active | discharged | cancelled  (default: scheduled)
department          string  required (max 100)
attendingPhysician  string  required (max 200)
roomBed             string? ward/bed assignment (max 50)
admissionReason     string? clinical reason for admission
dischargeDiagnosis  string? set on discharge
admittedAt          DateTimeOffset
dischargedAt        DateTimeOffset?
createdAt           DateTimeOffset
```

Indexes: `(patient_id, admitted_at DESC)`, partial `(status, admitted_at DESC) WHERE status = 'active'`, partial unique `(patient_id, encounter_type) WHERE status = 'ACTIVE'` (prevents duplicate active encounters of the same type per patient)

### AlertThreshold

```
id               Guid    PK
observationCode  string  required, unique (max 50)
displayName      string  required (max 200)
unit             string  required (max 20)
criticalLow      decimal(10,3)?
warningLow       decimal(10,3)?
warningHigh      decimal(10,3)?
criticalHigh     decimal(10,3)?
createdAt        DateTimeOffset
```

### Observation

```
id               Guid    PK
encounterId      UUID    FK → Encounter
observationCode  string  required (max 50)
value            decimal(10,3) required
unit             string  required (max 20)
source           string  DEVICE | MANUAL | LAB  (default: DEVICE)
idempotencyKey   string? optional, partial unique index
recordedAt       DateTimeOffset required
createdAt        DateTimeOffset
```

Indexes: partial unique `(idempotency_key) WHERE idempotency_key IS NOT NULL`, `(encounter_id, observation_code, recorded_at DESC)`

### ClinicalAlert

```
id              Guid    PK
encounterId     Guid    FK → Encounter
patientId       Guid    FK → Patient
observationId   Guid?   FK → Observation (null for NEWS2, GCS, SOFA composite alerts)
alertType       string  e.g. CRITICAL_HEART_RATE, QSOFA_SCREEN, SOFA_SEPSIS, NEWS2_WARNING, NEWS2_EMERGENCY, GCS_CRITICAL
severity        string  WARNING | CRITICAL
details         text    required
explanation     jsonb?  immutable structured explanation snapshot (score contributors, trend, medication context, narrative); null on legacy/threshold-only alerts
observationCode string? observation code that triggered this alert (e.g. HEART_RATE) — enables direct lookups without LIKE pattern matching
status          string  open | acknowledged | resolved | escalated  (default: open)
acknowledgedAt  DateTimeOffset?
acknowledgedBy  string?
resolvedAt      DateTimeOffset?
triggeredAt     DateTimeOffset
```

Indexes: `(encounter_id, triggered_at DESC)`, `(patient_id, triggered_at DESC)`, partial `(severity, triggered_at DESC) WHERE status = 'open'`, `(encounter_id, observation_code, status)`

### News2Score

```
id                    Guid    PK
encounterId           Guid    FK → Encounter
patientId             Guid    FK → Patient
totalScore            int     aggregate 0–20+
riskLevel             string  LOW | LOW_MEDIUM | MEDIUM | HIGH
respRateScore         int     component 0–3
spo2Score             int
systolicBpScore       int
heartRateScore        int
consciousnessScore    int
temperatureScore      int
supplementalO2Score   int
hasSingleParamThree   bool    true when any single parameter scored 3
calculatedAt          DateTimeOffset
```

Indexes: `(encounter_id, calculated_at DESC)`, `(patient_id, calculated_at DESC)`

### GcsScore

```
id              Guid    PK
encounterId     Guid    FK → Encounter
patientId       Guid    FK → Patient
eyeScore        int     1–4
verbalScore     int     1–5
motorScore      int     1–6
totalScore      int     3–15
classification  string  MILD | MODERATE | SEVERE
calculatedAt    DateTimeOffset
```

Indexes: `(encounter_id, calculated_at DESC)`

### SofaScore

```
id                  Guid    PK
encounterId         Guid    FK → Encounter
patientId           Guid    FK → Patient
totalScore          int     sum of six components (0–24)
respiratoryScore    int     0–4
coagulationScore    int     0–4
liverScore          int     0–4
cardiovascularScore int     0–4
cnsScore            int     0–4
renalScore          int     0–4
isBaseline          bool    true for admission baseline row
deltaFromBaseline   int?    current total minus baseline total
stalenessFlags      jsonb?  stale/missing components, SpO2 fallback flag
calculatedAt        DateTimeOffset
```

Indexes: `(encounter_id, calculated_at DESC)`, partial `(encounter_id) WHERE is_baseline = true`

### QsofaEvaluation

```
id                Guid    PK
encounterId       Guid    FK → Encounter
patientId         Guid    FK → Patient (via Encounter)
activeCriteria    int     0–3 (check constraint)
respRate          decimal? respiratory rate value at evaluation time
systolicBp        decimal? systolic BP value at evaluation time
avpu              decimal? AVPU/GCS value at evaluation time
screenAlertFired  bool    true if this evaluation triggered a QSOFA_SCREEN alert
evaluatedAt       DateTimeOffset
createdAt         DateTimeOffset
```

Indexes: `(encounter_id, evaluated_at)`

### Order

```
id            Guid    PK
encounterId   Guid    FK → Encounter
orderType     string  LAB | MEDICATION | IMAGING
description   string  required (max 500)
orderedBy     string  required (max 200)
status        string  pending | in_progress | resulted | cancelled  (default: pending)
orderedAt     DateTimeOffset
resultedAt    DateTimeOffset?
resultSummary string? Free-text result summary (set on record result)
```

Indexes: `(encounter_id, ordered_at DESC)`, partial `(status, ordered_at) WHERE status IN ('pending', 'in_progress')`

### SepsisBundle

```
id                    Guid    PK
encounterId           Guid    FK → Encounter
triggeringAlertId     Guid    FK → ClinicalAlert
triggeringAlertType   string  required (max 50) — SOFA_SEPSIS
recognizedAt          DateTimeOffset
deadlineAt            DateTimeOffset — recognizedAt + 1 hour
complianceStatus      string  IN_PROGRESS | COMPLIANT | NON_COMPLIANT  (default: IN_PROGRESS)
completedAt           DateTimeOffset?
```

Indexes: `(encounter_id, recognized_at DESC)`, `(compliance_status)`, `(triggering_alert_id)`, partial unique `(encounter_id) WHERE compliance_status = 'IN_PROGRESS'` (prevents TOCTOU race on concurrent bundle creation)

Check constraint: `compliance_status IN ('IN_PROGRESS', 'COMPLIANT', 'NON_COMPLIANT')`

### SepsisBundleElement

```
id            Guid    PK
bundleId      Guid    FK → SepsisBundle (CASCADE)
elementType   string  required (max 40) — BLOOD_CULTURES | SERUM_LACTATE | BROAD_SPECTRUM_ANTIBIOTICS | IV_FLUID_RESUSCITATION
status        string  PENDING | COMPLETED  (default: PENDING)
orderId       Guid?   FK → Order (SET NULL)
completedAt   DateTimeOffset?
```

Indexes: unique `(bundle_id, element_type)`, `(order_id)`

Check constraints: `element_type IN (...)`, `status IN ('PENDING', 'COMPLETED')`

### MedicationAdministration

```
id              Guid    PK
encounterId     Guid    FK → Encounter (Restrict on delete)
drugName        string  required (max 200)
dose            decimal(10,4) required
doseUnit        string  required (max 20)
route           string  required (max 20)
administeredAt  DateTimeOffset required
administeredBy  string  required (max 200)
```

Indexes: `(encounter_id, administered_at)`, `(encounter_id, drug_name)`

### OutboxEvent

```
id           Guid    PK
topic        string  required (max 200)
partitionKey string? — encounterId for per-encounter ordering
payload      JSONB   required
createdAt    DateTimeOffset
processedAt  DateTimeOffset?
retryCount   int     default 0 — Kafka produce attempt counter
lastError    string? — last Kafka produce failure reason
failedAt     DateTimeOffset? — set when retryCount exceeds OutboxMaxRetries (permanently failed)
```

Partial index: `(created_at) WHERE processed_at IS NULL AND failed_at IS NULL`

### ExternalResourceIdentifier

```
id              Guid    PK
resourceType    string  PATIENT | ENCOUNTER
internalId      Guid    FK → Patient or Encounter (logical, not enforced)
system          string  required — identifier system URI (e.g. http://hospital.example/mrn)
value           string  required — identifier value (e.g. MRN-001)
createdAt       DateTimeOffset
```

Unique index: `(resource_type, system, value)` — one mapping per external identifier

### ClinicalUser

```
id              Guid    PK
username        string  required, unique (max 100)
passwordHash    string  required (BCrypt)
displayName     string  required (max 200)
role            string  NURSE | PHYSICIAN | ADMIN | INTEGRATION
isActive        bool    default true
createdAt       DateTimeOffset
lastLoginAt     DateTimeOffset?
```

### RefreshToken

```
id          Guid    PK
token       string  required, unique (max 256) — opaque base64 token (64 random bytes)
userId      Guid    FK → ClinicalUser (CASCADE)
expiresAt   DateTimeOffset required
createdAt   DateTimeOffset
revokedAt   DateTimeOffset? — set on refresh rotation or explicit logout
```

Indexes: unique `(token)`, `(user_id)`

### ClinicalAuditLog

```
id                Guid    PK
action            string  required (max 50) — THRESHOLD_CREATED | THRESHOLD_UPDATED | THRESHOLD_DELETED | ALERT_ACKNOWLEDGED | ALERT_RESOLVED | ENCOUNTER_STATUS_CHANGED | PATIENT_REGISTERED | SUPPRESSION_WINDOW_SET | USER_LOGIN | AUTHORIZATION_DENIED | USER_LOGOUT | TOKEN_REFRESHED
entityType        string  required (max 100) — e.g. AlertThreshold, ClinicalAlert, Encounter, Patient, ClinicalUser
entityId          Guid    required
userId            Guid?   FK → ClinicalUser (null for system-initiated actions)
userDisplayName   string? (max 200)
previousValueJson jsonb?  state before the action
newValueJson      jsonb?  state after the action
reason            string? optional clinician-provided reason
ipAddress         string? (max 45) — IPv4 or IPv6
correlationId     string? (max 100) — links to request correlation header
createdAt         DateTimeOffset
```

Append-only — no UPDATE or DELETE from application code.

Indexes: `(entity_type)`, `(entity_id)`, `(user_id)`, `(created_at)`

### ClinicalSite

```
id          Guid    PK
siteCode    string  required, unique (max 32) — uppercase alphanumeric with hyphens
name        string  required (max 200)
address     string? free text
active      bool    default true
createdAt   DateTimeOffset
```

Indexes: unique `(site_code)`

### WardGateway

```
id                    Guid    PK
siteId                Guid    FK → ClinicalSite (RESTRICT)
gatewayCode           string  required (max 64)
department            string  required (max 100)
status                string  ONLINE | DEGRADED | OFFLINE  (default: OFFLINE)
reportedBufferDepth   int     default 0
lastHeartbeatAt       DateTimeOffset?
lastSyncAt            DateTimeOffset?
createdAt             DateTimeOffset
```

Indexes: unique `(site_id, gateway_code)`, `(site_id, department)`, partial `(status) WHERE status != 'ONLINE'`

Check constraint: `status IN ('ONLINE', 'DEGRADED', 'OFFLINE')`

### ReconciliationAlert

```
id            Guid    PK
checkType     string  UNACKNOWLEDGED_CRITICAL_ALERT | PENDING_ORDER_NO_RESULT | ACTIVE_INPATIENT_NO_OBSERVATION
encounterId   Guid?   FK → Encounter
patientId     Guid?   FK → Patient
details       text    required
resolvedAt    DateTimeOffset?
createdAt     DateTimeOffset
```

### AlertFeedback

```
id            Guid    PK
alertId       Guid    FK → ClinicalAlert
userId        Guid    FK → ClinicalUser
feedbackType  string  USEFUL | TOO_EARLY | TOO_LATE | FALSE_POSITIVE | MISSING_CONTEXT | WOULD_ACT
comment       string? optional free-text
createdAt     DateTimeOffset
```

Unique index: `(alert_id, user_id)` — one feedback per user per alert

### AlertQualityMetric

```
id                      Guid    PK
alertType               string  alert type (DB literal)
windowStart             DateTimeOffset
windowEnd               DateTimeOffset
totalAlerts             int
acknowledgedCount       int
resolvedCount           int
escalatedCount          int
feedbackUsefulCount     int
feedbackFalsePositiveCount int
feedbackWouldActCount   int
feedbackCount           int
acknowledgementRate     double
falsePositiveRate       double
usefulRate              double
wouldActRate            double
avgSecondsToAcknowledge double
avgSecondsToResolution  double
computedAt              DateTimeOffset
```

Indexes: `(alert_type, window_start)`

---

## Elasticsearch Index Shapes

### `patient_encounters`

```json
{
  "encounterId": "uuid",
  "patientId": "uuid",
  "mrn": "MRN-000001",
  "patientName": "Jane Smith",
  "department": "ICU",
  "status": "active",
  "attendingPhysician": "Dr. Osei",
  "roomBed": "ICU-4B",
  "admissionReason": "Chest pain, rule out MI",
  "admittedAt": "2025-01-01T08:00:00Z",
  "openAlertCount": 2,
  "news2Score": 6,
  "news2RiskLevel": "MEDIUM",
  "sepsisBundleStatus": "IN_PROGRESS",
  "sepsisBundleElementsCompleted": 2,
  "sepsisBundleDeadlineAt": "2025-01-01T09:00:00Z",
  "lastObservationAt": "2025-01-01T09:45:00Z"
}
```

`news2Score` and `news2RiskLevel` are optional — populated by `EsIndexerService` when a `NEWS2_WARNING` or `NEWS2_EMERGENCY` alert is indexed (payload fields `news2Score` / `news2RiskLevel` from `News2Detector`). LOW-risk scores with no alert are not projected to Elasticsearch.

`sepsisBundleStatus`, `sepsisBundleElementsCompleted`, and `sepsisBundleDeadlineAt` are optional — populated by `EsIndexerService` from `sepsis.bundle.created` and `sepsis.bundle.updated` Kafka events. Enables department dashboards to filter/sort encounters by sepsis bundle compliance in real time.

### `observations`

```json
{
  "observationId": "uuid",
  "encounterId": "uuid",
  "patientId": "uuid",
  "mrn": "MRN-000001",
  "observationCode": "HEART_RATE",
  "value": 118.0,
  "unit": "bpm",
  "source": "DEVICE",
  "recordedAt": "2025-01-01T09:45:00Z"
}
```

### `clinical_alerts`

```json
{
  "alertId": "uuid",
  "encounterId": "uuid",
  "patientId": "uuid",
  "department": "ICU",
  "alertType": "THRESHOLD_BREACH",
  "severity": "CRITICAL",
  "status": "open",
  "triggeredAt": "2025-01-01T09:45:00Z"
}
```

---

## RabbitMQ Exchange Topology

Exchange: `clinical.notifications.exchange` (direct)

| Queue | Purpose | DLQ |
|---|---|---|
| `alerts.paging.queue` | Physician paging jobs; prefetch=3 | → `alerts.paging.dlq` on NACK |
| `alerts.paging.dlq` | Dead-letter queue; `x-message-ttl = 300000ms` | → `alerts.escalation.queue` on TTL expiry |
| `alerts.escalation.queue` | On-call backup paging | — |
| `notifications.discharge.queue` | Discharge summary PDF generation + MinIO upload | — |
| `notifications.reconciliation.queue` | Reconciliation safety findings from scheduled checks | — |
| `notifications.appointment.queue` | Appointment reminder SMS | — |

---

## Kafka Topics

| Topic | Partition key | Consumer groups |
|---|---|---|
| `observation.recorded` | `encounterId` | `es-indexer`, `sepsis-engine` (qSOFA), `warning-evaluator`, `news2-scoring`, `gcs-scoring`, `sofa-scoring`, `trend-analyzer`, `data-lake-writer` |
| `alert.generated` | `encounterId` | `es-indexer`, `notification-publisher`, `data-lake-writer` |
| `encounter.status.changed` | `encounterId` | `es-indexer`, `data-lake-writer` |
| `gcs.scored` | `encounterId` | `sofa-scoring` |
| `sepsis.bundle.created` | `encounterId` | `es-indexer` |
| `sepsis.bundle.updated` | `encounterId` | `es-indexer` |

All topics use 6 partitions. `KAFKA_AUTO_CREATE_TOPICS_ENABLE=false` — topics (including `gcs.scored`) are provisioned explicitly by `KafkaTopicProvisioner` on API startup.

**`alert.generated` payload (minimum fields for downstream consumers):**

| Field | Required by | Notes |
|---|---|---|
| `alertId`, `encounterId`, `patientId` | ES indexer, data lake, paging | UUIDs |
| `alertType`, `severity`, `triggeredAt` | All consumers | DB string literals for type/severity |
| `details` | Data lake Parquet | Human-readable breach summary; always set on new alerts |
| `department` | ES indexer | Optional; critical ingest alerts include it |
| `news2Score`, `news2RiskLevel` | ES indexer | Optional; set on `NEWS2_WARNING` / `NEWS2_EMERGENCY` alerts for encounter document projection |
| `explanation` | Dashboard, analytics | Optional; structured score contributors, trend, medication context, and narrative summary on explainable alerts (NEWS2, SOFA, GCS, rapid deterioration). Omitted on legacy and threshold-only alerts. Existing consumers that ignore unknown fields remain compatible. |
| `partitionKey` | Outbox relay | Same as `encounterId` |

---

---

## qSOFA Screening (Sepsis-3 Bedside Tool)

The qSOFA (quick Sequential Organ Failure Assessment) engine evaluates three organ-dysfunction criteria per encounter within the `SepsisEngineService` Kafka consumer. Redis keys use a 30-minute TTL sliding window:

| Criterion | Observation Code | Trigger |
|---|---|---|
| Tachypnea | `RESP_RATE` | ≥ 22 breaths/min |
| Hypotension | `SYSTOLIC_BP` | ≤ 100 mmHg |
| Altered mentation | `GCS` / `AVPU` | GCS < 15 or AVPU ≥ 1 (any non-Alert state) |

Redis key pattern: `qsofa:{encounterId}:{code}` with 30-minute TTL. When a criterion normalizes, the key is deleted immediately. When ≥ 2 of 3 criteria are active simultaneously and no open `QSOFA_SCREEN` alert exists, the engine inserts a `WARNING`-level screening alert with details formatted as `"qSOFA score 2/3: RESP_RATE=24, SYSTOLIC_BP=95 — recommend SOFA lab panel"`.

**Clinical role:** qSOFA is a bedside screening tool — it identifies patients who should have SOFA labs ordered. It does **not** trigger the sepsis bundle directly. Only `SOFA_SEPSIS` (delta ≥ 2 from baseline) triggers bundle creation. This matches the Sepsis-3 two-tier workflow: screen → confirm → treat.

**API:** `GET /encounters/{id}/qsofa/current` returns `activeCriteria` (0–3) and per-criterion values from Redis via `QsofaService` — used by ward dashboards and the simulator poll loop. `GET /encounters/{id}/qsofa/history` returns cursor-paginated evaluation history from the `qsofa_evaluations` table, including criteria values and whether a screen alert was fired — used by the `QsofaHistory.vue` dashboard chart.

---

## Sepsis Bundle Compliance (SEP-1)

When a `SOFA_SEPSIS` alert fires (delta ≥ 2 from baseline), `SepsisAlertHandler` calls `SepsisBundleService.TryCreateBundleAsync()` to initiate a four-element treatment bundle with a one-hour compliance deadline:

| Bundle Element | Order Type | Auto-Created Order Description |
|---|---|---|
| `BLOOD_CULTURES` | Lab | SEP-1: Blood cultures |
| `SERUM_LACTATE` | Lab | SEP-1: Serum lactate |
| `BROAD_SPECTRUM_ANTIBIOTICS` | Medication | SEP-1: Broad-spectrum antibiotics |
| `IV_FLUID_RESUSCITATION` | Procedure | SEP-1: IV fluid bolus |

**Lifecycle:**

1. `SOFA_SEPSIS` alert fires → `SepsisAlertHandler` → `SepsisBundleService.TryCreateBundleAsync()`
2. Bundle created with `complianceStatus = IN_PROGRESS`, `deadlineAt = recognizedAt + 1 hour`
3. Four orders created (`orderedBy: sepsis-bundle-engine`), each linked to a bundle element
4. Outbox event → Kafka topic `sepsis.bundle.created` → ES indexer projects `sepsisBundleStatus` on encounter
5. Clinicians work through orders; `PATCH /orders/{id}/result` → `OrderService` → `SepsisBundleService.OnOrderResultedAsync()`
6. Each resulted order marks its bundle element `COMPLETED`; outbox event → `sepsis.bundle.updated` → ES update
7. When all four elements are complete: `complianceStatus = COMPLIANT` (within deadline) or `NON_COMPLIANT` (past deadline); Prometheus `sepsis_bundle_compliance_total{status}` incremented
8. If the deadline passes with incomplete elements, `SepsisBundleMonitorService` (polling every 5 min) marks the bundle `NON_COMPLIANT` — elements remain `PENDING` but the bundle status reflects the missed deadline

**Idempotency:** Only one in-progress bundle can exist per encounter, enforced by a partial unique index `(encounter_id) WHERE compliance_status = 'IN_PROGRESS'`. Bundle creation wraps order and bundle inserts in a single database transaction — if the unique constraint rejects a concurrent duplicate, the transaction rolls back all associated orders, preventing orphaned order records. A second alert for the same encounter returns early without side effects.

---

## NEWS2 Scoring

The NEWS2 engine evaluates seven observation codes that overlap with the expanded vital-sign vocabulary from Phase 10:

| Parameter | Observation Code | Score range |
|---|---|---|
| Respiratory rate | `RESP_RATE` | 0–3 |
| Oxygen saturation (Scale 1) | `SPO2` | 0–3 |
| Systolic blood pressure | `SYSTOLIC_BP` | 0–3 |
| Heart rate | `HEART_RATE` | 0–3 |
| Consciousness (AVPU) | `AVPU` | 0 or 3 |
| Temperature | `TEMP_C` | 0–3 |
| Supplemental oxygen | `SUPPLEMENTAL_O2` | 0 or 2 |

**Risk levels** (aggregate score):

| Total score | Risk level | Alert |
|---|---|---|
| 0–4 (no single param = 3) | `LOW` | None |
| Any single param = 3 (total under 5) | `LOW_MEDIUM` | `NEWS2_WARNING` |
| 5–6 | `MEDIUM` | `NEWS2_WARNING` |
| ≥ 7 | `HIGH` | `NEWS2_EMERGENCY` (CRITICAL) |

All seven parameters must be present in Redis (4-hour TTL per key) before a score is computed. Each new observation after completeness triggers a new `news2_scores` row; alert creation is idempotent per encounter and alert type while an alert remains open.

---

## Elasticsearch Index Replay

If the Elasticsearch indices need to be rebuilt (e.g., after a mapping change or data loss):

```bash
# 1. Stop the indexer consumer group (set consumer group to a known-good offset, or reset to beginning)
# 2. Delete existing indices
curl -X DELETE http://localhost:9200/patient_encounters
curl -X DELETE http://localhost:9200/observations
curl -X DELETE http://localhost:9200/clinical_alerts

# 3. Reset the es-indexer consumer group offset to the beginning
docker exec -it <kafka-container> kafka-consumer-groups.sh \
  --bootstrap-server localhost:9092 \
  --group es-indexer \
  --topic observation.recorded \
  --reset-offsets --to-earliest --execute

# 4. Restart the application — EsIndexerService will replay all events from offset 0
dotnet run
```

The indices rebuild from the full Kafka history. Document count should match PostgreSQL row count when complete. This is only possible because Kafka retains events after consumption.

---

## Data Lake Replay

The MinIO Parquet archive is a pure Kafka projection — rebuildable without touching PostgreSQL. See `docs/plans/phase-9-plan.md` for the full procedure. Summary:

```bash
# Reset data-lake-writer offsets to earliest
docker compose exec -T kafka /opt/kafka/bin/kafka-consumer-groups.sh \
  --bootstrap-server localhost:9092 \
  --group data-lake-writer \
  --reset-offsets --to-earliest --all-topics --execute

# Clear Parquet prefixes in MinIO (mc alias localvc http://localhost:9005 minioadmin minioadmin)
mc rm --recursive --force localvc/vigilcare/observations/
mc rm --recursive --force localvc/vigilcare/alerts/
mc rm --recursive --force localvc/vigilcare/encounters/

# Restart the API — DataLakeWriterService replays from offset 0
dotnet run
```

Verify with `./scripts/run-phase9-verification.sh`.

---

## Pagination

List endpoints use offset pagination:

| Param | Default | Description |
|---|---|---|
| `page` | 1 | Page number (1-based) |
| `pageSize` | 20 | Items per page (max 100) |

Response shape:

```json
{
  "items": [],
  "page": 1,
  "pageSize": 20,
  "totalCount": 42,
  "totalPages": 3
}
```

Observation history uses cursor pagination on `(recorded_at DESC, id DESC)`. Offset pagination would shift results as new observations arrive continuously. The cursor is opaque and returned in the response; pass it as `?cursor=` on the next request.

---

## Implemented Phases

Thirty-three phases from the project roadmap are implemented and verified, including the **Site & Gateway Registry** (Phase 20), the **Ward Gateway Service** (Phase 21), the **Dashboard Gap Analysis Fixes** (Phase 22), the **Degraded Operations Visibility** (Phase 23), the **Sepsis-3 clinical refactor** (Phases 27–29), the **FHIR R4 Inbound Facade** (Phase 30), **RBAC with clinical audit logging** (Phase 31), the **Alert Quality Analytics** (Phase 33), the **Explainable Alerts** (Phase 34), the **MIMIC-IV Replay Scenario Generator** (Phase 35), and the **Enhanced Dashboard** (department overview, sepsis bundle board, critical alert notifications, shift handoff reports, vitals entry, sortable/filterable ward table). Integration tests (`dotnet test`) and per-phase verification scripts cover Phases 8–15, 20–23, 25–31, 33–35. Phases 17–19 add the Vue dashboard and clinician feedback (Vitest in `vigilcare-dashboard/`).

| Phase | Feature | Status |
|---|---|---|
| 1 | Schema, EF Core migrations, patient/encounter CRUD, alert threshold CRUD, encounter status machine, Redis threshold pre-load, seed data | Done |
| 2 | Observation ingest — idempotency, plausibility validation, synchronous critical alert creation, outbox event, cursor-paginated history; alert lifecycle (acknowledge, resolve); integration tests | Done |
| 3 | Outbox relay (`IHostedService`, 500ms poll); Kafka topics with 6 partitions; `encounterId` partition key; relay survives Kafka restart | Done |
| 4 | Elasticsearch CQRS projection (`EsIndexerService`); patient search; observation trend; alert summary; population aggregation; replay procedure | Done |
| 5 | Sepsis engine (`SepsisEngineService`); Redis-based qSOFA screening (SIRS removed in Phase 27); idempotent alert creation; integration tests | Done |
| 6 | RabbitMQ exchange and queue topology; `NotificationPublisherService`; `PagingWorkerService`; DLQ escalation (`EscalationWorkerService`); discharge summary (`DischargeSummaryWorkerService` → MinIO); integration tests | Done |
| 7 | Reconciliation scheduler — unacknowledged critical alerts, stale pending orders, disconnected monitors; `reconciliation_alerts` table; RabbitMQ publish; integration tests | Done |
| 8 | Prometheus metrics (`GET /metrics`); ten metric families and three collectors; Grafana clinical dashboard; `ObservabilityPhase8Tests`; `run-phase8-verification.sh` | Done |
| 9 | Data lake writer — `data-lake-writer` consumer group; date-partitioned Parquet flush to MinIO; `DataLakePhase9Tests`; `run-phase9-verification.sh`; design doc in `docs/decisions/data-lake-design.md` | Done |
| 10 | Clinical data model expansion — `BloodType`, patient allergies/emergency contact, encounter room/bed/admission/discharge fields; five new observation codes (`SYSTOLIC_BP`, `DIASTOLIC_BP`, `LACTATE_MMOL_L`, `AVPU`, `SUPPLEMENTAL_O2`); `GLUCOSE_MG_DL` threshold fix; 12 seeded thresholds; `ClinicalDemographicsAndObservationTests`; `run-phase10-verification.sh` | Done |
| 11 | Warning alert consumer (`WarningAlertService` / `warning-evaluator`); 10 `Warning*` alert types; Orders API (`OrdersController`, `OrderService`); FluentValidation on all request DTOs; `WarningAlertTests`, `OrderLifecycleTests`, `ValidationTests`; `run-phase11-verification.sh` | Done |
| 12 | NEWS2 composite scoring (`News2Calculator`, `News2Detector`, `News2ScoringService`); `news2_scores` table; `NEWS2_WARNING` / `NEWS2_EMERGENCY` alert types; `News2Controller` (current + history); ES `news2Score` / `news2RiskLevel` projection; Prometheus NEWS2 metrics; `News2CalculatorTests`, `News2DetectorTests`; `run-phase12-verification.sh` | Done |
| 13 | Trend detection (`TrendCalculator`, `TrendDetector`, `TrendAnalyzerService`); `RAPID_DETERIORATION` alert type; alert suppression windows (`AlertSuppressionService`, Redis `suppress:{enc}:{type}`); `TrendCalculatorTests`, `TrendDetectorTests`, `AlertSuppressionTests`; `run-phase13-verification.sh` | Done |
| 14 | qSOFA scoring engine (`QsofaCalculator`, `QsofaDetector`); sepsis bundle compliance (`SepsisBundle`, `SepsisBundleElement`, `SepsisBundleService`); auto-created treatment orders with 1-hour deadline; `SepsisAlertHandler` bridge; `SepsisBundleMonitorService` (5-min overdue scan); `SepsisBundlesController` API; ES projection of bundle status; Kafka topics `sepsis.bundle.created` / `sepsis.bundle.updated`; Prometheus `qsofa_detections_total` and `sepsis_bundle_compliance_total`; `QsofaCalculatorTests`, `QsofaDetectorTests`, `SepsisBundleTests` (bundle trigger updated to SOFA_SEPSIS in Phase 27) | Done |
| 15 | Medication administration (`MedicationAdministration`, `MedicationsController`, `MedicationService`); drug-vital correlation config (`MedicationCorrelationOptions`); `MedicationCorrelationHelper` annotates `WarningEvaluator` and `News2Detector` alert details; `medication_administrations` table + migration; `MedicationServiceTests`, `MedicationCorrelationTests`, `MedicationValidationTests`; `run-phase15-verification.sh`; design doc in `docs/decisions/medication-correlation-design.md` | Done |
| 16 | Console replay simulator (`VigilCare.Simulator`); scenario JSON schema; CLI commands `replay`, `replay-all`, `validate`, `dry-run`; speed multiplier and optional API polling; eight sample scenarios; `docs/simulator-guide.md` | Done |
| 20 | **Site & Gateway Registry + Clinical Sync Contracts** — `VigilCare.ClinicalContracts` shared class library with sync DTOs (`ClinicalSyncBatchRequest`, `SyncedObservation`, `SyncedAlertEvent`, `GatewayHeartbeatRequest`); `ClinicalSite` and `WardGateway` domain entities with EF Core configurations and migrations; `GatewayApiKeyAuthenticationHandler` (constant-time `X-Api-Key` validation + `X-Gateway-Id` claim) registered alongside JWT bearer; `SitesController` (create, list, get) and `GatewaysController` (register, list, get, heartbeat) with dual auth — JWT + `users:admin` for admin CRUD, gateway API key for heartbeat; `SiteService`, `GatewayRegistryService`; FluentValidation on `CreateSiteRequest`, `RegisterGatewayRequest`, `GatewayHeartbeatRequest`; `GatewayRegistrySeeder` with fixed GUIDs for demo site and gateway; `WardGatewayMetricsCollector` (60s periodic) exports `ward_gateways_offline_gauge` and `ward_gateway_buffer_depth`; `GatewayRegistryTests` (register, heartbeat, API key 401, degraded status, department filter); `ClinicalContractsTests` (JSON round-trip); `run-phase20-verification.sh` | Done |
| 21 | **Ward Gateway Service (Local-First Clinical Path)** — `VigilCare.WardGateway` standalone ASP.NET Core 8 deployable with its own PostgreSQL (`vigilcare_ward`), Redis, and RabbitMQ; domain entities mirror central API (`ReplicaPatient`, `ReplicaEncounter`, `LocalObservation`, `LocalClinicalAlert`, `ReplicaAlertThreshold`); `LocalObservationService` ingests observations locally with plausibility validation and synchronous critical alert creation; `LocalWarningEvaluator` creates warning-range alerts from Redis-cached thresholds; `BufferedSyncWriter` writes observation and alert events to `buffered_sync_items` table for upload when online; `EncounterReplicaSyncService` pulls patient/encounter data from central API on startup; `ThresholdCacheLoader` fetches alert thresholds from central API into local Redis; `CentralReachabilityService` polls central API health every 30s; `GatewayHeartbeatService` reports gateway status and buffer depth to central registry; `SyncUploaderService` batches buffered sync items and uploads to central API using `ClinicalSyncBatchRequest` contracts when online; local RabbitMQ paging (`LocalPagingWorkerService`) and escalation (`LocalEscalationWorkerService`) for ward-level clinician notification; `EncounterReadService` provides ward encounter list and detail views; Docker Compose `ward-gateway` profile with separate PostgreSQL, Redis, and RabbitMQ; health checks (Redis, RabbitMQ, encounter replica readiness); `WardGatewayLocalPathTests` and `WardGatewayPartitionTests` integration tests with Testcontainers; `run-phase21-verification.sh` | Done |
| 22 | **Dashboard Gap Analysis Fixes** — SOFA history chart (`SofaHistory.vue`) with organ-system breakdown; GCS history chart (`GcsHistory.vue`) with component tracking; qSOFA evaluation history (`QsofaHistory.vue`) backed by new `qsofa_evaluations` table and `GET /qsofa/history` API; patient banner (`PatientBanner.vue`) with demographics, age, blood type, allergies, emergency contact; encounter timeline (`EncounterTimeline.vue`) with merged chronological status/observation/alert events; medication administration markers on vital trend charts (`medicationMarkerPlugin.js`); composables `patientFormat.js`, `timelineFormat.js`, `chartMedications.js`; `GET /encounters/{id}/gcs/history` cursor-paginated GCS history endpoint; `QsofaDetector` now persists every evaluation; `GapAnalysisFixTests` integration tests; Vitest tests for all new components; `run-phase22-verification.sh`; `docs/dashboard-gap-analysis.md` | Done |
| 17 | Ward dashboard shell — Vue 3 + Vite + Pinia + Tailwind; virtual ward table (NEWS2-sorted, department filter); patient detail (vitals, scores, alerts, orders, sepsis bundle); alert center (global acknowledge/resolve); API polling; CORS-backed `GET /encounters` ward list | Done |
| 18 | Clinical review mode — Chart.js vital sign trends (5 charts), NEWS2 history chart, local replay controls, alert reasoning panel, medication context on alerts; `fetchNews2History` / `fetchMedications`; Vitest composable and component tests; `docs/dashboard-guide.md` | Done |
| 19 | Clinician feedback mode — six rating buttons per alert, optional notes, Feedback Summary with aggregate stats, JSON/CSV export, localStorage persistence; `docs/clinical-testing-guide.md` for doctor/nurse evaluation sessions | Done |
| 25 | Glasgow Coma Scale — `GcsCalculator`, `GcsDetector`, `GcsScoringService`; `gcs_scores` table; `GCS_CRITICAL` / `GCS_WARNING` alerts; `gcs.scored` outbox topic; NEWS2 consciousness GCS-first; qSOFA altered mentation sync; `GcsController`; Prometheus `gcs_scores_total`; `GcsScoringTests`; `run-phase25-verification.sh` | Done |
| 26 | SOFA scoring — `SofaCalculator`, `SofaDetector`, `SofaLabCache`, `SofaVasopressorResolver`, `SofaScoringService`; `sofa_scores` table with baseline + delta; `SOFA_SEPSIS` / `SOFA_WARNING` alerts; six new observation codes; `SofaController`; Kafka topic `gcs.scored` provisioned for CNS re-score; stale-encounter guard for Kafka replay; Prometheus `sofa_scores_total`; `SofaScoringTests`; `run-phase26-verification.sh` | Done |
| 27 | **Sepsis-3 clinical refactor** — SIRS removed (`SirsDetector`, `SirsEvaluator` deleted); qSOFA repositioned as bedside screening (`QSOFA_SCREEN` replaces `QSOFA_WARNING`); sepsis bundle now triggered only by `SOFA_SEPSIS` (delta ≥ 2) via `SepsisAlertHandler`; `AlertCreationGuard` prevents deprecated `SEPSIS_WARNING` creation; legacy alert types retained `[Obsolete]` for historical queries; migration `AddQsofaScreenAlertType`; `SepsisRefactorTests`, `AlertCreationGuardTests`; `run-phase27-verification.sh` | Done |
| 28 | **Frontend GCS + SOFA + sepsis UI refactor** — `GcsEntryForm.vue` (bedside GCS component entry); `SofaScorePanel.vue` (organ-system breakdown with staleness indicators); `useGcs` / `useSofa` composables; `scoring` Pinia store; `ScoresPanel` updated with GCS/SOFA display; `SepsisBundlePanel` and `AlertReasoning` refactored for Sepsis-3 alert types; Vitest tests for GCS entry, SOFA panel, scores panel, alert labels; `run-phase28-verification.sh` | Done |
| 29 | **Simulator scenario expansion + clinical validation** — three new scenarios (`neurological-decline-gcs-01`, `sepsis-sofa-progression-01`, `sofa-partial-spo2-fallback-01`); existing scenarios enriched with GCS/SOFA observations; `ScenarioReplayHelper` for end-to-end test replay; `ClinicalRefactorEndToEndTests` validates qSOFA screen → SOFA labs → bundle workflow; simulator polls GCS/SOFA scores; `run-phase29-verification.sh` | Done |
| 30 | **FHIR R4 Inbound Facade** — `FhirIngestController` (`POST /fhir/R4/{Patient,Encounter,Observation,MedicationAdministration}`); `FhirMetadataController` (CapabilityStatement); `FhirBundleProcessor` (transaction Bundles in dependency order); `LoincCodeMapper` (19 LOINC + 3 SNOMED CT → internal codes); `FhirUnitConverter` (°F→°C); `ExternalResourceIdentifier` table + `ExternalIdentifierService` for hospital MRN/visit number ↔ internal UUID linking; `FhirApiKeyMiddleware` (`X-Api-Key` auth); `FhirExceptionFilter` (→ OperationOutcome); `PatientFhirMapper`, `EncounterFhirMapper`, `ObservationFhirMapper`, `MedicationAdministrationFhirMapper`, `FhirReferenceResolver`; idempotent patient/encounter upserts (`RegisterOrUpdateByIdentifierAsync`, `OpenOrUpdateByIdentifierAsync`); configurable identifier systems, department codes, encounter class maps (`FhirOptions`); Prometheus `fhir_ingest_total`, `fhir_mapping_errors_total`; Mirth Connect integration guide; `FhirIngestTests`; `run-phase30-verification.sh` | Done |
| 31 | **RBAC + Clinical Audit Logging + Token Refresh** — JWT bearer authentication (`AuthService`, `AuthController`); four clinical roles (`Nurse`, `Physician`, `Admin`, `Integration`) with 18 granular permissions; `AuthorizePermission` attribute on all controller actions; `PermissionAuthorizationHandler` + `PermissionPolicyProvider` resolve `perm:*` policies; `CurrentUserService` extracts identity from JWT claims; `ClinicalUser` entity with BCrypt password hashing; `RefreshToken` entity with DB-backed opaque token storage, rotation on use, and server-side revocation; short-lived access tokens (15 min) paired with long-lived refresh tokens (7 days); `POST /auth/refresh` and `POST /auth/logout` endpoints; `ClinicalAuditLog` append-only table with before/after JSONB, user identity, IP, and correlation ID; `AuditService` writes log entries on clinical write actions (12 audit actions including `USER_LOGOUT` and `TOKEN_REFRESHED`); `AuditLogsController` admin-only query with filters; `FhirApiKeyOrJwtMiddleware` dual auth for FHIR routes (JWT or X-Api-Key with multi-key rotation); alert `acknowledgedBy` set from authenticated user, not request body; four seeded demo users; frontend `LoginView` + `auth` Pinia store with proactive token refresh, 401 auto-retry, session expiry redirect, and logout button in header/sidebar/mobile nav; Vue router auth guard; `RbacTests`; `run-phase31-verification.sh` | Done |
| 23 | **Degraded Operations Visibility** — `GatewayStaleDetectorService` background service auto-marks gateways OFFLINE when heartbeat exceeds configurable `StaleThresholdMinutes`; `OperationsController` exposes gateway fleet listing (`GET /operations/gateways` with status/site filters), gateway detail (`GET /operations/gateways/{id}`), and site summary (`GET /operations/sites/{siteId}/summary`); `DischargeSummaryService` with `GET /encounters/{id}/discharge-summary` (info) and `GET /encounters/{id}/discharge-summary/content` (MinIO PDF download); `UsersController` (`GET /users`, `POST /users`, `PATCH /users/{id}`) for admin user account management; frontend: `GatewayOperations.vue` operations dashboard, `DegradedModeBanner.vue` warning banner, `DischargeSummaryPanel.vue` on patient detail, `ThresholdManagementView.vue` with `ThresholdFormModal.vue`, `UserManagementView.vue` with `UserFormModal.vue`, `AuditLogView.vue`, `ReconciliationView.vue`; role-aware admin sidebar navigation; `roleAccess.js` composable; `useChartTheme.js`, `useFocusTrap.js`, `useApiMode.js` composables; `CollapsibleSection.vue`, `SeverityBadge.vue` UI components; `OperationsApiTests`; `run-phase23-verification.sh` | Done |
| 33 | **Alert Quality Analytics** — `AlertFeedback` entity with per-user-per-alert constraint; `POST /alerts/{id}/feedback` server-side feedback submission with `alerts:feedback` permission (Nurse, Physician, Admin); `AlertQualityMetric` entity stores per-alert-type quality snapshots (acknowledgement rate, false positive rate, useful rate, would-act rate, avg seconds to acknowledge/resolve); `AlertQualityAggregatorService` background service computes metrics periodically; `AlertQualityMetricsController` exposes `GET /alerts/quality-metrics` (time-range + alert type filter) and `GET /alerts/quality-metrics/summary`; `AlertFeedbackConfiguration` and `AlertQualityMetricConfiguration` EF Core configs; `SubmitAlertFeedbackRequestValidator`; Prometheus `alert_quality_useful_rate` and `alert_quality_false_positive_rate` gauges; Grafana `alert-quality-dashboard.json`; frontend `AlertQualityAnalytics.vue` with `AlertQualityChart.vue` and `alertQuality` Pinia store; `AlertQualityAnalyticsTests`; `run-phase33-verification.sh` | Done |
| 34 | **Explainable Alerts** — `AlertExplanation` value object (`ScoreContributor`, `TrendContext`, `MedicationContext`, `NarrativeSummary`); JSONB `ClinicalAlert.Explanation` column (immutable at creation); contributor builders for NEWS2, SOFA, GCS; `TrendContextBuilder`; `AlertExplanationBuilder` + `ClinicalAlertFactory`; NEWS2, SOFA, GCS, and `TrendDetector` wire explanation and include `explanation` in `alert.generated` outbox; `MedicationCorrelationHelper.TryGetContextAsync()` for structured medication context; `AlertResponse` DTO + `AlertResponseMapper`; GET/list/acknowledge/resolve return `AlertResponse`; ES indexer projects `NarrativeSummary`; data lake Parquet `explanation_json`; ward gateway `LocalClinicalAlert.ExplanationJson` + sync; dashboard `AlertReasoning.vue` + `alertExplanation.js`; simulator `ExpectedOutcomeValidator` with `narrativeContains`; `ExplainableAlertsTests`; `run-phase34-verification.sh` | Done |
| 35 | **MIMIC-IV Replay Scenario Generator** — offline CLI tool in `VigilCare.Simulator/Mimic/` that reads MIMIC-IV CSV files (100 patients, 140 ICU stays, 668K chart events, 107K lab events from `docs/MIMIC-IV/`) and generates standard VigilCare scenario JSONs; `MimicCsvReader` streaming CSV parser with header-index lookup and filter predicate (memory-efficient for large files); `MimicItemMap` maps 17 chart event items (vitals, GCS, FiO₂, PaO₂, labs) and 8 lab event items to VigilCare observation codes with GCS text-to-numeric fallback dictionary, Fahrenheit-to-Celsius conversion, and blood pressure priority (non-invasive preferred over arterial); `MimicCareUnitMap` maps care units to departments and generates tags; `MimicDataLoader` streams chartevents/labevents/prescriptions filtered by stay_id + item ID set; `MimicScenarioBuilder` deduplicates BP, enforces 10-observation-per-cluster limit with priority-based splitting, computes offsetMinutes, parses medication doses; `MimicListCommand` (`mimic-list`) displays Spectre.Console table of available stays; `MimicGenerateCommand` (`mimic-generate`) produces scenario JSON with `--max-hours`, `--no-medications`, `--no-labs`, `--validate` options; generated scenarios pass `ScenarioValidator` and replay through the standard `replay` command | Done |

**Ward dashboard:** backend APIs (`GET /encounters` ward list with extended summary fields including SOFA/GCS/attending/admitted-at, `GET /qsofa/current`, `GET /qsofa/history`, `GET /gcs/history`, `GET /sepsis-bundles` hospital-wide list, `GET /operations/gateways` fleet management, `GET /users` user management, `GET /alerts/quality-metrics` alert quality, `GET /alerts/{id}` with structured explanation, CORS) and frontend SPA — `EncountersListTests`, `QsofaCurrentTests`, `GapAnalysisFixTests`, `OperationsApiTests`, `AlertQualityAnalyticsTests`, `ExplainableAlertsTests`, `vigilcare-dashboard` Vitest suite (replay scrubbing, feedback store, FeedbackButtons, FeedbackSummary, alert components, AlertReasoning, charts, ward table, ward sort, ward filter, department format, sepsis format, alert acknowledge, critical alert detect, handoff report, vitals form, GCS entry/history, SOFA panel/history, qSOFA history, scores panel, alert labels, PatientBanner, EncounterTimeline, medication chart markers, AcknowledgeModal, CriticalAlertBanner, DepartmentOverviewView, SepsisBoardView, VitalsEntryForm, useAlertStore, useWardStore, roleAccess, ThresholdManagementView, DischargeSummaryPanel, GatewayOperations, alertQuality).

**Enhanced Dashboard (post-Phase 22):** Major dashboard feature expansion addressing clinical workflow gaps. **Department Overview** (`/departments`) — unit-level snapshot cards showing patient count, critical/alert/bundle totals per department with acuity distribution bars; click-through to ward filtered by department. **Sepsis Bundle Board** (`/sepsis`) — real-time bundle compliance tracking with countdown timers to 1-hour deadline, urgency-sorted (overdue → at-risk → on-track), live 1-second tick updates. **Critical Alert Notifications** — `CriticalAlertBanner` surfaces new critical alerts from polling cycle with audible 880Hz two-tone alert, browser title flash, and native `Notification` API integration; mute toggle persisted in settings. **Shift Handoff Report** — `HandoffReport.vue` generates SBAR-format (Situation, Background, Assessment, Recommendation) structured reports for all ward patients, enriched with latest vitals, open alerts, pending orders, and sepsis bundle status; ward summary with department stats; print/PDF export. **Vitals Entry Form** — `VitalsEntryForm.vue` on patient detail page enables manual observation recording (7 vital parameters with AVPU dropdown) with client-side plausibility validation matching server-side ranges. **Ward Table Enhancements** — multi-column sorting (room, patient, department, NEWS2, qSOFA, sepsis, alerts) with sortable column headers, debounced patient search (name/MRN), quick-filter toggles (critical, has alerts, active sepsis), clear-all filters. **Acknowledge Modal** — role-aware acknowledgment with clinician identity pre-populated from JWT, role-specific guidance text, and acknowledgment note preview. Backend additions: `GET /sepsis-bundles` paginated hospital-wide list with `SepsisBundleSummary` (patient demographics, elements, deadlines); `WardEncounterSummary` extended with `sofaScore`, `sofaDelta`, `gcsScore`, `gcsClassification`, `lastObservationAt`, `attendingPhysician`, `admittedAt`.

**Site & Gateway Registry (Phase 20):** Central API manages clinical sites and ward edge nodes (gateways). Gateways authenticate via API key for heartbeat and sync upload. Shared `VigilCare.ClinicalContracts` class library defines sync DTOs consumed by both central API and ward gateway projects. Prometheus fleet health gauges track offline gateways and buffer depth per site.

**Ward Gateway (Phase 21):** `VigilCare.WardGateway` is a separate ASP.NET deployable with its own PostgreSQL (`vigilcare_ward`), Redis, and RabbitMQ — a local-first clinical path for ward edge nodes. Docker Compose services use the `ward-gateway` profile — start with `docker compose --profile ward-gateway up -d`. Observations are ingested locally with threshold evaluation and critical alert creation, then buffered for upload to the central API when the network link is available. Background services replicate encounter/patient data and alert thresholds from central on startup, report heartbeat status, and batch-upload buffered sync items. Local RabbitMQ provides ward-level paging and escalation independent of central connectivity. Integration tests (`WardGatewayLocalPathTests`, `WardGatewayPartitionTests`) validate the local ingest path and network partition/recovery workflow with Testcontainers.

**Dashboard gap analysis (Phase 22):** Addresses P0–P1 clinical gaps identified in `docs/dashboard-gap-analysis.md`. SOFA, GCS, and qSOFA now have history charts matching the existing NEWS2 history pattern. Patient detail gains a demographic banner (age, blood type, allergies, emergency contact) and an encounter timeline merging status changes, observation summaries, and alerts into a single chronological view. Vital trend charts overlay medication administration markers so clinicians can correlate drug timing with vital changes. Backend additions: `GET /gcs/history` cursor-paginated endpoint, `qsofa_evaluations` table with `GET /qsofa/history` for evaluation persistence.

**Scoring pipeline (Phases 25–26):** GCS components → `gcs_scores` + `gcs.scored` → SOFA CNS organ system; SOFA lab/vital observations → `sofa_scores` with baseline tracking → delta sepsis alerts when organ dysfunction worsens.

**Sepsis-3 refactor (Phases 27–29):** SIRS removed; qSOFA repositioned as bedside screening (`QSOFA_SCREEN`); SOFA delta ≥ 2 triggers `SOFA_SEPSIS` → sepsis bundle. Frontend gains GCS entry form and SOFA score panel. Twelve simulator scenarios validate the full clinical pipeline end-to-end.

**FHIR R4 integration (Phase 30):** Inbound facade accepts FHIR R4 JSON from integration engines (Mirth Connect, Rhapsody). Supports per-resource endpoints and transaction Bundles for ADT admit workflows. LOINC/SNOMED code mapping, Fahrenheit conversion, and external identifier linking enable drop-in EHR integration without changing the internal clinical pipeline.

**RBAC + audit logging + token refresh (Phase 31):** JWT authentication with role-based permission gating on every endpoint. Four clinical roles with 18 granular permissions. Short-lived access tokens (15 min) paired with rotating opaque refresh tokens (7 days) stored in PostgreSQL — `POST /auth/refresh` rotates tokens, `POST /auth/logout` revokes server-side. Frontend auto-refreshes before expiry, retries on 401, and redirects to login on refresh failure; logout button in header, sidebar, and mobile nav. Append-only audit logging records who did what, when, and why — with before/after state snapshots for compliance and incident review, including `USER_LOGOUT` and `TOKEN_REFRESHED` actions.

**Degraded Operations Visibility (Phase 23):** Gateway fleet operations panel with stale gateway auto-detection (`GatewayStaleDetectorService`), discharge summary API with MinIO PDF retrieval, admin panels for user management, threshold management, audit log browsing, and reconciliation viewing. Frontend adds role-aware sidebar navigation, degraded-mode banner for offline gateways, and comprehensive admin CRUD views.

**Alert Quality Analytics (Phase 33):** Server-side clinician feedback persisted as `AlertFeedback` entities (one per user per alert, six feedback types). `AlertQualityAggregatorService` periodically computes per-alert-type quality metrics (acknowledgement rate, false positive rate, useful rate, would-act rate, response times). REST API exposes quality metric snapshots and aggregate summaries. Grafana dashboard visualizes alert quality trends. Frontend analytics view with quality charts.

**Explainable Alerts (Phase 34):** Composite alerts (NEWS2, SOFA, GCS, rapid deterioration) carry an immutable JSONB `explanation` snapshot at creation — score contributors with raw values and normal ranges, trend context (percent change, duration, direction), structured medication context, and a bedside `NarrativeSummary`. `AlertResponse` exposes explanation on GET/list/acknowledge/resolve. Downstream consumers (Elasticsearch indexer, data lake Parquet, ward gateway sync, Kafka `alert.generated`) propagate explanation without breaking legacy consumers. Dashboard `AlertReasoning.vue` renders structured reasoning. Simulator validates `narrativeContains` on key scenarios.

**MIMIC-IV Replay Scenario Generator (Phase 35):** Offline CLI tool that converts real de-identified ICU data from MIT's MIMIC-IV dataset into VigilCare scenario JSONs. `mimic-list` browses 140 ICU stays across 100 patients with demographics, care unit, LOS, and outcome. `mimic-generate` produces a scenario from a specific stay ID with options for duration capping, medication/lab exclusion, and inline validation. The streaming CSV parser handles 668K-row chartevents efficiently by filtering at the string level before allocating records. Item mappings cover 17 chart event items (vitals, GCS text-to-numeric, FiO₂, PaO₂, ICU labs) and 8 lab event items (creatinine, platelets, bilirubin, lactate, WBC, potassium, glucose, PaO₂). Blood pressure deduplication prefers non-invasive over arterial readings. The 10-observation-per-cluster limit is enforced by priority-based splitting (vitals first, labs spill to the next offset). Generated scenarios are structurally identical to hand-crafted ones and replay through the existing `replay` command, driving NEWS2, SOFA, GCS, qSOFA, trend detection, and alerting on real patient trajectories.

**Post-phase hardening (after Phase 31):**
- **FHIR R4 read/search** — `FhirReadController` adds `GET /fhir/R4/Patient/{id}`, `GET /fhir/R4/Patient` (search by `identifier`), `GET /fhir/R4/Encounter/{id}`, `GET /fhir/R4/Encounter` (search by `patient`/`status`); new `fhir:read` permission for Admin and Integration roles; CapabilityStatement updated to advertise `read` and `searchType` interactions for Patient and Encounter
- **Alert threshold deletion** — `DELETE /alert-thresholds/{id}` with `THRESHOLD_DELETED` audit action and Redis cache invalidation
- **FHIR API key rotation** — `Fhir:ApiKeys` array alongside existing `Fhir:ApiKey` for zero-downtime key rotation; constant-time comparison via `CryptographicOperations.FixedTimeEquals` prevents timing attacks
- **Authorization failure logging** — `PermissionAuthorizationHandler` logs denied requests with structured details (username, user ID, role, required permission, endpoint); Prometheus `authorization_failures_total` counter with `permission` and `role` labels
- **JWT signing key validation** — startup guard rejects keys shorter than 256 bits (HMAC-SHA256 minimum); prevents silent misconfiguration that would weaken token verification
- **Token refresh and revocation** — `RefreshToken` entity with DB-backed opaque token storage; `POST /auth/refresh` rotates access + refresh tokens (previous refresh token revoked on each use); `POST /auth/logout` revokes refresh token server-side; access token reduced from 8 hours to 15 minutes; refresh token valid for 7 days; frontend auto-refreshes 1 minute before expiry with 401 retry fallback; logout button in header, sidebar, and mobile nav with session redirect; `USER_LOGOUT` and `TOKEN_REFRESHED` audit actions
- **Concurrency hardening** — `SepsisBundleService.TryCreateBundleAsync` wraps order + bundle creation in a single database transaction so the unique constraint rollback also reverts orphaned orders; `PatientService.OpenEncounterAsync` enforced by new partial unique index `ix_encounters_patient_active_type` on `(patient_id, encounter_type) WHERE status = 'ACTIVE'` with constraint-violation catch returning 409 Conflict; `ConcurrencyTests` validates parallel patient registration, sepsis bundle creation, observation idempotency, and encounter open race conditions
- **New Prometheus metrics** — `fhir_read_total` (resource_type, interaction, outcome), `authorization_failures_total` (permission, role)
- **New audit actions** — `THRESHOLD_DELETED`, `AUTHORIZATION_DENIED`, `USER_LOGOUT`, `TOKEN_REFRESHED`

**Optional follow-up:** execute and document the Kafka replay demonstration for the data lake (reset `data-lake-writer` offsets, clear MinIO prefixes, restart API, confirm Parquet rebuild). See `docs/plans/phase-9-plan.md` § Replay demonstration.
