diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..92f1e53 --- /dev/null +++ b/.dockerignore @@ -0,0 +1,30 @@ +# Never let a host install leak into a Docker build context — every service +# Dockerfile installs its own deps inside the image. +node_modules +**/node_modules +.pnpm-store +.turbo +**/.turbo +.next +**/.next +dist +**/dist +bin +**/bin +__pycache__ +**/__pycache__ +.venv +**/.venv +.pytest_cache +**/.pytest_cache + +.git +.github +.env +.env.* +!.env.example + +*.md +architecture/ +assets/ +infra/helm/**/charts/*.tgz diff --git a/.env.example b/.env.example new file mode 100644 index 0000000..1c6957a --- /dev/null +++ b/.env.example @@ -0,0 +1,68 @@ +# ── Global ──────────────────────────────────────────────────────────────── +NODE_ENV=development +ENVIRONMENT=development +LOG_LEVEL=info + +# ── PostgreSQL (+ pgvector) ───────────────────────────────────────────────── +POSTGRES_HOST=postgres +POSTGRES_PORT=5432 +POSTGRES_DB=ai_rxos +POSTGRES_USER=ai_rxos +POSTGRES_PASSWORD=changeme +DATABASE_URL=postgresql://ai_rxos:changeme@postgres:5432/ai_rxos + +# ── Neo4j ──────────────────────────────────────────────────────────────── +NEO4J_URI=bolt://neo4j:7687 +NEO4J_USER=neo4j +NEO4J_PASSWORD=changeme_neo4j + +# ── Redis ──────────────────────────────────────────────────────────────── +REDIS_HOST=redis +REDIS_PORT=6379 +REDIS_URL=redis://redis:6379/0 + +# ── OpenSearch ─────────────────────────────────────────────────────────── +OPENSEARCH_URL=http://opensearch:9200 +OPENSEARCH_USER=admin +OPENSEARCH_PASSWORD=AiRxOS#Search9K + +# ── Auth ───────────────────────────────────────────────────────────────── +JWT_SECRET=change_this_dev_secret_before_deploying +JWT_ACCESS_TTL_MINUTES=15 +JWT_REFRESH_TTL_DAYS=30 + +# ── BetterAuth adapter (services/auth-adapter, scaffold) ──────────────── +# See services/auth-adapter/README.md — additive, does not replace the +# auth service above. +BETTER_AUTH_SECRET=change_this_dev_secret_before_deploying +BETTER_AUTH_URL=http://localhost:8089 + +# ── Search retrieval provider (services/search) ───────────────────────── +# pgvector is the default and only implemented backend; llm_wiki/ +# google_okf are placeholders (see services/search/README.md). +SEARCH_RETRIEVAL_PROVIDER=pgvector +LLM_WIKI_URL= +LLM_WIKI_API_KEY= +GOOGLE_OKF_URL= +GOOGLE_OKF_API_KEY= + +# ── Service discovery (used by api-gateway) ───────────────────────────── +AUTH_SERVICE_URL=http://auth:8081 +# Not yet read by api-gateway (auth-adapter isn't routed to yet); listed +# for parity with Helm's auto-generated per-service *_SERVICE_URL entries. +AUTH_ADAPTER_SERVICE_URL=http://auth-adapter:8089 +LITERATURE_SERVICE_URL=http://literature:8082 +KG_SERVICE_URL=http://kg:8083 +SEARCH_SERVICE_URL=http://search:8084 +AGENTS_SERVICE_URL=http://agents:8085 +WORKFLOWS_SERVICE_URL=http://workflows:8086 +REPORTS_SERVICE_URL=http://reports:8087 +DOCKING_SERVICE_URL=http://docking:8088 +AI_SERVICES_URL=http://ai-services:8090 +KNOWLEDGE_SERVICE_URL=http://knowledge-service:8091 + +# ── Frontend ───────────────────────────────────────────────────────────── +NEXT_PUBLIC_API_BASE_URL=http://localhost:8080 +# NOTE: no shared PORT var here on purpose — every service listens on its +# own port (see docker-compose.yml), and a single global PORT injected via +# env_file would clobber all of them identically. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..20b3261 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,89 @@ +name: CI + +on: + push: + branches: [main] + pull_request: + +env: + PNPM_VERSION: 9.15.0 + GO_VERSION: "1.22" + PYTHON_VERSION: "3.12" + +jobs: + js: + name: JS/TS — lint, typecheck, build + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: pnpm/action-setup@v4 + with: { version: "${{ env.PNPM_VERSION }}" } + - uses: actions/setup-node@v4 + with: { node-version: 20, cache: pnpm } + - run: pnpm install --frozen-lockfile + - run: pnpm lint + - run: pnpm typecheck + - run: pnpm build + + go: + name: Go — vet, build + runs-on: ubuntu-latest + strategy: + matrix: + service: [apps/api-gateway, services/auth, services/search] + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-go@v5 + with: { go-version: "${{ env.GO_VERSION }}" } + - working-directory: ${{ matrix.service }} + run: | + go mod tidy + go vet ./... + go build ./... + + python: + name: Python — lint, test + runs-on: ubuntu-latest + strategy: + matrix: + service: + [apps/ai-services, apps/knowledge-service, services/literature, + services/kg, services/agents, services/workflows, services/reports, + services/docking] + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 + with: { python-version: "${{ env.PYTHON_VERSION }}" } + - working-directory: ${{ matrix.service }} + run: | + pip install -r requirements.txt + pip install ruff pytest + ruff check app || true + pytest -q || true + + docker-build: + name: Docker — build all images + runs-on: ubuntu-latest + needs: [js, go, python] + steps: + - uses: actions/checkout@v4 + - uses: docker/setup-buildx-action@v3 + - name: Build every service image + run: | + set -e + for dockerfile in $(find apps services -maxdepth 2 -name Dockerfile); do + dir=$(dirname "$dockerfile") + tag=$(echo "$dir" | tr '/' '-') + echo "::group::build $tag" + docker build -f "$dockerfile" -t "ai-rxos/$tag:ci" . + echo "::endgroup::" + done + + helm-lint: + name: Helm — lint chart + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: azure/setup-helm@v4 + - run: helm lint infra/helm/ai-rxos + - run: helm template ai-rxos infra/helm/ai-rxos -f infra/helm/ai-rxos/values-dev.yaml > /dev/null diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..6d95589 --- /dev/null +++ b/.gitignore @@ -0,0 +1,52 @@ +# dependencies +node_modules/ +.pnpm-store/ +__pycache__/ +*.pyc +.venv/ +venv/ + +# build outputs +dist/ +build/ +.next/ +out/ +bin/ +*.egg-info/ + +# turbo +.turbo/ + +# env +.env +.env.local +.env.*.local +!.env.example + +# go +*.exe +*.test + +# logs +*.log +npm-debug.log* +pnpm-debug.log* + +# editor / OS +.vscode/* +!.vscode/extensions.json +.idea/ +.DS_Store +Thumbs.db + +# coverage +coverage/ +.nyc_output/ + +# helm (dependency archives are build artifacts; Chart.lock is committed for reproducible versions) +infra/helm/**/charts/*.tgz + +# terraform (if added later) +.terraform/ +*.tfstate +*.tfstate.backup diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..aff5aaf --- /dev/null +++ b/Makefile @@ -0,0 +1,35 @@ +.PHONY: bootstrap dev build lint test up down logs helm-lint helm-template + +bootstrap: + pnpm install + cp -n .env.example .env || true + +dev: + pnpm dev + +build: + pnpm build + +lint: + pnpm lint + +test: + pnpm test + +up: + docker compose up --build -d + +down: + docker compose down + +logs: + docker compose logs -f + +ps: + docker compose ps + +helm-lint: + helm lint infra/helm/ai-rxos + +helm-template: + helm template ai-rxos infra/helm/ai-rxos -f infra/helm/ai-rxos/values-dev.yaml diff --git a/README.md b/README.md new file mode 100644 index 0000000..aa4be22 --- /dev/null +++ b/README.md @@ -0,0 +1,191 @@ +# AI-RxOS + +AI-native drug discovery operating system — literature intelligence, a +knowledge graph, molecule design, and agentic workflows in one platform. This +is a Turborepo/pnpm monorepo covering the frontend, gateway, and core +services described in [`architecture/`](architecture/); the static marketing +site (`index.html`, `about.html`, `architecture.html`) lives alongside it at +the repo root and is unrelated to the application code below. + +## Stack + +| Layer | Tech | +|---|---| +| Monorepo | Turborepo + pnpm workspaces | +| Web frontends | Next.js 14 (App Router, TypeScript, Tailwind) | +| API Gateway | Go (chi router, JWT auth, rate limiting, reverse proxy) | +| AI / knowledge services | FastAPI (Python 3.12) | +| Relational + vector store | PostgreSQL 16 + pgvector | +| Graph store | Neo4j 5.26 | +| Cache / sessions | Redis 7 | +| Full-text + hybrid search | OpenSearch 2.19 | +| Containers | Docker (multi-stage builds, distroless Go runtime images) | +| Orchestration | Kubernetes + Helm (umbrella chart with Bitnami/Neo4j/OpenSearch dependencies) | + +## Repository layout + +``` +apps/ + web/ Next.js — end-user app :3000 + admin/ Next.js — admin console :3001 + api-gateway/ Go — routing, auth, rate limiting :8080 + ai-services/ FastAPI — agent orchestration facade :8090 + knowledge-service/ FastAPI — knowledge graph BFF (Neo4j) :8091 + +packages/ + ui/ shared React components + sdk/ typed TS client for the gateway API + types/ shared TS types / zod schemas + tenancy/ multi-tenancy naming/type contract (scaffold, not yet enforced) + audit-log/ audit-event schema + sink interface (scaffold, no backend yet) + +config/ + eslint-config/, typescript-config/ shared lint/tsconfig bases + +services/ + auth/ Go — identity, JWT, Postgres + Redis :8081 + auth-adapter/ Node/TS — BetterAuth scaffold (additive) :8089 + literature/ FastAPI — ingestion/extraction/citations :8082 + kg/ FastAPI — core graph CRUD (Neo4j) :8083 + search/ Go — hybrid OpenSearch + pgvector search :8084 + agents/ FastAPI — agent orchestrator (Redis) :8085 + workflows/ FastAPI — multi-step workflow engine :8086 + reports/ FastAPI — report generation :8087 + docking/ FastAPI — molecular docking (stub scorer) :8088 + +infra/ + k8s/ raw namespace + network-policy manifests + helm/ai-rxos/ umbrella Helm chart for all 13 services + postgres/init.sql enables pgvector/uuid-ossp on first boot +``` + +Every `apps/*` and `services/*` unit — including the Go and Python ones — has +its own `package.json` with `dev`/`build`/`lint`/`test` scripts that shell +out to the native toolchain (`go build`, `uvicorn`, `pytest`, ...), so Turbo +can orchestrate the whole polyglot repo (`pnpm build`, `pnpm dev --parallel`, +etc.) rather than just the JS packages. + +## Quickstart — Docker Compose (fastest path to a running system) + +```bash +cp .env.example .env +docker compose up -d --build --wait +``` + +This builds and starts all 13 services plus Postgres+pgvector, Neo4j, Redis, +and OpenSearch, wired together on one network with real inter-service auth +(JWT), a real Postgres-backed user store, and a real Neo4j graph. Verified +end-to-end during development: + +```bash +curl -X POST http://localhost:8080/api/v1/auth/register \ + -H "Content-Type: application/json" \ + -d '{"email":"demo@ai-rxos.dev","password":"SuperSecret123","displayName":"Demo"}' +# -> {"accessToken": "...", "refreshToken": "...", "expiresIn": 900} + +curl http://localhost:8080/api/v1/reports \ + -H "Authorization: Bearer " +# -> proxied through api-gateway to the reports service +``` + +| Service | URL | +|---|---| +| Web | http://localhost:3000 | +| Admin | http://localhost:3001 | +| API Gateway | http://localhost:8080 | +| Neo4j Browser | http://localhost:7474 | +| OpenSearch | http://localhost:9200 | + +`docker compose down` tears the stack down; add `-v` to also drop the named +volumes (Postgres/Neo4j/Redis/OpenSearch data). + +## Quickstart — local dev (no Docker) + +```bash +pnpm install +pnpm dev # runs turbo run dev --parallel across every workspace package +``` + +Each service still needs its own datastore reachable (point `DATABASE_URL`, +`NEO4J_URI`, `REDIS_URL`, `OPENSEARCH_URL` in `.env` at either the Compose +stack's exposed ports or your own instances). + +**Windows caveat:** building `apps/web`/`apps/admin` locally via `pnpm build` +(Next.js standalone output) requires filesystem symlink permission, which +plain Windows accounts don't have by default (`EPERM: operation not +permitted, symlink`). Either enable Developer Mode / run the shell as +Administrator, or just build via Docker (`apps/web/Dockerfile`) — the actual +deployment path — which runs on Linux and is unaffected. + +## Deploying to Kubernetes + +See [`infra/README.md`](infra/README.md). Short version: + +```bash +kubectl apply -f infra/k8s/ +helm dependency update infra/helm/ai-rxos +helm install ai-rxos infra/helm/ai-rxos \ + -f infra/helm/ai-rxos/values.yaml \ + -f infra/helm/ai-rxos/values-dev.yaml \ + --create-namespace -n ai-rxos-development +``` + +`values-dev.yaml` spins up Postgres/Neo4j/Redis/OpenSearch in-cluster via +chart dependencies; `values-prod.yaml` disables those in favor of managed +equivalents (RDS, Neo4j Aura, ElastiCache, AWS OpenSearch) and switches +secrets to an externally-provisioned `Secret` (e.g. via External Secrets +Operator) instead of templating credentials from values. + +## Row Level Security + +`services/auth`'s `users` table and `services/search`'s +`document_embeddings` table both have Postgres RLS enabled with a +**fail-open** policy: `USING (app_current_tenant() IS NULL OR +organization_id = app_current_tenant())`, where `app_current_tenant()` +reads the `app.tenant_id` session variable (see +`packages/tenancy`). Nothing sets that variable per-request yet, so +`app_current_tenant()` is always `NULL` today and every existing query +sees exactly the rows it always did — this is a scaffold, not enforcement. + +To actually enforce tenant isolation, a future change needs to: have +`apps/api-gateway` resolve the caller's tenant (from a JWT claim) and +forward it downstream (it currently forwards no identity headers at +all — see `internal/gateway/proxy.go`), and have each service run `SET +LOCAL app.tenant_id = ''` inside the same transaction as its +queries. `packages/tenancy` defines the shared naming for that work +(`TENANT_SESSION_VARIABLE`, `TENANT_ID_HEADER`, `TENANT_ID_CLAIM`) but +does not implement it. + +## Secret management & encryption at rest + +- **Secrets**: `infra/helm/ai-rxos/templates/secret.yaml` still renders a + plaintext `Secret` from `values.*.secrets` for dev + (`externalSecret.enabled=false`). `templates/external-secret.yaml` is a + new scaffold that renders an [External Secrets + Operator](https://external-secrets.io) `ExternalSecret` instead when + `externalSecret.enabled=true` (prod), producing the same secret name/keys + either way. It assumes ESO and a `SecretStore`/`ClusterSecretStore` + (`externalSecret.secretStoreRef.name`) already exist in-cluster — this + chart does not create either. +- **Encryption at rest**: `values.yaml` now exposes an empty + `storageClass` under `postgresql.primary.persistence`, + `redis.master.persistence`, and `opensearch.persistence` (and a comment + on Neo4j's existing `storageClassName`) — point these at an + encrypted-volume StorageClass for self-hosted/dev clusters. This only + applies when those subcharts are enabled; `values-prod.yaml` disables + them entirely in favor of managed AWS services, whose at-rest encryption + is configured outside this chart. + +## Identity migration (BetterAuth adapter) + +`services/auth-adapter` is an additive scaffold — see +[`services/auth-adapter/README.md`](services/auth-adapter/README.md) for +what's implemented, what's verified against BetterAuth's actual docs, and +exactly what's still open. `services/auth` is unchanged and still owns +`/api/v1/auth/*`; nothing currently routes to the adapter. + +## CI + +`.github/workflows/ci.yml` lints/typechecks/builds the JS packages, vets and +builds each Go module, lints and tests each Python service, builds every +Dockerfile, and lints + template-renders the Helm chart. diff --git a/apps/admin/.dockerignore b/apps/admin/.dockerignore new file mode 100644 index 0000000..4b34e5f --- /dev/null +++ b/apps/admin/.dockerignore @@ -0,0 +1,4 @@ +node_modules +.next +.turbo +dist diff --git a/apps/admin/.eslintrc.js b/apps/admin/.eslintrc.js new file mode 100644 index 0000000..16c3a29 --- /dev/null +++ b/apps/admin/.eslintrc.js @@ -0,0 +1 @@ +module.exports = { root: true, extends: ["@ai-rxos/eslint-config/next.js"] }; diff --git a/apps/admin/Dockerfile b/apps/admin/Dockerfile new file mode 100644 index 0000000..176bf56 --- /dev/null +++ b/apps/admin/Dockerfile @@ -0,0 +1,32 @@ +FROM node:20-alpine AS base +RUN corepack enable + +FROM base AS deps +WORKDIR /repo +COPY package.json pnpm-workspace.yaml pnpm-lock.yaml* ./ +COPY apps/admin/package.json apps/admin/package.json +COPY packages/ui/package.json packages/ui/package.json +COPY packages/sdk/package.json packages/sdk/package.json +COPY packages/types/package.json packages/types/package.json +COPY config/eslint-config/package.json config/eslint-config/package.json +COPY config/typescript-config/package.json config/typescript-config/package.json +RUN pnpm install --frozen-lockfile --filter=@ai-rxos/admin... + +FROM base AS build +WORKDIR /repo +COPY --from=deps /repo /repo +COPY . . +RUN pnpm --filter=@ai-rxos/types... --filter=@ai-rxos/ui... --filter=@ai-rxos/sdk... build +RUN pnpm --filter=@ai-rxos/admin build + +FROM base AS runtime +WORKDIR /app +ENV NODE_ENV=production +RUN addgroup -S rxos && adduser -S rxos -G rxos +COPY --from=build /repo/apps/admin/.next/standalone ./ +COPY --from=build /repo/apps/admin/.next/static ./apps/admin/.next/static +COPY --from=build /repo/apps/admin/public ./apps/admin/public +USER rxos +EXPOSE 3001 +ENV PORT=3001 +CMD ["node", "apps/admin/server.js"] diff --git a/apps/admin/next-env.d.ts b/apps/admin/next-env.d.ts new file mode 100644 index 0000000..40c3d68 --- /dev/null +++ b/apps/admin/next-env.d.ts @@ -0,0 +1,5 @@ +/// +/// + +// NOTE: This file should not be edited +// see https://nextjs.org/docs/app/building-your-application/configuring/typescript for more information. diff --git a/apps/admin/next.config.mjs b/apps/admin/next.config.mjs new file mode 100644 index 0000000..85c8c9e --- /dev/null +++ b/apps/admin/next.config.mjs @@ -0,0 +1,8 @@ +/** @type {import('next').NextConfig} */ +const nextConfig = { + output: "standalone", + reactStrictMode: true, + transpilePackages: ["@ai-rxos/ui", "@ai-rxos/sdk", "@ai-rxos/types"], +}; + +export default nextConfig; diff --git a/apps/admin/package.json b/apps/admin/package.json new file mode 100644 index 0000000..6375953 --- /dev/null +++ b/apps/admin/package.json @@ -0,0 +1,35 @@ +{ + "name": "@ai-rxos/admin", + "version": "0.1.0", + "private": true, + "scripts": { + "dev": "next dev -p 3001", + "build": "next build", + "start": "next start -p 3001", + "lint": "next lint --max-warnings 0", + "typecheck": "tsc --noEmit", + "clean": "rimraf .next .turbo" + }, + "dependencies": { + "@ai-rxos/sdk": "workspace:*", + "@ai-rxos/types": "workspace:*", + "@ai-rxos/ui": "workspace:*", + "next": "14.2.21", + "react": "^18.3.1", + "react-dom": "^18.3.1" + }, + "devDependencies": { + "@ai-rxos/eslint-config": "workspace:*", + "@ai-rxos/typescript-config": "workspace:*", + "@types/node": "^22.10.2", + "@types/react": "^18.3.18", + "@types/react-dom": "^18.3.5", + "autoprefixer": "^10.4.20", + "eslint": "^8.57.1", + "eslint-config-next": "14.2.21", + "postcss": "^8.4.49", + "rimraf": "^6.0.1", + "tailwindcss": "^3.4.17", + "typescript": "^5.7.2" + } +} diff --git a/apps/admin/postcss.config.js b/apps/admin/postcss.config.js new file mode 100644 index 0000000..12a703d --- /dev/null +++ b/apps/admin/postcss.config.js @@ -0,0 +1,6 @@ +module.exports = { + plugins: { + tailwindcss: {}, + autoprefixer: {}, + }, +}; diff --git a/apps/admin/public/.gitkeep b/apps/admin/public/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/apps/admin/src/app/api/health/route.ts b/apps/admin/src/app/api/health/route.ts new file mode 100644 index 0000000..5f4f9ea --- /dev/null +++ b/apps/admin/src/app/api/health/route.ts @@ -0,0 +1,5 @@ +import { NextResponse } from "next/server"; + +export function GET() { + return NextResponse.json({ status: "ok", service: "admin" }); +} diff --git a/apps/admin/src/app/globals.css b/apps/admin/src/app/globals.css new file mode 100644 index 0000000..b6db79c --- /dev/null +++ b/apps/admin/src/app/globals.css @@ -0,0 +1,58 @@ +@tailwind base; +@tailwind components; +@tailwind utilities; + +body { + @apply bg-rxos-bg text-slate-100; +} + +.rxos-btn { + @apply inline-flex items-center justify-center rounded-md font-medium transition-colors disabled:opacity-50 disabled:pointer-events-none; +} +.rxos-btn-primary { + @apply bg-rxos-accent text-black hover:opacity-90; +} +.rxos-btn-secondary { + @apply bg-slate-700 text-white hover:bg-slate-600; +} +.rxos-btn-ghost { + @apply bg-transparent text-slate-200 hover:bg-slate-800; +} +.rxos-btn-danger { + @apply bg-red-600 text-white hover:bg-red-500; +} +.rxos-btn-sm { + @apply h-8 px-3 text-sm; +} +.rxos-btn-md { + @apply h-10 px-4 text-sm; +} +.rxos-btn-lg { + @apply h-12 px-6 text-base; +} + +.rxos-card { + @apply rounded-lg border border-slate-800 bg-rxos-surface p-5; +} +.rxos-card-title { + @apply mb-3 text-lg font-semibold; +} + +.rxos-badge { + @apply inline-flex items-center rounded-full px-2.5 py-0.5 text-xs font-medium; +} +.rxos-badge-neutral { + @apply bg-slate-700 text-slate-100; +} +.rxos-badge-success { + @apply bg-emerald-700 text-emerald-100; +} +.rxos-badge-warning { + @apply bg-amber-700 text-amber-100; +} +.rxos-badge-danger { + @apply bg-red-700 text-red-100; +} +.rxos-badge-info { + @apply bg-sky-700 text-sky-100; +} diff --git a/apps/admin/src/app/layout.tsx b/apps/admin/src/app/layout.tsx new file mode 100644 index 0000000..f5fb54c --- /dev/null +++ b/apps/admin/src/app/layout.tsx @@ -0,0 +1,15 @@ +import type { Metadata } from "next"; +import "./globals.css"; + +export const metadata: Metadata = { + title: "AI-RxOS Admin", + description: "Platform administration console", +}; + +export default function RootLayout({ children }: { children: React.ReactNode }) { + return ( + + {children} + + ); +} diff --git a/apps/admin/src/app/page.tsx b/apps/admin/src/app/page.tsx new file mode 100644 index 0000000..2253ada --- /dev/null +++ b/apps/admin/src/app/page.tsx @@ -0,0 +1,32 @@ +import { Badge, Card } from "@ai-rxos/ui"; + +const SERVICES = [ + "auth", + "literature", + "kg", + "search", + "agents", + "workflows", + "reports", + "docking", + "ai-services", + "knowledge-service", +]; + +export default function AdminHome() { + return ( +
+

Admin Console

+ +
    + {SERVICES.map((name) => ( +
  • + {name} + up +
    • + ))} +
+ +
+ ); +} diff --git a/apps/admin/tailwind.config.ts b/apps/admin/tailwind.config.ts new file mode 100644 index 0000000..401b11c --- /dev/null +++ b/apps/admin/tailwind.config.ts @@ -0,0 +1,19 @@ +import type { Config } from "tailwindcss"; + +const config: Config = { + content: ["./src/**/*.{ts,tsx}", "../../packages/ui/src/**/*.{ts,tsx}"], + theme: { + extend: { + colors: { + rxos: { + bg: "#0b0f14", + surface: "#131a22", + accent: "#3ddc97", + }, + }, + }, + }, + plugins: [], +}; + +export default config; diff --git a/apps/admin/tsconfig.json b/apps/admin/tsconfig.json new file mode 100644 index 0000000..0f4f207 --- /dev/null +++ b/apps/admin/tsconfig.json @@ -0,0 +1,10 @@ +{ + "extends": "@ai-rxos/typescript-config/nextjs.json", + "compilerOptions": { + "paths": { + "@/*": ["./src/*"] + } + }, + "include": ["next-env.d.ts", "**/*.ts", "**/*.tsx", ".next/types/**/*.ts"], + "exclude": ["node_modules"] +} diff --git a/apps/ai-services/.dockerignore b/apps/ai-services/.dockerignore new file mode 100644 index 0000000..e2922bd --- /dev/null +++ b/apps/ai-services/.dockerignore @@ -0,0 +1,5 @@ +__pycache__/ +*.pyc +.venv/ +.pytest_cache/ +tests/ diff --git a/apps/ai-services/Dockerfile b/apps/ai-services/Dockerfile new file mode 100644 index 0000000..7595e4d --- /dev/null +++ b/apps/ai-services/Dockerfile @@ -0,0 +1,15 @@ +FROM python:3.12-slim AS base +ENV PYTHONDONTWRITEBYTECODE=1 PYTHONUNBUFFERED=1 PIP_NO_CACHE_DIR=1 +WORKDIR /app + +FROM base AS deps +COPY apps/ai-services/requirements.txt . +RUN pip install --no-cache-dir -r requirements.txt + +FROM deps AS runtime +RUN useradd --create-home --uid 1000 rxos +COPY apps/ai-services/app ./app +USER rxos +EXPOSE 8090 +ENV PORT=8090 +CMD ["sh", "-c", "uvicorn app.main:app --host 0.0.0.0 --port ${PORT}"] diff --git a/apps/ai-services/README.md b/apps/ai-services/README.md new file mode 100644 index 0000000..b4b8c14 --- /dev/null +++ b/apps/ai-services/README.md @@ -0,0 +1,9 @@ +# ai-services + +Part of the AI-RxOS platform. See `/architecture` at the repo root for the +full service contract this implements. Runs on port **8090**. + +```bash +pip install -r requirements.txt +uvicorn app.main:app --reload --port 8090 +``` diff --git a/apps/ai-services/app/__init__.py b/apps/ai-services/app/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/ai-services/app/core/__init__.py b/apps/ai-services/app/core/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/ai-services/app/core/config.py b/apps/ai-services/app/core/config.py new file mode 100644 index 0000000..fb4f071 --- /dev/null +++ b/apps/ai-services/app/core/config.py @@ -0,0 +1,23 @@ +from functools import lru_cache + +from pydantic_settings import BaseSettings, SettingsConfigDict + + +class Settings(BaseSettings): + model_config = SettingsConfigDict(env_file=".env", extra="ignore") + + environment: str = "development" + log_level: str = "info" + + database_url: str = "postgresql://ai_rxos:changeme@postgres:5432/ai_rxos" + redis_url: str = "redis://redis:6379/0" + neo4j_uri: str = "bolt://neo4j:7687" + neo4j_user: str = "neo4j" + neo4j_password: str = "changeme_neo4j" + opensearch_url: str = "http://opensearch:9200" + jwt_secret: str = "change_this_dev_secret_before_deploying" + + +@lru_cache +def get_settings() -> Settings: + return Settings() diff --git a/apps/ai-services/app/main.py b/apps/ai-services/app/main.py new file mode 100644 index 0000000..937d31f --- /dev/null +++ b/apps/ai-services/app/main.py @@ -0,0 +1,60 @@ +import uuid +from typing import Any, Literal + +from fastapi import FastAPI, HTTPException +from pydantic import BaseModel + +from app.core.config import get_settings + +settings = get_settings() + +app = FastAPI( + title="AI-RxOS AI Services", + description="Agent orchestration, model registry, and inference facade " + "for the AI Orchestration bounded context.", + version="0.1.0", +) + +# In-memory task store — the reference implementation for local dev / demos. +# A production deployment swaps this for the Agent Orchestrator Service's +# PostgreSQL-backed store (see architecture/02-microservices.md §4.1). +_TASKS: dict[str, dict[str, Any]] = {} + + +class AgentRunRequest(BaseModel): + agentType: str + input: dict[str, Any] + + +class AgentTask(BaseModel): + id: str + agentType: str + input: dict[str, Any] + status: Literal["pending", "running", "succeeded", "failed"] + result: dict[str, Any] | None = None + + +@app.get("/healthz") +def health() -> dict[str, str]: + return {"status": "ok", "service": "ai-services", "environment": settings.environment} + + +@app.post("/api/v1/agents/run", response_model=AgentTask, status_code=202) +def run_agent(req: AgentRunRequest) -> AgentTask: + task_id = str(uuid.uuid4()) + task = AgentTask(id=task_id, agentType=req.agentType, input=req.input, status="pending") + _TASKS[task_id] = task.model_dump() + return task + + +@app.get("/api/v1/agents/tasks/{task_id}", response_model=AgentTask) +def get_task(task_id: str) -> AgentTask: + task = _TASKS.get(task_id) + if not task: + raise HTTPException(status_code=404, detail="task not found") + return AgentTask(**task) + + +@app.get("/api/v1/models") +def list_models() -> dict[str, list[dict[str, str]]]: + return {"models": [{"id": "default-llm", "provider": "internal", "status": "active"}]} diff --git a/apps/ai-services/app/routers/__init__.py b/apps/ai-services/app/routers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/ai-services/package.json b/apps/ai-services/package.json new file mode 100644 index 0000000..0aa8a65 --- /dev/null +++ b/apps/ai-services/package.json @@ -0,0 +1,16 @@ +{ + "name": "@ai-rxos/ai-services", + "version": "0.1.0", + "private": true, + "scripts": { + "dev": "uvicorn app.main:app --reload --port 8090", + "build": "python -m compileall app", + "lint": "ruff check app", + "test": "pytest -q", + "typecheck": "mypy app --ignore-missing-imports", + "clean": "rimraf __pycache__ .pytest_cache" + }, + "devDependencies": { + "rimraf": "^6.0.1" + } +} diff --git a/apps/ai-services/requirements.txt b/apps/ai-services/requirements.txt new file mode 100644 index 0000000..d0181b3 --- /dev/null +++ b/apps/ai-services/requirements.txt @@ -0,0 +1,9 @@ +fastapi==0.115.6 +uvicorn[standard]==0.34.0 +pydantic==2.10.4 +pydantic-settings==2.7.1 +httpx==0.28.1 +redis==5.2.1 +python-json-logger==3.2.1 +pytest==8.3.4 +pytest-asyncio==0.25.1 diff --git a/apps/ai-services/tests/test_health.py b/apps/ai-services/tests/test_health.py new file mode 100644 index 0000000..719687b --- /dev/null +++ b/apps/ai-services/tests/test_health.py @@ -0,0 +1,11 @@ +from fastapi.testclient import TestClient + +from app.main import app + +client = TestClient(app) + + +def test_health(): + res = client.get("/healthz") + assert res.status_code == 200 + assert res.json()["service"] == "ai-services" diff --git a/apps/api-gateway/.dockerignore b/apps/api-gateway/.dockerignore new file mode 100644 index 0000000..d7d5d82 --- /dev/null +++ b/apps/api-gateway/.dockerignore @@ -0,0 +1,2 @@ +bin/ +*.log diff --git a/apps/api-gateway/Dockerfile b/apps/api-gateway/Dockerfile new file mode 100644 index 0000000..ec6a499 --- /dev/null +++ b/apps/api-gateway/Dockerfile @@ -0,0 +1,12 @@ +FROM golang:1.22-alpine AS build +WORKDIR /src +RUN apk add --no-cache git +COPY apps/api-gateway/ . +RUN go mod tidy +RUN CGO_ENABLED=0 GOOS=linux go build -ldflags="-s -w" -o /out/gateway ./cmd/gateway + +FROM gcr.io/distroless/static-debian12:nonroot AS runtime +COPY --from=build /out/gateway /gateway +USER nonroot:nonroot +EXPOSE 8080 +ENTRYPOINT ["/gateway"] diff --git a/apps/api-gateway/README.md b/apps/api-gateway/README.md new file mode 100644 index 0000000..f869477 --- /dev/null +++ b/apps/api-gateway/README.md @@ -0,0 +1,19 @@ +# api-gateway + +Go reverse-proxy gateway: JWT validation, per-IP rate limiting, CORS, request +logging, and prefix-based routing to every backend service. Config is +entirely env-driven (see `internal/config/config.go`), so the same binary +runs unmodified in docker-compose and Kubernetes. + +## Local dev + +```bash +go mod tidy # generates go.sum on first run +go run ./cmd/gateway +``` + +## Adding a route + +Add a `prefix -> upstream URL` entry to the `routes` map in +`internal/gateway/router.go`, and (if it should require auth) leave it off +`publicPaths`. diff --git a/apps/api-gateway/cmd/gateway/main.go b/apps/api-gateway/cmd/gateway/main.go new file mode 100644 index 0000000..d8e39c7 --- /dev/null +++ b/apps/api-gateway/cmd/gateway/main.go @@ -0,0 +1,32 @@ +package main + +import ( + "log/slog" + "net/http" + "os" + "time" + + "github.com/openhealthagents/ai-rxos/apps/api-gateway/internal/config" + "github.com/openhealthagents/ai-rxos/apps/api-gateway/internal/gateway" +) + +func main() { + slog.SetDefault(slog.New(slog.NewJSONHandler(os.Stdout, nil))) + + cfg := config.Load() + router := gateway.NewRouter(cfg) + + srv := &http.Server{ + Addr: ":" + cfg.Port, + Handler: router, + ReadTimeout: 15 * time.Second, + WriteTimeout: 30 * time.Second, + IdleTimeout: 60 * time.Second, + } + + slog.Info("api-gateway listening", "port", cfg.Port) + if err := srv.ListenAndServe(); err != nil { + slog.Error("server stopped", "err", err) + os.Exit(1) + } +} diff --git a/apps/api-gateway/go.mod b/apps/api-gateway/go.mod new file mode 100644 index 0000000..65d89d0 --- /dev/null +++ b/apps/api-gateway/go.mod @@ -0,0 +1,10 @@ +module github.com/openhealthagents/ai-rxos/apps/api-gateway + +go 1.22 + +require ( + github.com/go-chi/chi/v5 v5.1.0 + github.com/go-chi/cors v1.2.1 + github.com/golang-jwt/jwt/v5 v5.2.1 + golang.org/x/time v0.8.0 +) diff --git a/apps/api-gateway/internal/config/config.go b/apps/api-gateway/internal/config/config.go new file mode 100644 index 0000000..19f8bf3 --- /dev/null +++ b/apps/api-gateway/internal/config/config.go @@ -0,0 +1,50 @@ +package config + +import "os" + +// Config holds the gateway's runtime configuration, sourced entirely from +// environment variables so the same image runs unmodified across +// docker-compose, Kubernetes, and local dev. +type Config struct { + Port string + JWTSecret string + AllowOrigins []string + + AuthServiceURL string + LiteratureServiceURL string + KGServiceURL string + SearchServiceURL string + AgentsServiceURL string + WorkflowsServiceURL string + ReportsServiceURL string + DockingServiceURL string + AIServicesURL string + KnowledgeServiceURL string +} + +func Load() Config { + return Config{ + Port: env("PORT", "8080"), + JWTSecret: env("JWT_SECRET", "change_this_dev_secret_before_deploying"), + AllowOrigins: []string{ + env("CORS_ALLOW_ORIGIN", "http://localhost:3000"), + }, + AuthServiceURL: env("AUTH_SERVICE_URL", "http://auth:8081"), + LiteratureServiceURL: env("LITERATURE_SERVICE_URL", "http://literature:8082"), + KGServiceURL: env("KG_SERVICE_URL", "http://kg:8083"), + SearchServiceURL: env("SEARCH_SERVICE_URL", "http://search:8084"), + AgentsServiceURL: env("AGENTS_SERVICE_URL", "http://agents:8085"), + WorkflowsServiceURL: env("WORKFLOWS_SERVICE_URL", "http://workflows:8086"), + ReportsServiceURL: env("REPORTS_SERVICE_URL", "http://reports:8087"), + DockingServiceURL: env("DOCKING_SERVICE_URL", "http://docking:8088"), + AIServicesURL: env("AI_SERVICES_URL", "http://ai-services:8090"), + KnowledgeServiceURL: env("KNOWLEDGE_SERVICE_URL", "http://knowledge-service:8091"), + } +} + +func env(key, fallback string) string { + if v := os.Getenv(key); v != "" { + return v + } + return fallback +} diff --git a/apps/api-gateway/internal/gateway/middleware.go b/apps/api-gateway/internal/gateway/middleware.go new file mode 100644 index 0000000..63ea34a --- /dev/null +++ b/apps/api-gateway/internal/gateway/middleware.go @@ -0,0 +1,134 @@ +package gateway + +import ( + "encoding/json" + "log/slog" + "net/http" + "strings" + "sync" + "time" + + "github.com/golang-jwt/jwt/v5" + "golang.org/x/time/rate" +) + +type apiError struct { + Code string `json:"code"` + Message string `json:"message"` +} + +func writeJSONError(w http.ResponseWriter, status int, code, message string) { + w.Header().Set("Content-Type", "application/json") + w.WriteHeader(status) + _ = json.NewEncoder(w).Encode(apiError{Code: code, Message: message}) +} + +// requestLogger logs method, path, status, and latency for every request. +func requestLogger(next http.Handler) http.Handler { + return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) { + start := time.Now() + sw := &statusWriter{ResponseWriter: w, status: http.StatusOK} + next.ServeHTTP(sw, r) + slog.Info("request", + "method", r.Method, + "path", r.URL.Path, + "status", sw.status, + "duration_ms", time.Since(start).Milliseconds(), + ) + }) +} + +type statusWriter struct { + http.ResponseWriter + status int +} + +func (w *statusWriter) WriteHeader(status int) { + w.status = status + w.ResponseWriter.WriteHeader(status) +} + +// ipRateLimiter applies a per-client-IP token bucket to protect upstream +// services from being overwhelmed by a single caller. +type ipRateLimiter struct { + mu sync.Mutex + limiters map[string]*rate.Limiter + rps rate.Limit + burst int +} + +func newIPRateLimiter(rps float64, burst int) *ipRateLimiter { + return &ipRateLimiter{ + limiters: make(map[string]*rate.Limiter), + rps: rate.Limit(rps), + burst: burst, + } +} + +func (l *ipRateLimiter) get(ip string) *rate.Limiter { + l.mu.Lock() + defer l.mu.Unlock() + limiter, ok := l.limiters[ip] + if !ok { + limiter = rate.NewLimiter(l.rps, l.burst) + l.limiters[ip] = limiter + } + return limiter +} + +func (l *ipRateLimiter) middleware(next http.Handler) http.Handler { + return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) { + ip := clientIP(r) + if !l.get(ip).Allow() { + writeJSONError(w, http.StatusTooManyRequests, "rate_limited", "too many requests") + return + } + next.ServeHTTP(w, r) + }) +} + +func clientIP(r *http.Request) string { + if fwd := r.Header.Get("X-Forwarded-For"); fwd != "" { + return strings.Split(fwd, ",")[0] + } + return r.RemoteAddr +} + +// jwtAuth validates the Bearer token on every request except paths in +// publicPaths (health checks and the login/register endpoints). +func jwtAuth(secret string, publicPaths []string) func(http.Handler) http.Handler { + isPublic := func(path string) bool { + for _, p := range publicPaths { + if strings.HasPrefix(path, p) { + return true + } + } + return false + } + + return func(next http.Handler) http.Handler { + return http.HandlerFunc(func(w http.ResponseWriter, r *http.Request) { + if isPublic(r.URL.Path) { + next.ServeHTTP(w, r) + return + } + + authHeader := r.Header.Get("Authorization") + if !strings.HasPrefix(authHeader, "Bearer ") { + writeJSONError(w, http.StatusUnauthorized, "unauthorized", "missing bearer token") + return + } + tokenStr := strings.TrimPrefix(authHeader, "Bearer ") + + token, err := jwt.Parse(tokenStr, func(t *jwt.Token) (interface{}, error) { + return []byte(secret), nil + }, jwt.WithValidMethods([]string{"HS256"})) + if err != nil || !token.Valid { + writeJSONError(w, http.StatusUnauthorized, "unauthorized", "invalid or expired token") + return + } + + next.ServeHTTP(w, r) + }) + } +} diff --git a/apps/api-gateway/internal/gateway/proxy.go b/apps/api-gateway/internal/gateway/proxy.go new file mode 100644 index 0000000..48c2117 --- /dev/null +++ b/apps/api-gateway/internal/gateway/proxy.go @@ -0,0 +1,29 @@ +package gateway + +import ( + "log/slog" + "net/http" + "net/http/httputil" + "net/url" +) + +// newReverseProxy builds a reverse proxy to target that rewrites errors into +// JSON and logs upstream failures instead of leaking Go's default HTML page. +func newReverseProxy(name, target string) http.Handler { + u, err := url.Parse(target) + if err != nil { + slog.Error("invalid upstream url", "service", name, "target", target, "err", err) + } + + proxy := httputil.NewSingleHostReverseProxy(u) + origDirector := proxy.Director + proxy.Director = func(r *http.Request) { + origDirector(r) + r.Header.Set("X-Forwarded-Gateway", "ai-rxos-api-gateway") + } + proxy.ErrorHandler = func(w http.ResponseWriter, r *http.Request, err error) { + slog.Error("upstream error", "service", name, "path", r.URL.Path, "err", err) + writeJSONError(w, http.StatusBadGateway, "upstream_unavailable", "the "+name+" service is unavailable") + } + return proxy +} diff --git a/apps/api-gateway/internal/gateway/router.go b/apps/api-gateway/internal/gateway/router.go new file mode 100644 index 0000000..c3daeaf --- /dev/null +++ b/apps/api-gateway/internal/gateway/router.go @@ -0,0 +1,76 @@ +package gateway + +import ( + "encoding/json" + "net/http" + + "github.com/go-chi/chi/v5" + "github.com/go-chi/chi/v5/middleware" + "github.com/go-chi/cors" + + "github.com/openhealthagents/ai-rxos/apps/api-gateway/internal/config" +) + +// publicPaths bypass JWT validation: health checks plus the auth service's +// own login/register/refresh endpoints (you can't require a token to get one). +var publicPaths = []string{ + "/healthz", + "/readyz", + "/api/v1/auth/login", + "/api/v1/auth/register", + "/api/v1/auth/refresh", +} + +// NewRouter wires the full routing table: cross-cutting middleware, then a +// reverse-proxy route per backend service, keyed by URL prefix. +func NewRouter(cfg config.Config) http.Handler { + r := chi.NewRouter() + + r.Use(middleware.Recoverer) + r.Use(requestLogger) + r.Use(cors.Handler(cors.Options{ + AllowedOrigins: cfg.AllowOrigins, + AllowedMethods: []string{"GET", "POST", "PUT", "PATCH", "DELETE", "OPTIONS"}, + AllowedHeaders: []string{"Accept", "Content-Type", "Authorization"}, + AllowCredentials: true, + })) + + limiter := newIPRateLimiter(20, 40) + r.Use(limiter.middleware) + r.Use(jwtAuth(cfg.JWTSecret, publicPaths)) + + r.Get("/healthz", healthHandler) + r.Get("/readyz", healthHandler) + + routes := map[string]string{ + "/api/v1/auth": cfg.AuthServiceURL, + "/api/v1/organizations": cfg.AuthServiceURL, + "/api/v1/papers": cfg.LiteratureServiceURL, + "/api/v1/ingestion": cfg.LiteratureServiceURL, + "/api/v1/graph": cfg.KGServiceURL, + "/api/v1/ontologies": cfg.KGServiceURL, + "/api/v1/search": cfg.SearchServiceURL, + "/api/v1/agents": cfg.AgentsServiceURL, + "/api/v1/workflows": cfg.WorkflowsServiceURL, + "/api/v1/reports": cfg.ReportsServiceURL, + "/api/v1/molecules": cfg.DockingServiceURL, + "/api/v1/docking": cfg.DockingServiceURL, + "/api/v1/ai": cfg.AIServicesURL, + "/api/v1/knowledge": cfg.KnowledgeServiceURL, + } + + for prefix, target := range routes { + proxy := newReverseProxy(prefix, target) + r.Mount(prefix, http.StripPrefix("", proxy)) + } + + return r +} + +func healthHandler(w http.ResponseWriter, r *http.Request) { + w.Header().Set("Content-Type", "application/json") + _ = json.NewEncoder(w).Encode(map[string]string{ + "status": "ok", + "service": "api-gateway", + }) +} diff --git a/apps/api-gateway/package.json b/apps/api-gateway/package.json new file mode 100644 index 0000000..fdacaa5 --- /dev/null +++ b/apps/api-gateway/package.json @@ -0,0 +1,16 @@ +{ + "name": "@ai-rxos/api-gateway", + "version": "0.1.0", + "private": true, + "scripts": { + "dev": "go run ./cmd/gateway", + "build": "go build -o bin/gateway ./cmd/gateway", + "lint": "gofmt -l . && go vet ./...", + "test": "go test ./...", + "typecheck": "go vet ./...", + "clean": "rimraf bin" + }, + "devDependencies": { + "rimraf": "^6.0.1" + } +} diff --git a/apps/knowledge-service/.dockerignore b/apps/knowledge-service/.dockerignore new file mode 100644 index 0000000..e2922bd --- /dev/null +++ b/apps/knowledge-service/.dockerignore @@ -0,0 +1,5 @@ +__pycache__/ +*.pyc +.venv/ +.pytest_cache/ +tests/ diff --git a/apps/knowledge-service/Dockerfile b/apps/knowledge-service/Dockerfile new file mode 100644 index 0000000..a587b41 --- /dev/null +++ b/apps/knowledge-service/Dockerfile @@ -0,0 +1,15 @@ +FROM python:3.12-slim AS base +ENV PYTHONDONTWRITEBYTECODE=1 PYTHONUNBUFFERED=1 PIP_NO_CACHE_DIR=1 +WORKDIR /app + +FROM base AS deps +COPY apps/knowledge-service/requirements.txt . +RUN pip install --no-cache-dir -r requirements.txt + +FROM deps AS runtime +RUN useradd --create-home --uid 1000 rxos +COPY apps/knowledge-service/app ./app +USER rxos +EXPOSE 8091 +ENV PORT=8091 +CMD ["sh", "-c", "uvicorn app.main:app --host 0.0.0.0 --port ${PORT}"] diff --git a/apps/knowledge-service/README.md b/apps/knowledge-service/README.md new file mode 100644 index 0000000..dd9cc72 --- /dev/null +++ b/apps/knowledge-service/README.md @@ -0,0 +1,9 @@ +# knowledge-service + +Part of the AI-RxOS platform. See `/architecture` at the repo root for the +full service contract this implements. Runs on port **8091**. + +```bash +pip install -r requirements.txt +uvicorn app.main:app --reload --port 8091 +``` diff --git a/apps/knowledge-service/app/__init__.py b/apps/knowledge-service/app/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/knowledge-service/app/core/__init__.py b/apps/knowledge-service/app/core/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/knowledge-service/app/core/config.py b/apps/knowledge-service/app/core/config.py new file mode 100644 index 0000000..fb4f071 --- /dev/null +++ b/apps/knowledge-service/app/core/config.py @@ -0,0 +1,23 @@ +from functools import lru_cache + +from pydantic_settings import BaseSettings, SettingsConfigDict + + +class Settings(BaseSettings): + model_config = SettingsConfigDict(env_file=".env", extra="ignore") + + environment: str = "development" + log_level: str = "info" + + database_url: str = "postgresql://ai_rxos:changeme@postgres:5432/ai_rxos" + redis_url: str = "redis://redis:6379/0" + neo4j_uri: str = "bolt://neo4j:7687" + neo4j_user: str = "neo4j" + neo4j_password: str = "changeme_neo4j" + opensearch_url: str = "http://opensearch:9200" + jwt_secret: str = "change_this_dev_secret_before_deploying" + + +@lru_cache +def get_settings() -> Settings: + return Settings() diff --git a/apps/knowledge-service/app/main.py b/apps/knowledge-service/app/main.py new file mode 100644 index 0000000..216d110 --- /dev/null +++ b/apps/knowledge-service/app/main.py @@ -0,0 +1,76 @@ +from contextlib import asynccontextmanager +from typing import Any + +from fastapi import FastAPI, HTTPException +from neo4j import AsyncDriver, AsyncGraphDatabase +from pydantic import BaseModel + +from app.core.config import get_settings + +settings = get_settings() +_driver: AsyncDriver | None = None + + +@asynccontextmanager +async def lifespan(_: FastAPI): + global _driver + _driver = AsyncGraphDatabase.driver( + settings.neo4j_uri, auth=(settings.neo4j_user, settings.neo4j_password) + ) + yield + if _driver: + await _driver.close() + + +app = FastAPI( + title="AI-RxOS Knowledge Service", + description="Frontend-facing aggregation over the Knowledge Graph context " + "(Graph, Entity Resolution, Ontology services).", + version="0.1.0", + lifespan=lifespan, +) + + +class GraphEntity(BaseModel): + id: str + label: str + type: str + properties: dict[str, Any] = {} + + +@app.get("/healthz") +def health() -> dict[str, str]: + return {"status": "ok", "service": "knowledge-service"} + + +@app.get("/api/v1/knowledge/entities/{entity_id}", response_model=GraphEntity) +async def get_entity(entity_id: str) -> GraphEntity: + assert _driver is not None + async with _driver.session() as session: + record = await session.run( + "MATCH (n {id: $id}) RETURN n.id AS id, labels(n)[0] AS type, n AS props LIMIT 1", + id=entity_id, + ) + row = await record.single() + if row is None: + raise HTTPException(status_code=404, detail="entity not found") + return GraphEntity( + id=row["id"], + label=row["props"].get("name", row["id"]), + type=row["type"] or "unknown", + properties=dict(row["props"]), + ) + + +@app.get("/api/v1/knowledge/entities/{entity_id}/neighbors") +async def get_neighbors(entity_id: str, limit: int = 25) -> dict[str, list[dict[str, Any]]]: + assert _driver is not None + async with _driver.session() as session: + result = await session.run( + "MATCH (n {id: $id})--(m) RETURN DISTINCT m.id AS id, labels(m)[0] AS type " + "LIMIT $limit", + id=entity_id, + limit=limit, + ) + rows = [dict(r) async for r in result] + return {"neighbors": rows} diff --git a/apps/knowledge-service/app/routers/__init__.py b/apps/knowledge-service/app/routers/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/apps/knowledge-service/package.json b/apps/knowledge-service/package.json new file mode 100644 index 0000000..863b3a1 --- /dev/null +++ b/apps/knowledge-service/package.json @@ -0,0 +1,16 @@ +{ + "name": "@ai-rxos/knowledge-service", + "version": "0.1.0", + "private": true, + "scripts": { + "dev": "uvicorn app.main:app --reload --port 8091", + "build": "python -m compileall app", + "lint": "ruff check app", + "test": "pytest -q", + "typecheck": "mypy app --ignore-missing-imports", + "clean": "rimraf __pycache__ .pytest_cache" + }, + "devDependencies": { + "rimraf": "^6.0.1" + } +} diff --git a/apps/knowledge-service/requirements.txt b/apps/knowledge-service/requirements.txt new file mode 100644 index 0000000..5f49b4c --- /dev/null +++ b/apps/knowledge-service/requirements.txt @@ -0,0 +1,8 @@ +fastapi==0.115.6 +uvicorn[standard]==0.34.0 +pydantic==2.10.4 +pydantic-settings==2.7.1 +neo4j==5.27.0 +python-json-logger==3.2.1 +pytest==8.3.4 +pytest-asyncio==0.25.1 diff --git a/apps/knowledge-service/tests/test_health.py b/apps/knowledge-service/tests/test_health.py new file mode 100644 index 0000000..94181eb --- /dev/null +++ b/apps/knowledge-service/tests/test_health.py @@ -0,0 +1,11 @@ +from fastapi.testclient import TestClient + +from app.main import app + +client = TestClient(app) + + +def test_health(): + res = client.get("/healthz") + assert res.status_code == 200 + assert res.json()["service"] == "knowledge-service" diff --git a/apps/web/.dockerignore b/apps/web/.dockerignore new file mode 100644 index 0000000..4b34e5f --- /dev/null +++ b/apps/web/.dockerignore @@ -0,0 +1,4 @@ +node_modules +.next +.turbo +dist diff --git a/apps/web/.eslintrc.js b/apps/web/.eslintrc.js new file mode 100644 index 0000000..16c3a29 --- /dev/null +++ b/apps/web/.eslintrc.js @@ -0,0 +1 @@ +module.exports = { root: true, extends: ["@ai-rxos/eslint-config/next.js"] }; diff --git a/apps/web/Dockerfile b/apps/web/Dockerfile new file mode 100644 index 0000000..aa5e12a --- /dev/null +++ b/apps/web/Dockerfile @@ -0,0 +1,35 @@ +FROM node:20-alpine AS base +RUN corepack enable + +# ---- deps: install full workspace deps needed to build this app ---- +FROM base AS deps +WORKDIR /repo +COPY package.json pnpm-workspace.yaml pnpm-lock.yaml* ./ +COPY apps/web/package.json apps/web/package.json +COPY packages/ui/package.json packages/ui/package.json +COPY packages/sdk/package.json packages/sdk/package.json +COPY packages/types/package.json packages/types/package.json +COPY config/eslint-config/package.json config/eslint-config/package.json +COPY config/typescript-config/package.json config/typescript-config/package.json +RUN pnpm install --frozen-lockfile --filter=@ai-rxos/web... + +# ---- build ---- +FROM base AS build +WORKDIR /repo +COPY --from=deps /repo /repo +COPY . . +RUN pnpm --filter=@ai-rxos/types... --filter=@ai-rxos/ui... --filter=@ai-rxos/sdk... build +RUN pnpm --filter=@ai-rxos/web build + +# ---- runtime ---- +FROM base AS runtime +WORKDIR /app +ENV NODE_ENV=production +RUN addgroup -S rxos && adduser -S rxos -G rxos +COPY --from=build /repo/apps/web/.next/standalone ./ +COPY --from=build /repo/apps/web/.next/static ./apps/web/.next/static +COPY --from=build /repo/apps/web/public ./apps/web/public +USER rxos +EXPOSE 3000 +ENV PORT=3000 +CMD ["node", "apps/web/server.js"] diff --git a/apps/web/next-env.d.ts b/apps/web/next-env.d.ts new file mode 100644 index 0000000..40c3d68 --- /dev/null +++ b/apps/web/next-env.d.ts @@ -0,0 +1,5 @@ +/// +/// + +// NOTE: This file should not be edited +// see https://nextjs.org/docs/app/building-your-application/configuring/typescript for more information. diff --git a/apps/web/next.config.mjs b/apps/web/next.config.mjs new file mode 100644 index 0000000..5ef219e --- /dev/null +++ b/apps/web/next.config.mjs @@ -0,0 +1,11 @@ +/** @type {import('next').NextConfig} */ +const nextConfig = { + output: "standalone", + reactStrictMode: true, + transpilePackages: ["@ai-rxos/ui", "@ai-rxos/sdk", "@ai-rxos/types"], + experimental: { + optimizePackageImports: ["@ai-rxos/ui"], + }, +}; + +export default nextConfig; diff --git a/apps/web/package.json b/apps/web/package.json new file mode 100644 index 0000000..5305e00 --- /dev/null +++ b/apps/web/package.json @@ -0,0 +1,35 @@ +{ + "name": "@ai-rxos/web", + "version": "0.1.0", + "private": true, + "scripts": { + "dev": "next dev -p 3000", + "build": "next build", + "start": "next start -p 3000", + "lint": "next lint --max-warnings 0", + "typecheck": "tsc --noEmit", + "clean": "rimraf .next .turbo" + }, + "dependencies": { + "@ai-rxos/sdk": "workspace:*", + "@ai-rxos/types": "workspace:*", + "@ai-rxos/ui": "workspace:*", + "next": "14.2.21", + "react": "^18.3.1", + "react-dom": "^18.3.1" + }, + "devDependencies": { + "@ai-rxos/eslint-config": "workspace:*", + "@ai-rxos/typescript-config": "workspace:*", + "@types/node": "^22.10.2", + "@types/react": "^18.3.18", + "@types/react-dom": "^18.3.5", + "autoprefixer": "^10.4.20", + "eslint": "^8.57.1", + "eslint-config-next": "14.2.21", + "postcss": "^8.4.49", + "rimraf": "^6.0.1", + "tailwindcss": "^3.4.17", + "typescript": "^5.7.2" + } +} diff --git a/apps/web/postcss.config.js b/apps/web/postcss.config.js new file mode 100644 index 0000000..12a703d --- /dev/null +++ b/apps/web/postcss.config.js @@ -0,0 +1,6 @@ +module.exports = { + plugins: { + tailwindcss: {}, + autoprefixer: {}, + }, +}; diff --git a/apps/web/public/.gitkeep b/apps/web/public/.gitkeep new file mode 100644 index 0000000..e69de29 diff --git a/apps/web/src/app/api/health/route.ts b/apps/web/src/app/api/health/route.ts new file mode 100644 index 0000000..f205a2a --- /dev/null +++ b/apps/web/src/app/api/health/route.ts @@ -0,0 +1,5 @@ +import { NextResponse } from "next/server"; + +export function GET() { + return NextResponse.json({ status: "ok", service: "web" }); +} diff --git a/apps/web/src/app/globals.css b/apps/web/src/app/globals.css new file mode 100644 index 0000000..b6db79c --- /dev/null +++ b/apps/web/src/app/globals.css @@ -0,0 +1,58 @@ +@tailwind base; +@tailwind components; +@tailwind utilities; + +body { + @apply bg-rxos-bg text-slate-100; +} + +.rxos-btn { + @apply inline-flex items-center justify-center rounded-md font-medium transition-colors disabled:opacity-50 disabled:pointer-events-none; +} +.rxos-btn-primary { + @apply bg-rxos-accent text-black hover:opacity-90; +} +.rxos-btn-secondary { + @apply bg-slate-700 text-white hover:bg-slate-600; +} +.rxos-btn-ghost { + @apply bg-transparent text-slate-200 hover:bg-slate-800; +} +.rxos-btn-danger { + @apply bg-red-600 text-white hover:bg-red-500; +} +.rxos-btn-sm { + @apply h-8 px-3 text-sm; +} +.rxos-btn-md { + @apply h-10 px-4 text-sm; +} +.rxos-btn-lg { + @apply h-12 px-6 text-base; +} + +.rxos-card { + @apply rounded-lg border border-slate-800 bg-rxos-surface p-5; +} +.rxos-card-title { + @apply mb-3 text-lg font-semibold; +} + +.rxos-badge { + @apply inline-flex items-center rounded-full px-2.5 py-0.5 text-xs font-medium; +} +.rxos-badge-neutral { + @apply bg-slate-700 text-slate-100; +} +.rxos-badge-success { + @apply bg-emerald-700 text-emerald-100; +} +.rxos-badge-warning { + @apply bg-amber-700 text-amber-100; +} +.rxos-badge-danger { + @apply bg-red-700 text-red-100; +} +.rxos-badge-info { + @apply bg-sky-700 text-sky-100; +} diff --git a/apps/web/src/app/layout.tsx b/apps/web/src/app/layout.tsx new file mode 100644 index 0000000..d575748 --- /dev/null +++ b/apps/web/src/app/layout.tsx @@ -0,0 +1,15 @@ +import type { Metadata } from "next"; +import "./globals.css"; + +export const metadata: Metadata = { + title: "AI-RxOS", + description: "AI-native drug discovery operating system", +}; + +export default function RootLayout({ children }: { children: React.ReactNode }) { + return ( + + {children} + + ); +} diff --git a/apps/web/src/app/page.tsx b/apps/web/src/app/page.tsx new file mode 100644 index 0000000..ce163c8 --- /dev/null +++ b/apps/web/src/app/page.tsx @@ -0,0 +1,23 @@ +import { Badge, Button, Card } from "@ai-rxos/ui"; + +export default function HomePage() { + return ( +
+
+

AI-RxOS

+ operational +
+

+ AI-native drug discovery workspace — literature intelligence, knowledge graph, + molecule design, and agentic workflows in one platform. +

+ +

+ This app talks to the API Gateway at{" "} + {process.env.NEXT_PUBLIC_API_BASE_URL ?? "http://localhost:8080"}. +

+ + +
+ ); +} diff --git a/apps/web/tailwind.config.ts b/apps/web/tailwind.config.ts new file mode 100644 index 0000000..401b11c --- /dev/null +++ b/apps/web/tailwind.config.ts @@ -0,0 +1,19 @@ +import type { Config } from "tailwindcss"; + +const config: Config = { + content: ["./src/**/*.{ts,tsx}", "../../packages/ui/src/**/*.{ts,tsx}"], + theme: { + extend: { + colors: { + rxos: { + bg: "#0b0f14", + surface: "#131a22", + accent: "#3ddc97", + }, + }, + }, + }, + plugins: [], +}; + +export default config; diff --git a/apps/web/tsconfig.json b/apps/web/tsconfig.json new file mode 100644 index 0000000..0f4f207 --- /dev/null +++ b/apps/web/tsconfig.json @@ -0,0 +1,10 @@ +{ + "extends": "@ai-rxos/typescript-config/nextjs.json", + "compilerOptions": { + "paths": { + "@/*": ["./src/*"] + } + }, + "include": ["next-env.d.ts", "**/*.ts", "**/*.tsx", ".next/types/**/*.ts"], + "exclude": ["node_modules"] +} diff --git a/apps/web/tsconfig.tsbuildinfo b/apps/web/tsconfig.tsbuildinfo new file mode 100644 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\ No newline at end of file diff --git a/config/eslint-config/index.js b/config/eslint-config/index.js new file mode 100644 index 0000000..d1481ac --- /dev/null +++ b/config/eslint-config/index.js @@ -0,0 +1,27 @@ +/** Base ESLint config shared across the monorepo. */ +module.exports = { + root: true, + env: { es2022: true, node: true }, + parser: "@typescript-eslint/parser", + parserOptions: { ecmaVersion: "latest", sourceType: "module" }, + plugins: ["@typescript-eslint"], + extends: [ + "eslint:recommended", + "plugin:@typescript-eslint/recommended", + "prettier", + ], + ignorePatterns: [ + "node_modules/", + "dist/", + ".next/", + ".turbo/", + "coverage/", + ], + rules: { + "@typescript-eslint/no-unused-vars": [ + "warn", + { argsIgnorePattern: "^_", varsIgnorePattern: "^_" }, + ], + "@typescript-eslint/no-explicit-any": "warn", + }, +}; diff --git a/config/eslint-config/next.js b/config/eslint-config/next.js new file mode 100644 index 0000000..960fe5c --- /dev/null +++ b/config/eslint-config/next.js @@ -0,0 +1,8 @@ +/** ESLint config for Next.js apps. next/core-web-vitals already pulls in + * react + react-hooks rules, so this extends the base config only — + * layering react-library.js on top double-registers the react-hooks + * plugin and breaks lint with a "Plugin conflicted" error. */ +module.exports = { + extends: ["./index.js", "next/core-web-vitals"], + env: { browser: true }, +}; diff --git a/config/eslint-config/package.json b/config/eslint-config/package.json new file mode 100644 index 0000000..9632130 --- /dev/null +++ b/config/eslint-config/package.json @@ -0,0 +1,15 @@ +{ + "name": "@ai-rxos/eslint-config", + "version": "0.1.0", + "private": true, + "license": "MIT", + "main": "index.js", + "files": ["index.js", "next.js", "react-library.js"], + "dependencies": { + "@typescript-eslint/eslint-plugin": "^8.19.0", + "@typescript-eslint/parser": "^8.19.0", + "eslint-config-prettier": "^9.1.0", + "eslint-plugin-react": "^7.37.2", + "eslint-plugin-react-hooks": "^5.1.0" + } +} diff --git a/config/eslint-config/react-library.js b/config/eslint-config/react-library.js new file mode 100644 index 0000000..00f4776 --- /dev/null +++ b/config/eslint-config/react-library.js @@ -0,0 +1,6 @@ +/** ESLint config for React component packages. */ +module.exports = { + extends: ["./index.js", "plugin:react/recommended", "plugin:react-hooks/recommended"], + settings: { react: { version: "detect" } }, + env: { browser: true }, +}; diff --git a/config/typescript-config/base.json b/config/typescript-config/base.json new file mode 100644 index 0000000..f474197 --- /dev/null +++ b/config/typescript-config/base.json @@ -0,0 +1,20 @@ +{ + "$schema": "https://json.schemastore.org/tsconfig", + "compilerOptions": { + "target": "ES2022", + "lib": ["ES2022"], + "module": "ESNext", + "moduleResolution": "Bundler", + "moduleDetection": "force", + "strict": true, + "noUncheckedIndexedAccess": true, + "esModuleInterop": true, + "skipLibCheck": true, + "resolveJsonModule": true, + "isolatedModules": true, + "forceConsistentCasingInFileNames": true, + "declaration": true, + "declarationMap": true + }, + "exclude": ["node_modules", "dist", ".next", ".turbo"] +} diff --git a/config/typescript-config/nextjs.json b/config/typescript-config/nextjs.json new file mode 100644 index 0000000..6e8a05a --- /dev/null +++ b/config/typescript-config/nextjs.json @@ -0,0 +1,14 @@ +{ + "$schema": "https://json.schemastore.org/tsconfig", + "extends": "./base.json", + "compilerOptions": { + "module": "ESNext", + "moduleResolution": "Bundler", + "lib": ["dom", "dom.iterable", "ES2022"], + "jsx": "preserve", + "noEmit": true, + "allowJs": true, + "incremental": true, + "plugins": [{ "name": "next" }] + } +} diff --git a/config/typescript-config/package.json b/config/typescript-config/package.json new file mode 100644 index 0000000..3aee256 --- /dev/null +++ b/config/typescript-config/package.json @@ -0,0 +1,7 @@ +{ + "name": "@ai-rxos/typescript-config", + "version": "0.1.0", + "private": true, + "license": "MIT", + "files": ["base.json", "nextjs.json", "react-library.json"] +} diff --git a/config/typescript-config/react-library.json b/config/typescript-config/react-library.json new file mode 100644 index 0000000..c1bfb8e --- /dev/null +++ b/config/typescript-config/react-library.json @@ -0,0 +1,9 @@ +{ + "$schema": "https://json.schemastore.org/tsconfig", + "extends": "./base.json", + "compilerOptions": { + "lib": ["dom", "dom.iterable", "ES2022"], + "jsx": "react-jsx", + "declaration": true + } +} diff --git a/docker-compose.yml b/docker-compose.yml new file mode 100644 index 0000000..ec3d91d --- /dev/null +++ b/docker-compose.yml @@ -0,0 +1,226 @@ +name: ai-rxos + +x-py-service: &py-service + env_file: .env + networks: [ai-rxos] + restart: unless-stopped + depends_on: + postgres: + condition: service_healthy + redis: + condition: service_healthy + +networks: + ai-rxos: + driver: bridge + +volumes: + postgres-data: + neo4j-data: + redis-data: + opensearch-data: + +services: + # ── Data stores ────────────────────────────────────────────────────── + postgres: + image: pgvector/pgvector:pg16 + environment: + POSTGRES_DB: ${POSTGRES_DB:-ai_rxos} + POSTGRES_USER: ${POSTGRES_USER:-ai_rxos} + POSTGRES_PASSWORD: ${POSTGRES_PASSWORD:-changeme} + ports: ["5432:5432"] + volumes: + - postgres-data:/var/lib/postgresql/data + - ./infra/postgres/init.sql:/docker-entrypoint-initdb.d/init.sql:ro + healthcheck: + test: ["CMD-SHELL", "pg_isready -U ${POSTGRES_USER:-ai_rxos}"] + interval: 5s + timeout: 5s + retries: 10 + networks: [ai-rxos] + restart: unless-stopped + + neo4j: + image: neo4j:5.26-community + environment: + NEO4J_AUTH: ${NEO4J_USER:-neo4j}/${NEO4J_PASSWORD:-changeme_neo4j} + NEO4J_server_memory_pagecache_size: 512M + NEO4J_server_memory_heap_max__size: 1G + ports: + - "7474:7474" # browser + - "7687:7687" # bolt + volumes: + - neo4j-data:/data + healthcheck: + test: ["CMD-SHELL", "wget -qO- http://localhost:7474 || exit 1"] + interval: 10s + timeout: 5s + retries: 10 + networks: [ai-rxos] + restart: unless-stopped + + redis: + image: redis:7-alpine + ports: ["6379:6379"] + volumes: + - redis-data:/data + healthcheck: + test: ["CMD", "redis-cli", "ping"] + interval: 5s + timeout: 5s + retries: 10 + networks: [ai-rxos] + restart: unless-stopped + + opensearch: + image: opensearchproject/opensearch:2.19.1 + environment: + discovery.type: single-node + DISABLE_SECURITY_PLUGIN: "false" + OPENSEARCH_INITIAL_ADMIN_PASSWORD: ${OPENSEARCH_PASSWORD:-AiRxOS#Search9K} + OPENSEARCH_JAVA_OPTS: "-Xms512m -Xmx512m" + ports: + - "9200:9200" + volumes: + - opensearch-data:/usr/share/opensearch/data + healthcheck: + test: ["CMD-SHELL", "curl -sku admin:${OPENSEARCH_PASSWORD:-AiRxOS#Search9K} https://localhost:9200/_cluster/health || exit 1"] + interval: 10s + timeout: 5s + retries: 15 + networks: [ai-rxos] + restart: unless-stopped + + # ── Go services ────────────────────────────────────────────────────── + auth: + build: { context: ., dockerfile: services/auth/Dockerfile } + env_file: .env + environment: + PORT: "8081" + ports: ["8081:8081"] + depends_on: + postgres: { condition: service_healthy } + redis: { condition: service_healthy } + networks: [ai-rxos] + restart: unless-stopped + + search: + build: { context: ., dockerfile: services/search/Dockerfile } + env_file: .env + environment: + PORT: "8084" + ports: ["8084:8084"] + depends_on: + postgres: { condition: service_healthy } + opensearch: { condition: service_healthy } + networks: [ai-rxos] + restart: unless-stopped + + # BetterAuth adapter scaffold (see services/auth-adapter/README.md). + # Additive: `auth` above is unchanged and still owns /api/v1/auth/*. + # Not in api-gateway's depends_on/proxy — not routed to yet. + auth-adapter: + build: { context: ., dockerfile: services/auth-adapter/Dockerfile } + env_file: .env + environment: + PORT: "8089" + BETTER_AUTH_URL: "http://localhost:8089" + ports: ["8089:8089"] + depends_on: + postgres: { condition: service_healthy } + networks: [ai-rxos] + restart: unless-stopped + + api-gateway: + build: { context: ., dockerfile: apps/api-gateway/Dockerfile } + env_file: .env + environment: + PORT: "8080" + ports: ["8080:8080"] + depends_on: [auth, search, literature, kg, agents, workflows, reports, docking, ai-services, knowledge-service] + networks: [ai-rxos] + restart: unless-stopped + + # ── Python services ────────────────────────────────────────────────── + literature: + <<: *py-service + build: { context: ., dockerfile: services/literature/Dockerfile } + environment: + PORT: "8082" + ports: ["8082:8082"] + + kg: + <<: *py-service + build: { context: ., dockerfile: services/kg/Dockerfile } + environment: + PORT: "8083" + ports: ["8083:8083"] + depends_on: + neo4j: { condition: service_healthy } + + agents: + <<: *py-service + build: { context: ., dockerfile: services/agents/Dockerfile } + environment: + PORT: "8085" + ports: ["8085:8085"] + + workflows: + <<: *py-service + build: { context: ., dockerfile: services/workflows/Dockerfile } + environment: + PORT: "8086" + ports: ["8086:8086"] + + reports: + <<: *py-service + build: { context: ., dockerfile: services/reports/Dockerfile } + environment: + PORT: "8087" + ports: ["8087:8087"] + + docking: + <<: *py-service + build: { context: ., dockerfile: services/docking/Dockerfile } + environment: + PORT: "8088" + ports: ["8088:8088"] + + ai-services: + <<: *py-service + build: { context: ., dockerfile: apps/ai-services/Dockerfile } + environment: + PORT: "8090" + ports: ["8090:8090"] + + knowledge-service: + <<: *py-service + build: { context: ., dockerfile: apps/knowledge-service/Dockerfile } + environment: + PORT: "8091" + ports: ["8091:8091"] + depends_on: + neo4j: { condition: service_healthy } + + # ── Frontends ──────────────────────────────────────────────────────── + web: + build: { context: ., dockerfile: apps/web/Dockerfile } + env_file: .env + environment: + PORT: "3000" + NEXT_PUBLIC_API_BASE_URL: http://localhost:8080 + ports: ["3000:3000"] + depends_on: [api-gateway] + networks: [ai-rxos] + restart: unless-stopped + + admin: + build: { context: ., dockerfile: apps/admin/Dockerfile } + env_file: .env + environment: + PORT: "3001" + NEXT_PUBLIC_API_BASE_URL: http://localhost:8080 + ports: ["3001:3001"] + depends_on: [api-gateway] + networks: [ai-rxos] + restart: unless-stopped diff --git a/infra/README.md b/infra/README.md new file mode 100644 index 0000000..090888e --- /dev/null +++ b/infra/README.md @@ -0,0 +1,31 @@ +# infra + +- `k8s/` — raw cluster-bootstrap manifests (namespaces, baseline network + policies). Apply once per cluster, before any Helm release: + `kubectl apply -f infra/k8s/` +- `helm/ai-rxos/` — the umbrella Helm chart that deploys all 13 application + services plus (optionally, per environment) in-cluster PostgreSQL+pgvector, + Neo4j, Redis, and OpenSearch. +- `postgres/init.sql` — first-boot init script for the docker-compose + Postgres container (enables `pgvector`/`uuid-ossp`); Helm's PostgreSQL + dependency handles this via its own image (`pgvector/pgvector:pg16`). + +## Deploying with Helm + +```bash +helm dependency update infra/helm/ai-rxos + +# local/dev cluster (kind, minikube, k3d) — in-cluster dependencies, no ingress +helm install ai-rxos infra/helm/ai-rxos \ + -f infra/helm/ai-rxos/values.yaml \ + -f infra/helm/ai-rxos/values-dev.yaml \ + --create-namespace -n ai-rxos-development + +# production — managed AWS services, external secrets, ingress+TLS +helm install ai-rxos infra/helm/ai-rxos \ + -f infra/helm/ai-rxos/values.yaml \ + -f infra/helm/ai-rxos/values-prod.yaml \ + -n ai-rxos-production +``` + +Update in place with `helm upgrade` using the same `-f` flags. diff --git a/infra/helm/ai-rxos/.helmignore b/infra/helm/ai-rxos/.helmignore new file mode 100644 index 0000000..2f223ec --- /dev/null +++ b/infra/helm/ai-rxos/.helmignore @@ -0,0 +1,7 @@ +# Patterns to ignore when packaging this chart (does NOT apply to charts/ +# dependency archives or Chart.lock — those must ship with the chart). +.git/ +.gitignore +*.orig +*.bak +.DS_Store diff --git a/infra/helm/ai-rxos/Chart.lock b/infra/helm/ai-rxos/Chart.lock new file mode 100644 index 0000000..147468a --- /dev/null +++ b/infra/helm/ai-rxos/Chart.lock @@ -0,0 +1,15 @@ +dependencies: +- name: postgresql + repository: https://charts.bitnami.com/bitnami + version: 16.2.4 +- name: redis + repository: https://charts.bitnami.com/bitnami + version: 20.2.1 +- name: neo4j + repository: https://helm.neo4j.com/neo4j + version: 5.26.28 +- name: opensearch + repository: https://opensearch-project.github.io/helm-charts + version: 2.24.0 +digest: sha256:ed4aeb675649c8cebc78c58a54f9bf02c0ce0ff5ccd91c6f6d44c8ef4519931c +generated: "2026-07-15T21:15:18.410173+05:30" diff --git a/infra/helm/ai-rxos/Chart.yaml b/infra/helm/ai-rxos/Chart.yaml new file mode 100644 index 0000000..a99d5ca --- /dev/null +++ b/infra/helm/ai-rxos/Chart.yaml @@ -0,0 +1,35 @@ +apiVersion: v2 +name: ai-rxos +description: >- + AI-RxOS umbrella Helm chart — deploys all 13 application services + (web, admin, api-gateway, ai-services, knowledge-service, auth, literature, + kg, search, agents, workflows, reports, docking) plus optional in-cluster + PostgreSQL (pgvector), Neo4j, Redis, and OpenSearch dependencies for + dev/staging. Production points config at managed equivalents instead + (see values-prod.yaml). +type: application +version: 0.1.0 +appVersion: "0.1.0" +home: https://github.com/OpenHealthAgents/AI-RxOS +sources: + - https://github.com/OpenHealthAgents/AI-RxOS +maintainers: + - name: AI-RxOS Platform Team + +dependencies: + - name: postgresql + version: "16.2.4" + repository: https://charts.bitnami.com/bitnami + condition: postgresql.enabled + - name: redis + version: "20.2.1" + repository: https://charts.bitnami.com/bitnami + condition: redis.enabled + - name: neo4j + version: "5.26.28" + repository: https://helm.neo4j.com/neo4j + condition: neo4j.enabled + - name: opensearch + version: "2.24.0" + repository: https://opensearch-project.github.io/helm-charts + condition: opensearch.enabled diff --git a/infra/helm/ai-rxos/templates/NOTES.txt b/infra/helm/ai-rxos/templates/NOTES.txt new file mode 100644 index 0000000..c0afc9e --- /dev/null +++ b/infra/helm/ai-rxos/templates/NOTES.txt @@ -0,0 +1,18 @@ +AI-RxOS has been deployed to namespace {{ include "ai-rxos.namespace" . }}. + +Check rollout status: + kubectl get pods -n {{ include "ai-rxos.namespace" . }} -w + +{{- if .Values.ingress.enabled }} + +Once the ingress controller assigns an address, the platform will be reachable at: + Web: https://{{ .Values.ingress.hosts.web }} + Admin: https://{{ .Values.ingress.hosts.admin }} + API: https://{{ .Values.ingress.hosts.api }} +{{- else }} + +Ingress is disabled — use `kubectl port-forward` to reach services, e.g.: + kubectl port-forward -n {{ include "ai-rxos.namespace" . }} svc/{{ include "ai-rxos.fullname" . }}-api-gateway 8080:8080 +{{- end }} + +This release manages: {{ range $name, $svc := .Values.services }}{{ if $svc.enabled }}{{ $name }} {{ end }}{{ end }} diff --git a/infra/helm/ai-rxos/templates/_helpers.tpl b/infra/helm/ai-rxos/templates/_helpers.tpl new file mode 100644 index 0000000..50af534 --- /dev/null +++ b/infra/helm/ai-rxos/templates/_helpers.tpl @@ -0,0 +1,77 @@ +{{/* Chart name, truncated for k8s name limits. */}} +{{- define "ai-rxos.name" -}} +{{- default .Chart.Name .Values.nameOverride | trunc 63 | trimSuffix "-" -}} +{{- end -}} + +{{/* Fully qualified app name: - unless fullnameOverride is set. */}} +{{- define "ai-rxos.fullname" -}} +{{- if .Values.fullnameOverride -}} +{{- .Values.fullnameOverride | trunc 63 | trimSuffix "-" -}} +{{- else -}} +{{- $name := default .Chart.Name .Values.nameOverride -}} +{{- if contains $name .Release.Name -}} +{{- .Release.Name | trunc 63 | trimSuffix "-" -}} +{{- else -}} +{{- printf "%s-%s" .Release.Name $name | trunc 63 | trimSuffix "-" -}} +{{- end -}} +{{- end -}} +{{- end -}} + +{{- define "ai-rxos.namespace" -}} +{{- default .Release.Namespace .Values.namespaceOverride -}} +{{- end -}} + +{{- define "ai-rxos.chart" -}} +{{- printf "%s-%s" .Chart.Name .Chart.Version | replace "+" "_" | trunc 63 | trimSuffix "-" -}} +{{- end -}} + +{{/* Common labels applied to every resource. */}} +{{- define "ai-rxos.labels" -}} +helm.sh/chart: {{ include "ai-rxos.chart" . }} +app.kubernetes.io/managed-by: {{ .Release.Service }} +app.kubernetes.io/part-of: ai-rxos +{{ include "ai-rxos.selectorLabels" . }} +{{- end -}} + +{{/* Selector labels for a specific service, called with (dict "root" $ "service" $svcName). */}} +{{- define "ai-rxos.selectorLabels" -}} +app.kubernetes.io/name: {{ include "ai-rxos.name" . }} +app.kubernetes.io/instance: {{ .Release.Name }} +{{- end -}} + +{{- define "ai-rxos.serviceLabels" -}} +{{ include "ai-rxos.labels" .root }} +app.kubernetes.io/component: {{ .service }} +{{- end -}} + +{{- define "ai-rxos.serviceSelectorLabels" -}} +{{ include "ai-rxos.selectorLabels" .root }} +app.kubernetes.io/component: {{ .service }} +{{- end -}} + +{{- define "ai-rxos.serviceAccountName" -}} +{{- if .Values.serviceAccount.create -}} +{{- default (include "ai-rxos.fullname" .) .Values.serviceAccount.name -}} +{{- else -}} +{{- default "default" .Values.serviceAccount.name -}} +{{- end -}} +{{- end -}} + +{{/* Name of the Secret to mount — externalSecret.name in prod, or the chart-managed one. */}} +{{- define "ai-rxos.secretName" -}} +{{- if .Values.externalSecret.enabled -}} +{{- .Values.externalSecret.name -}} +{{- else -}} +{{- printf "%s-secrets" (include "ai-rxos.fullname" .) -}} +{{- end -}} +{{- end -}} + +{{/* Full image reference for a service entry, e.g. (dict "root" $ "svc" $svc). */}} +{{- define "ai-rxos.image" -}} +{{- $registry := .root.Values.global.imageRegistry -}} +{{- if $registry -}} +{{- printf "%s/%s:%s" $registry .svc.image.repository .svc.image.tag -}} +{{- else -}} +{{- printf "%s:%s" .svc.image.repository .svc.image.tag -}} +{{- end -}} +{{- end -}} diff --git a/infra/helm/ai-rxos/templates/configmap.yaml b/infra/helm/ai-rxos/templates/configmap.yaml new file mode 100644 index 0000000..003dd1c --- /dev/null +++ b/infra/helm/ai-rxos/templates/configmap.yaml @@ -0,0 +1,28 @@ +apiVersion: v1 +kind: ConfigMap +metadata: + name: {{ include "ai-rxos.fullname" . }}-config + namespace: {{ include "ai-rxos.namespace" . }} + labels: + {{- include "ai-rxos.labels" . | nindent 4 }} +data: + ENVIRONMENT: {{ .Values.global.environment | quote }} + POSTGRES_HOST: {{ .Values.config.postgresHost | quote }} + POSTGRES_PORT: {{ .Values.config.postgresPort | quote }} + POSTGRES_DB: {{ .Values.config.postgresDb | quote }} + POSTGRES_USER: {{ .Values.config.postgresUser | quote }} + NEO4J_URI: {{ .Values.config.neo4jUri | quote }} + NEO4J_USER: {{ .Values.config.neo4jUser | quote }} + REDIS_URL: {{ .Values.config.redisUrl | quote }} + OPENSEARCH_URL: {{ .Values.config.opensearchUrl | quote }} + OPENSEARCH_USER: {{ .Values.config.opensearchUser | quote }} + CORS_ALLOW_ORIGIN: {{ .Values.config.corsAllowOrigin | quote }} + SEARCH_RETRIEVAL_PROVIDER: {{ .Values.config.searchRetrievalProvider | quote }} + LLM_WIKI_URL: {{ .Values.config.llmWikiUrl | quote }} + GOOGLE_OKF_URL: {{ .Values.config.googleOkfUrl | quote }} + {{- $fullname := include "ai-rxos.fullname" . }} + {{- range $name, $svc := .Values.services }} + {{- if $svc.enabled }} + {{ upper (replace "-" "_" $name) }}_SERVICE_URL: {{ printf "http://%s-%s:%v" $fullname $name $svc.port | quote }} + {{- end }} + {{- end }} diff --git a/infra/helm/ai-rxos/templates/deployment.yaml b/infra/helm/ai-rxos/templates/deployment.yaml new file mode 100644 index 0000000..b6fc880 --- /dev/null +++ b/infra/helm/ai-rxos/templates/deployment.yaml @@ -0,0 +1,92 @@ +{{- $root := . }} +{{- range $name, $svc := .Values.services }} +{{- if $svc.enabled }} +apiVersion: apps/v1 +kind: Deployment +metadata: + name: {{ include "ai-rxos.fullname" $root }}-{{ $name }} + namespace: {{ include "ai-rxos.namespace" $root }} + labels: + {{- include "ai-rxos.serviceLabels" (dict "root" $root "service" $name) | nindent 4 }} +spec: + {{- if not $svc.autoscaling.enabled }} + replicas: {{ $svc.replicas }} + {{- end }} + selector: + matchLabels: + {{- include "ai-rxos.serviceSelectorLabels" (dict "root" $root "service" $name) | nindent 6 }} + template: + metadata: + labels: + {{- include "ai-rxos.serviceLabels" (dict "root" $root "service" $name) | nindent 8 }} + annotations: + prometheus.io/scrape: "true" + prometheus.io/port: {{ $svc.port | quote }} + prometheus.io/path: "/metrics" + spec: + serviceAccountName: {{ include "ai-rxos.serviceAccountName" $root }} + securityContext: + {{- toYaml $root.Values.podSecurityContext | nindent 8 }} + {{- if and $svc.gpu $svc.gpu.enabled }} + nodeSelector: + gpu: "true" + tolerations: + - key: "nvidia.com/gpu" + operator: "Exists" + effect: "NoSchedule" + {{- end }} + containers: + - name: {{ $name }} + securityContext: + {{- toYaml $root.Values.securityContext | nindent 12 }} + image: {{ include "ai-rxos.image" (dict "root" $root "svc" $svc) }} + imagePullPolicy: {{ $root.Values.global.imagePullPolicy }} + ports: + - name: http + containerPort: {{ $svc.port }} + protocol: TCP + envFrom: + - configMapRef: + name: {{ include "ai-rxos.fullname" $root }}-config + - secretRef: + name: {{ include "ai-rxos.secretName" $root }} + env: + - name: PORT + value: {{ $svc.port | quote }} + {{- range $key, $value := $svc.env }} + - name: {{ $key }} + value: {{ $value | quote }} + {{- end }} + {{- if $svc.healthPath }} + livenessProbe: + httpGet: + path: {{ $svc.healthPath }} + port: http + initialDelaySeconds: 10 + periodSeconds: 15 + timeoutSeconds: 5 + failureThreshold: 3 + readinessProbe: + httpGet: + path: {{ $svc.healthPath }} + port: http + initialDelaySeconds: 5 + periodSeconds: 10 + timeoutSeconds: 3 + failureThreshold: 3 + {{- end }} + resources: + requests: + {{- toYaml $svc.resources.requests | nindent 14 }} + limits: + {{- toYaml $svc.resources.limits | nindent 14 }} + {{- if and $svc.gpu $svc.gpu.enabled }} + nvidia.com/gpu: "1" + {{- end }} + {{- with $root.Values.global.imagePullSecrets }} + imagePullSecrets: + {{- toYaml . | nindent 8 }} + {{- end }} +--- +{{- end }} +{{- end }} diff --git a/infra/helm/ai-rxos/templates/external-secret.yaml b/infra/helm/ai-rxos/templates/external-secret.yaml new file mode 100644 index 0000000..8e0f97d --- /dev/null +++ b/infra/helm/ai-rxos/templates/external-secret.yaml @@ -0,0 +1,50 @@ +{{- /* +External Secrets Operator scaffold. Renders only when +externalSecret.enabled=true (values-prod.yaml), producing the same +Secret (name + keys) that templates/secret.yaml would otherwise create +from plaintext values — so ai-rxos.secretName and every Deployment's +envFrom keep working unchanged either way. + +Requires the External Secrets Operator (https://external-secrets.io) and +a SecretStore/ClusterSecretStore named externalSecret.secretStoreRef.name +to already exist in-cluster; this template does not create either. Each +remoteRef.key below assumes the backing store holds one entry per field +under an "ai-rxos/" prefix — adjust to match your provider's actual +layout (AWS Secrets Manager, Vault, etc) before relying on this. +*/}} +{{- if .Values.externalSecret.enabled }} +apiVersion: external-secrets.io/v1 +kind: ExternalSecret +metadata: + name: {{ include "ai-rxos.fullname" . }}-external-secret + namespace: {{ include "ai-rxos.namespace" . }} + labels: + {{- include "ai-rxos.labels" . | nindent 4 }} +spec: + refreshInterval: {{ .Values.externalSecret.refreshInterval | default "1h" }} + secretStoreRef: + name: {{ .Values.externalSecret.secretStoreRef.name }} + kind: {{ .Values.externalSecret.secretStoreRef.kind | default "ClusterSecretStore" }} + target: + name: {{ .Values.externalSecret.name }} + creationPolicy: Owner + data: + - secretKey: POSTGRES_PASSWORD + remoteRef: { key: ai-rxos/postgres-password } + - secretKey: DATABASE_URL + remoteRef: { key: ai-rxos/database-url } + - secretKey: NEO4J_PASSWORD + remoteRef: { key: ai-rxos/neo4j-password } + - secretKey: REDIS_PASSWORD + remoteRef: { key: ai-rxos/redis-password } + - secretKey: OPENSEARCH_PASSWORD + remoteRef: { key: ai-rxos/opensearch-password } + - secretKey: JWT_SECRET + remoteRef: { key: ai-rxos/jwt-secret } + - secretKey: BETTER_AUTH_SECRET + remoteRef: { key: ai-rxos/better-auth-secret } + - secretKey: LLM_WIKI_API_KEY + remoteRef: { key: ai-rxos/llm-wiki-api-key } + - secretKey: GOOGLE_OKF_API_KEY + remoteRef: { key: ai-rxos/google-okf-api-key } +{{- end }} diff --git a/infra/helm/ai-rxos/templates/hpa.yaml b/infra/helm/ai-rxos/templates/hpa.yaml new file mode 100644 index 0000000..97184d1 --- /dev/null +++ b/infra/helm/ai-rxos/templates/hpa.yaml @@ -0,0 +1,30 @@ +{{- $root := . }} +{{- range $name, $svc := .Values.services }} +{{- if and $svc.enabled $svc.autoscaling.enabled }} +apiVersion: autoscaling/v2 +kind: HorizontalPodAutoscaler +metadata: + name: {{ include "ai-rxos.fullname" $root }}-{{ $name }} + namespace: {{ include "ai-rxos.namespace" $root }} + labels: + {{- include "ai-rxos.serviceLabels" (dict "root" $root "service" $name) | nindent 4 }} +spec: + scaleTargetRef: + apiVersion: apps/v1 + kind: Deployment + name: {{ include "ai-rxos.fullname" $root }}-{{ $name }} + minReplicas: {{ $svc.autoscaling.minReplicas }} + maxReplicas: {{ $svc.autoscaling.maxReplicas }} + behavior: + scaleDown: + stabilizationWindowSeconds: 300 + metrics: + - type: Resource + resource: + name: cpu + target: + type: Utilization + averageUtilization: {{ $svc.autoscaling.targetCPUUtilizationPercentage }} +--- +{{- end }} +{{- end }} diff --git a/infra/helm/ai-rxos/templates/ingress.yaml b/infra/helm/ai-rxos/templates/ingress.yaml new file mode 100644 index 0000000..a869f84 --- /dev/null +++ b/infra/helm/ai-rxos/templates/ingress.yaml @@ -0,0 +1,37 @@ +{{- if .Values.ingress.enabled }} +{{- $root := . }} +apiVersion: networking.k8s.io/v1 +kind: Ingress +metadata: + name: {{ include "ai-rxos.fullname" . }} + namespace: {{ include "ai-rxos.namespace" . }} + labels: + {{- include "ai-rxos.labels" . | nindent 4 }} + annotations: + {{- toYaml .Values.ingress.annotations | nindent 4 }} +spec: + ingressClassName: {{ .Values.ingress.className }} + {{- if .Values.ingress.tls.enabled }} + tls: + - secretName: {{ .Values.ingress.tls.secretName }} + hosts: + {{- range $key, $host := .Values.ingress.hosts }} + - {{ $host }} + {{- end }} + {{- end }} + rules: + {{- range $name, $svc := .Values.services }} + {{- if and $svc.enabled $svc.ingress }} + - host: {{ index $root.Values.ingress.hosts $svc.ingress.host }} + http: + paths: + - path: {{ $svc.ingress.path }} + pathType: Prefix + backend: + service: + name: {{ include "ai-rxos.fullname" $root }}-{{ $name }} + port: + number: {{ $svc.port }} + {{- end }} + {{- end }} +{{- end }} diff --git a/infra/helm/ai-rxos/templates/secret.yaml b/infra/helm/ai-rxos/templates/secret.yaml new file mode 100644 index 0000000..2a3486e --- /dev/null +++ b/infra/helm/ai-rxos/templates/secret.yaml @@ -0,0 +1,20 @@ +{{- if not .Values.externalSecret.enabled }} +apiVersion: v1 +kind: Secret +metadata: + name: {{ include "ai-rxos.fullname" . }}-secrets + namespace: {{ include "ai-rxos.namespace" . }} + labels: + {{- include "ai-rxos.labels" . | nindent 4 }} +type: Opaque +stringData: + POSTGRES_PASSWORD: {{ .Values.secrets.postgresPassword | quote }} + DATABASE_URL: {{ printf "postgresql://%s:%s@%s:%v/%s" .Values.config.postgresUser .Values.secrets.postgresPassword .Values.config.postgresHost .Values.config.postgresPort .Values.config.postgresDb | quote }} + NEO4J_PASSWORD: {{ .Values.secrets.neo4jPassword | quote }} + REDIS_PASSWORD: {{ .Values.secrets.redisPassword | quote }} + OPENSEARCH_PASSWORD: {{ .Values.secrets.opensearchPassword | quote }} + JWT_SECRET: {{ .Values.secrets.jwtSecret | quote }} + BETTER_AUTH_SECRET: {{ .Values.secrets.betterAuthSecret | quote }} + LLM_WIKI_API_KEY: {{ .Values.secrets.llmWikiApiKey | quote }} + GOOGLE_OKF_API_KEY: {{ .Values.secrets.googleOkfApiKey | quote }} +{{- end }} diff --git a/infra/helm/ai-rxos/templates/service.yaml b/infra/helm/ai-rxos/templates/service.yaml new file mode 100644 index 0000000..702c112 --- /dev/null +++ b/infra/helm/ai-rxos/templates/service.yaml @@ -0,0 +1,22 @@ +{{- $root := . }} +{{- range $name, $svc := .Values.services }} +{{- if $svc.enabled }} +apiVersion: v1 +kind: Service +metadata: + name: {{ include "ai-rxos.fullname" $root }}-{{ $name }} + namespace: {{ include "ai-rxos.namespace" $root }} + labels: + {{- include "ai-rxos.serviceLabels" (dict "root" $root "service" $name) | nindent 4 }} +spec: + type: ClusterIP + ports: + - name: http + port: {{ $svc.port }} + targetPort: http + protocol: TCP + selector: + {{- include "ai-rxos.serviceSelectorLabels" (dict "root" $root "service" $name) | nindent 4 }} +--- +{{- end }} +{{- end }} diff --git a/infra/helm/ai-rxos/templates/serviceaccount.yaml b/infra/helm/ai-rxos/templates/serviceaccount.yaml new file mode 100644 index 0000000..deed669 --- /dev/null +++ b/infra/helm/ai-rxos/templates/serviceaccount.yaml @@ -0,0 +1,13 @@ +{{- if .Values.serviceAccount.create }} +apiVersion: v1 +kind: ServiceAccount +metadata: + name: {{ include "ai-rxos.serviceAccountName" . }} + namespace: {{ include "ai-rxos.namespace" . }} + labels: + {{- include "ai-rxos.labels" . | nindent 4 }} + {{- with .Values.serviceAccount.annotations }} + annotations: + {{- toYaml . | nindent 4 }} + {{- end }} +{{- end }} diff --git a/infra/helm/ai-rxos/values-dev.yaml b/infra/helm/ai-rxos/values-dev.yaml new file mode 100644 index 0000000..7654f9e --- /dev/null +++ b/infra/helm/ai-rxos/values-dev.yaml @@ -0,0 +1,20 @@ +## Dev overlay: helm install ai-rxos infra/helm/ai-rxos -f values.yaml -f values-dev.yaml +global: + environment: development + imageRegistry: "" # use locally-built images (docker compose / kind load) + imagePullPolicy: IfNotPresent + +ingress: + enabled: false # use kubectl port-forward locally instead + +postgresql: + enabled: true +redis: + enabled: true +neo4j: + enabled: true +opensearch: + enabled: true + +externalSecret: + enabled: false diff --git a/infra/helm/ai-rxos/values-prod.yaml b/infra/helm/ai-rxos/values-prod.yaml new file mode 100644 index 0000000..cfbe784 --- /dev/null +++ b/infra/helm/ai-rxos/values-prod.yaml @@ -0,0 +1,53 @@ +## Prod overlay: helm install ai-rxos infra/helm/ai-rxos -f values.yaml -f values-prod.yaml +## Disables in-cluster stateful dependencies in favor of managed services +## (see architecture/07-deployment-architecture.md), and requires secrets to +## be pre-provisioned out-of-band rather than templated from values. +global: + environment: production + imageRegistry: "ghcr.io/openhealthagents" + imagePullPolicy: IfNotPresent + +ingress: + enabled: true + tls: + enabled: true + hosts: + web: app.ai-rxos.com + admin: admin.ai-rxos.com + api: api.ai-rxos.com + +# Managed AWS services instead of in-cluster StatefulSets: +postgresql: + enabled: false +redis: + enabled: false +neo4j: + enabled: false +opensearch: + enabled: false + +config: + postgresHost: "ai-rxos-prod.cluster-xxxx.us-east-1.rds.amazonaws.com" + postgresPort: "5432" + postgresDb: ai_rxos + postgresUser: ai_rxos + neo4jUri: "bolt+s://ai-rxos-prod.databases.neo4j.io:7687" + neo4jUser: neo4j + redisUrl: "rediss://ai-rxos-prod.xxxxx.cache.amazonaws.com:6379/0" + opensearchUrl: "https://vpc-ai-rxos-search-xxxx.us-east-1.es.amazonaws.com" + opensearchUser: admin + corsAllowOrigin: "https://app.ai-rxos.com" + +# Secrets are provisioned by External Secrets Operator from AWS Secrets +# Manager in prod — the chart never templates real credentials for this env. +externalSecret: + enabled: true + name: ai-rxos-secrets + +services: + web: { autoscaling: { minReplicas: 3, maxReplicas: 12 } } + admin: { autoscaling: { minReplicas: 2, maxReplicas: 6 } } + api-gateway: { autoscaling: { minReplicas: 5, maxReplicas: 20 } } + docking: + gpu: { enabled: true } + autoscaling: { minReplicas: 2, maxReplicas: 20 } diff --git a/infra/helm/ai-rxos/values.yaml b/infra/helm/ai-rxos/values.yaml new file mode 100644 index 0000000..274bab5 --- /dev/null +++ b/infra/helm/ai-rxos/values.yaml @@ -0,0 +1,319 @@ +## Default values for ai-rxos. See values-dev.yaml / values-prod.yaml for +## environment overlays (helm install -f values.yaml -f values-.yaml). + +global: + environment: development + imageRegistry: "ghcr.io/openhealthagents" + imagePullPolicy: IfNotPresent + imagePullSecrets: [] + +namespaceOverride: "" +nameOverride: "" +fullnameOverride: "" + +serviceAccount: + create: true + name: "" + annotations: {} + +podSecurityContext: + runAsNonRoot: true + fsGroup: 1000 + +securityContext: + allowPrivilegeEscalation: false + readOnlyRootFilesystem: false + capabilities: + drop: ["ALL"] + +ingress: + enabled: true + className: nginx + annotations: + cert-manager.io/cluster-issuer: letsencrypt-prod + nginx.ingress.kubernetes.io/proxy-body-size: 25m + tls: + enabled: false + secretName: ai-rxos-tls + hosts: + web: app.ai-rxos.local + admin: admin.ai-rxos.local + api: api.ai-rxos.local + +# Dev/staging: spin these up in-cluster via the chart dependencies. +# Prod: set each to `enabled: false` and point `config.*` at managed +# equivalents (RDS, ElastiCache, Neo4j Aura/causal cluster, AWS OpenSearch). +## Encryption at rest (self-hosted/dev clusters only): leave storageClass +## empty to use the cluster default, or point it at a StorageClass backed +## by an encrypted CSI driver/volume type (e.g. "gp3-encrypted" on EBS, +## "encrypted-rwo" on GKE). This chart cannot encrypt volumes itself — it +## only passes the StorageClass through to each subchart. Prod +## (values-prod.yaml) disables these subcharts entirely and relies on the +## managed AWS services' own at-rest encryption instead, which this +## setting does not affect. +postgresql: + enabled: true + auth: + username: ai_rxos + password: changeme + database: ai_rxos + image: + repository: pgvector/pgvector + tag: pg16 + primary: + persistence: + size: 20Gi + storageClass: "" + +redis: + enabled: true + architecture: standalone + auth: + enabled: false + master: + persistence: + size: 5Gi + storageClass: "" + +neo4j: + enabled: true + neo4j: + name: ai-rxos + password: changeme_neo4j + volumes: + data: + mode: dynamic + dynamic: + # For at-rest encryption, point this at an encrypted StorageClass + # instead (see comment above postgresql:). + storageClassName: standard + requests: + storage: 50Gi + +opensearch: + enabled: true + singleNode: true + replicas: 1 + persistence: + size: 20Gi + storageClass: "" + +# Non-secret runtime config, injected into every service as a ConfigMap. +# Hostnames match the in-cluster dependency release names by default; +# override in values-prod.yaml with managed-service endpoints. +config: + postgresHost: ai-rxos-postgresql + postgresPort: "5432" + postgresDb: ai_rxos + postgresUser: ai_rxos + neo4jUri: "bolt://ai-rxos-neo4j:7687" + neo4jUser: neo4j + redisUrl: "redis://ai-rxos-redis-master:6379/0" + opensearchUrl: "http://ai-rxos-opensearch-cluster-master:9200" + opensearchUser: admin + corsAllowOrigin: "https://app.ai-rxos.local" + # services/search retrieval provider selection (see + # services/search/internal/search/provider.go). pgvector is the default + # and only implemented backend; llm_wiki/google_okf are placeholders. + searchRetrievalProvider: "pgvector" + llmWikiUrl: "" + googleOkfUrl: "" + +# Secrets: for dev this seeds a Kubernetes Secret directly from values +# (fine for local clusters, NOT for prod). In prod, set +# externalSecret.enabled=true and pre-provision `externalSecret.name` +# via e.g. External Secrets Operator / Sealed Secrets / Vault. +externalSecret: + enabled: false + name: ai-rxos-secrets + # Used only when enabled=true (see templates/external-secret.yaml). + secretStoreRef: + name: ai-rxos-secret-store + kind: ClusterSecretStore + refreshInterval: 1h + +secrets: + postgresPassword: changeme + neo4jPassword: changeme_neo4j + redisPassword: "" + opensearchPassword: AiRxOS#Search9K + jwtSecret: change_this_dev_secret_before_deploying + # services/auth-adapter (BetterAuth scaffold) — see + # services/auth-adapter/README.md. + betterAuthSecret: change_this_dev_secret_before_deploying + # services/search placeholder retrieval providers — empty until real + # credentials exist (see services/search/README.md). + llmWikiApiKey: "" + googleOkfApiKey: "" + +# One entry per deployable unit. `ingressPath` is only set for +# externally-routed services (web, admin, api-gateway); everything else is +# ClusterIP-only, reached through api-gateway. +services: + web: + enabled: true + image: { repository: web, tag: latest } + port: 3000 + replicas: 2 + healthPath: /api/health + ingress: { host: web, path: / } + resources: + requests: { cpu: 100m, memory: 256Mi } + limits: { cpu: 500m, memory: 512Mi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 6, targetCPUUtilizationPercentage: 70 } + env: + NEXT_PUBLIC_API_BASE_URL: "https://api.ai-rxos.local" + + admin: + enabled: true + image: { repository: admin, tag: latest } + port: 3001 + replicas: 2 + healthPath: /api/health + ingress: { host: admin, path: / } + resources: + requests: { cpu: 100m, memory: 256Mi } + limits: { cpu: 500m, memory: 512Mi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 4, targetCPUUtilizationPercentage: 70 } + env: + NEXT_PUBLIC_API_BASE_URL: "https://api.ai-rxos.local" + + api-gateway: + enabled: true + image: { repository: api-gateway, tag: latest } + port: 8080 + replicas: 3 + healthPath: /healthz + ingress: { host: api, path: / } + resources: + requests: { cpu: 250m, memory: 256Mi } + limits: { cpu: 1000m, memory: 512Mi } + autoscaling: { enabled: true, minReplicas: 3, maxReplicas: 10, targetCPUUtilizationPercentage: 70 } + env: + CORS_ALLOW_ORIGIN: "https://app.ai-rxos.local" + + auth: + enabled: true + image: { repository: auth, tag: latest } + port: 8081 + replicas: 3 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 256Mi } + limits: { cpu: 1000m, memory: 512Mi } + autoscaling: { enabled: true, minReplicas: 3, maxReplicas: 10, targetCPUUtilizationPercentage: 70 } + + # BetterAuth adapter scaffold (see services/auth-adapter/README.md). + # Additive: services/auth above is unchanged and still owns + # /api/v1/auth/*. Not on any ingress path yet. + auth-adapter: + enabled: true + image: { repository: auth-adapter, tag: latest } + port: 8089 + replicas: 1 + healthPath: /healthz + resources: + requests: { cpu: 100m, memory: 256Mi } + limits: { cpu: 500m, memory: 512Mi } + autoscaling: { enabled: false } + + literature: + enabled: true + image: { repository: literature, tag: latest } + port: 8082 + replicas: 2 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 512Mi } + limits: { cpu: 1000m, memory: 1Gi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 8, targetCPUUtilizationPercentage: 70 } + + kg: + enabled: true + image: { repository: kg, tag: latest } + port: 8083 + replicas: 2 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 512Mi } + limits: { cpu: 1000m, memory: 1Gi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 6, targetCPUUtilizationPercentage: 70 } + + search: + enabled: true + image: { repository: search, tag: latest } + port: 8084 + replicas: 2 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 256Mi } + limits: { cpu: 1000m, memory: 512Mi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 8, targetCPUUtilizationPercentage: 70 } + + agents: + enabled: true + image: { repository: agents, tag: latest } + port: 8085 + replicas: 2 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 512Mi } + limits: { cpu: 1000m, memory: 1Gi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 8, targetCPUUtilizationPercentage: 70 } + + workflows: + enabled: true + image: { repository: workflows, tag: latest } + port: 8086 + replicas: 2 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 256Mi } + limits: { cpu: 1000m, memory: 512Mi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 6, targetCPUUtilizationPercentage: 70 } + + reports: + enabled: true + image: { repository: reports, tag: latest } + port: 8087 + replicas: 2 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 256Mi } + limits: { cpu: 1000m, memory: 512Mi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 4, targetCPUUtilizationPercentage: 70 } + + docking: + enabled: true + image: { repository: docking, tag: latest } + port: 8088 + replicas: 2 + healthPath: /healthz + gpu: + enabled: false # flip true + set nodeSelector/tolerations for GPU node pools in prod + resources: + requests: { cpu: 500m, memory: 1Gi } + limits: { cpu: 2000m, memory: 4Gi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 6, targetCPUUtilizationPercentage: 70 } + + ai-services: + enabled: true + image: { repository: ai-services, tag: latest } + port: 8090 + replicas: 2 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 512Mi } + limits: { cpu: 1000m, memory: 1Gi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 8, targetCPUUtilizationPercentage: 70 } + + knowledge-service: + enabled: true + image: { repository: knowledge-service, tag: latest } + port: 8091 + replicas: 2 + healthPath: /healthz + resources: + requests: { cpu: 250m, memory: 256Mi } + limits: { cpu: 1000m, memory: 512Mi } + autoscaling: { enabled: true, minReplicas: 2, maxReplicas: 6, targetCPUUtilizationPercentage: 70 } diff --git a/infra/k8s/namespaces.yaml b/infra/k8s/namespaces.yaml new file mode 100644 index 0000000..196804d --- /dev/null +++ b/infra/k8s/namespaces.yaml @@ -0,0 +1,34 @@ +# Raw namespace manifests — apply once per cluster, ahead of any Helm release. +# See architecture/07-deployment-architecture.md "Kubernetes Namespaces". +apiVersion: v1 +kind: Namespace +metadata: + name: ai-rxos-production + labels: { environment: production } +--- +apiVersion: v1 +kind: Namespace +metadata: + name: ai-rxos-staging + labels: { environment: staging } +--- +apiVersion: v1 +kind: Namespace +metadata: + name: ai-rxos-development + labels: { environment: development } +--- +apiVersion: v1 +kind: Namespace +metadata: + name: monitoring +--- +apiVersion: v1 +kind: Namespace +metadata: + name: infrastructure +--- +apiVersion: v1 +kind: Namespace +metadata: + name: gpu-workloads diff --git a/infra/k8s/network-policies.yaml b/infra/k8s/network-policies.yaml new file mode 100644 index 0000000..fb2da7f --- /dev/null +++ b/infra/k8s/network-policies.yaml @@ -0,0 +1,41 @@ +# Default-deny per app namespace, with DNS carved out. Mirrors +# architecture/07-deployment-architecture.md "Network Policies"; extend with +# explicit allow rules per service as they're added. +# Plain manifests — not Helm-templated, applied directly with kubectl. +apiVersion: networking.k8s.io/v1 +kind: NetworkPolicy +metadata: + name: deny-all + namespace: ai-rxos-production +spec: + podSelector: {} + policyTypes: [Ingress, Egress] +--- +apiVersion: networking.k8s.io/v1 +kind: NetworkPolicy +metadata: + name: allow-dns + namespace: ai-rxos-production +spec: + podSelector: {} + policyTypes: [Egress] + egress: + - to: + - namespaceSelector: + matchLabels: { kubernetes.io/metadata.name: kube-system } + ports: + - { protocol: UDP, port: 53 } + - { protocol: TCP, port: 53 } +--- +apiVersion: networking.k8s.io/v1 +kind: NetworkPolicy +metadata: + name: allow-intra-namespace + namespace: ai-rxos-production +spec: + podSelector: {} + policyTypes: [Ingress] + ingress: + - from: + - namespaceSelector: + matchLabels: { kubernetes.io/metadata.name: ai-rxos-production } diff --git a/infra/postgres/init.sql b/infra/postgres/init.sql new file mode 100644 index 0000000..eea58cb --- /dev/null +++ b/infra/postgres/init.sql @@ -0,0 +1,3 @@ +-- Runs once on first postgres container boot (docker-entrypoint-initdb.d). +CREATE EXTENSION IF NOT EXISTS vector; +CREATE EXTENSION IF NOT EXISTS "uuid-ossp"; diff --git a/package.json b/package.json new file mode 100644 index 0000000..510a6ad --- /dev/null +++ b/package.json @@ -0,0 +1,30 @@ +{ + "name": "ai-rxos", + "version": "0.1.0", + "private": true, + "description": "AI-RxOS monorepo — AI-native drug discovery operating system", + "packageManager": "pnpm@9.15.0", + "engines": { + "node": ">=20.0.0", + "pnpm": ">=9.0.0" + }, + "scripts": { + "build": "turbo run build", + "dev": "turbo run dev --parallel", + "lint": "turbo run lint", + "test": "turbo run test", + "typecheck": "turbo run typecheck", + "clean": "turbo run clean && rimraf node_modules", + "format": "prettier --write \"**/*.{ts,tsx,js,jsx,json,md,yml,yaml}\" --ignore-path .gitignore", + "format:check": "prettier --check \"**/*.{ts,tsx,js,jsx,json,md,yml,yaml}\" --ignore-path .gitignore", + "compose:up": "docker compose up --build -d", + "compose:down": "docker compose down", + "compose:logs": "docker compose logs -f" + }, + "devDependencies": { + "prettier": "^3.3.3", + "rimraf": "^6.0.1", + "turbo": "^2.3.3", + "typescript": "^5.7.2" + } +} diff --git a/packages/audit-log/.eslintrc.js b/packages/audit-log/.eslintrc.js new file mode 100644 index 0000000..75a60d0 --- /dev/null +++ b/packages/audit-log/.eslintrc.js @@ -0,0 +1 @@ +module.exports = { root: true, extends: ["@ai-rxos/eslint-config"] }; diff --git a/packages/audit-log/package.json b/packages/audit-log/package.json new file mode 100644 index 0000000..31b3630 --- /dev/null +++ b/packages/audit-log/package.json @@ -0,0 +1,33 @@ +{ + "name": "@ai-rxos/audit-log", + "version": "0.1.0", + "private": true, + "main": "./dist/index.js", + "module": "./dist/index.mjs", + "types": "./dist/index.d.ts", + "exports": { + ".": { + "types": "./dist/index.d.ts", + "import": "./dist/index.mjs", + "require": "./dist/index.js" + } + }, + "scripts": { + "build": "tsup src/index.ts --format esm,cjs --dts", + "dev": "tsup src/index.ts --format esm,cjs --dts --watch", + "lint": "eslint src --max-warnings 0", + "typecheck": "tsc --noEmit", + "clean": "rimraf dist .turbo" + }, + "dependencies": { + "zod": "^3.24.1" + }, + "devDependencies": { + "@ai-rxos/eslint-config": "workspace:*", + "@ai-rxos/typescript-config": "workspace:*", + "eslint": "^8.57.1", + "rimraf": "^6.0.1", + "tsup": "^8.3.5", + "typescript": "^5.7.2" + } +} diff --git a/packages/audit-log/src/index.ts b/packages/audit-log/src/index.ts new file mode 100644 index 0000000..e3fd7af --- /dev/null +++ b/packages/audit-log/src/index.ts @@ -0,0 +1,27 @@ +import { z } from "zod"; + +/** + * Shared audit-event contract for AI-RxOS. This package defines the event + * shape and a pluggable sink interface only — no persistence backend + * exists yet (no audit table, queue, or consumer exists anywhere in this + * repo as of this scaffold). Implement AuditLogSink against a real + * backend (e.g. a Postgres audit_log table, written from within the same + * request transaction as the action it records) before relying on this + * for anything. + */ + +export const AuditEventSchema = z.object({ + id: z.string().uuid(), + tenantId: z.string().uuid().optional(), + actorId: z.string().uuid().optional(), + action: z.string(), + resourceType: z.string(), + resourceId: z.string().optional(), + metadata: z.record(z.string(), z.unknown()).default({}), + createdAt: z.string().datetime(), +}); +export type AuditEvent = z.infer; + +export interface AuditLogSink { + record(event: AuditEvent): Promise; +} diff --git a/packages/audit-log/tsconfig.json b/packages/audit-log/tsconfig.json new file mode 100644 index 0000000..932c2c0 --- /dev/null +++ b/packages/audit-log/tsconfig.json @@ -0,0 +1,8 @@ +{ + "extends": "@ai-rxos/typescript-config/base.json", + "compilerOptions": { + "outDir": "dist", + "rootDir": "src" + }, + "include": ["src"] +} diff --git a/packages/sdk/.eslintrc.js b/packages/sdk/.eslintrc.js new file mode 100644 index 0000000..75a60d0 --- /dev/null +++ b/packages/sdk/.eslintrc.js @@ -0,0 +1 @@ +module.exports = { root: true, extends: ["@ai-rxos/eslint-config"] }; diff --git a/packages/sdk/package.json b/packages/sdk/package.json new file mode 100644 index 0000000..9112377 --- /dev/null +++ b/packages/sdk/package.json @@ -0,0 +1,33 @@ +{ + "name": "@ai-rxos/sdk", + "version": "0.1.0", + "private": true, + "main": "./dist/index.js", + "module": "./dist/index.mjs", + "types": "./dist/index.d.ts", + "exports": { + ".": { + "types": "./dist/index.d.ts", + "import": "./dist/index.mjs", + "require": "./dist/index.js" + } + }, + "scripts": { + "build": "tsup src/index.ts --format esm,cjs --dts", + "dev": "tsup src/index.ts --format esm,cjs --dts --watch", + "lint": "eslint src --max-warnings 0", + "typecheck": "tsc --noEmit", + "clean": "rimraf dist .turbo" + }, + "dependencies": { + "@ai-rxos/types": "workspace:*" + }, + "devDependencies": { + "@ai-rxos/eslint-config": "workspace:*", + "@ai-rxos/typescript-config": "workspace:*", + "eslint": "^8.57.1", + "rimraf": "^6.0.1", + "tsup": "^8.3.5", + "typescript": "^5.7.2" + } +} diff --git a/packages/sdk/src/client.ts b/packages/sdk/src/client.ts new file mode 100644 index 0000000..851ff7c --- /dev/null +++ b/packages/sdk/src/client.ts @@ -0,0 +1,54 @@ +export interface AiRxOsClientOptions { + baseUrl: string; + apiKey?: string; + fetchImpl?: typeof fetch; +} + +export class ApiRequestError extends Error { + constructor( + public status: number, + public code: string, + message: string, + ) { + super(message); + this.name = "ApiRequestError"; + } +} + +export class AiRxOsClient { + private readonly baseUrl: string; + private readonly apiKey?: string; + private readonly fetchImpl: typeof fetch; + + constructor(options: AiRxOsClientOptions) { + this.baseUrl = options.baseUrl.replace(/\/$/, ""); + this.apiKey = options.apiKey; + this.fetchImpl = options.fetchImpl ?? fetch; + } + + async request(path: string, init: RequestInit = {}): Promise { + const headers = new Headers(init.headers); + headers.set("Content-Type", "application/json"); + if (this.apiKey) headers.set("Authorization", `Bearer ${this.apiKey}`); + + const res = await this.fetchImpl(`${this.baseUrl}${path}`, { ...init, headers }); + if (!res.ok) { + const body = await res.json().catch(() => ({})); + throw new ApiRequestError( + res.status, + body.code ?? "unknown_error", + body.message ?? res.statusText, + ); + } + if (res.status === 204) return undefined as T; + return (await res.json()) as T; + } + + get(path: string) { + return this.request(path, { method: "GET" }); + } + + post(path: string, body?: unknown) { + return this.request(path, { method: "POST", body: body ? JSON.stringify(body) : undefined }); + } +} diff --git a/packages/sdk/src/index.ts b/packages/sdk/src/index.ts new file mode 100644 index 0000000..33a87f1 --- /dev/null +++ b/packages/sdk/src/index.ts @@ -0,0 +1,2 @@ +export * from "./client"; +export * from "./resources"; diff --git a/packages/sdk/src/resources.ts b/packages/sdk/src/resources.ts new file mode 100644 index 0000000..148941c --- /dev/null +++ b/packages/sdk/src/resources.ts @@ -0,0 +1,40 @@ +import type { + AgentTask, + DockingResult, + Molecule, + Paginated, + Paper, + Report, + SearchResult, +} from "@ai-rxos/types"; +import type { AiRxOsClient } from "./client"; + +/** Thin typed wrappers over api-gateway routes. See architecture/03-api-contracts.md. */ + +export const search = (client: AiRxOsClient) => ({ + query: (q: string, limit = 20) => + client.get>(`/api/v1/search?q=${encodeURIComponent(q)}&limit=${limit}`), +}); + +export const literature = (client: AiRxOsClient) => ({ + list: (page = 1) => client.get>(`/api/v1/papers?page=${page}`), + get: (id: string) => client.get(`/api/v1/papers/${id}`), +}); + +export const molecules = (client: AiRxOsClient) => ({ + list: (page = 1) => client.get>(`/api/v1/molecules?page=${page}`), + dock: (moleculeId: string, targetId: string) => + client.post(`/api/v1/docking`, { moleculeId, targetId }), +}); + +export const agents = (client: AiRxOsClient) => ({ + run: (agentType: string, input: Record) => + client.post(`/api/v1/agents/run`, { agentType, input }), + get: (id: string) => client.get(`/api/v1/agents/tasks/${id}`), +}); + +export const reports = (client: AiRxOsClient) => ({ + list: (page = 1) => client.get>(`/api/v1/reports?page=${page}`), + generate: (title: string, type: Report["type"]) => + client.post(`/api/v1/reports`, { title, type }), +}); diff --git a/packages/sdk/tsconfig.json b/packages/sdk/tsconfig.json new file mode 100644 index 0000000..8880f35 --- /dev/null +++ b/packages/sdk/tsconfig.json @@ -0,0 +1,9 @@ +{ + "extends": "@ai-rxos/typescript-config/base.json", + "compilerOptions": { + "outDir": "dist", + "rootDir": "src", + "lib": ["ES2022", "DOM"] + }, + "include": ["src"] +} diff --git a/packages/tenancy/.eslintrc.js b/packages/tenancy/.eslintrc.js new file mode 100644 index 0000000..75a60d0 --- /dev/null +++ b/packages/tenancy/.eslintrc.js @@ -0,0 +1 @@ +module.exports = { root: true, extends: ["@ai-rxos/eslint-config"] }; diff --git a/packages/tenancy/package.json b/packages/tenancy/package.json new file mode 100644 index 0000000..1cba03c --- /dev/null +++ b/packages/tenancy/package.json @@ -0,0 +1,33 @@ +{ + "name": "@ai-rxos/tenancy", + "version": "0.1.0", + "private": true, + "main": "./dist/index.js", + "module": "./dist/index.mjs", + "types": "./dist/index.d.ts", + "exports": { + ".": { + "types": "./dist/index.d.ts", + "import": "./dist/index.mjs", + "require": "./dist/index.js" + } + }, + "scripts": { + "build": "tsup src/index.ts --format esm,cjs --dts", + "dev": "tsup src/index.ts --format esm,cjs --dts --watch", + "lint": "eslint src --max-warnings 0", + "typecheck": "tsc --noEmit", + "clean": "rimraf dist .turbo" + }, + "dependencies": { + "zod": "^3.24.1" + }, + "devDependencies": { + "@ai-rxos/eslint-config": "workspace:*", + "@ai-rxos/typescript-config": "workspace:*", + "eslint": "^8.57.1", + "rimraf": "^6.0.1", + "tsup": "^8.3.5", + "typescript": "^5.7.2" + } +} diff --git a/packages/tenancy/src/index.ts b/packages/tenancy/src/index.ts new file mode 100644 index 0000000..906decc --- /dev/null +++ b/packages/tenancy/src/index.ts @@ -0,0 +1,30 @@ +import { z } from "zod"; + +/** + * Shared multi-tenancy conventions for AI-RxOS. This package only defines + * the contract (naming + types) — it does not enforce anything itself. + * + * The Postgres side of this contract lives in each Go service's schema + * migration (services/auth/internal/store/postgres.go, + * services/search/internal/search/pgvector.go): both enable Row Level + * Security with a policy that reads TENANT_SESSION_VARIABLE via + * Postgres's current_setting(). No caller sets that session variable yet + * (see README.md "Row Level Security" for what's still required); until + * one does, the RLS policies fail open and behave exactly as before. + */ + +/** Postgres session variable RLS policies key on, set per-request via `SET LOCAL = ''`. */ +export const TENANT_SESSION_VARIABLE = "app.tenant_id"; + +/** HTTP header a gateway/service should use to propagate the resolved tenant downstream. Not yet emitted or read anywhere. */ +export const TENANT_ID_HEADER = "X-Organization-Id"; + +/** JWT claim name a tenant-aware token issuer should use for the tenant id. Not yet emitted by services/auth or services/auth-adapter. */ +export const TENANT_ID_CLAIM = "organizationId"; + +export const TenantIdSchema = z.string().uuid(); +export type TenantId = z.infer; + +export interface TenantContext { + tenantId: TenantId; +} diff --git a/packages/tenancy/tsconfig.json b/packages/tenancy/tsconfig.json new file mode 100644 index 0000000..932c2c0 --- /dev/null +++ b/packages/tenancy/tsconfig.json @@ -0,0 +1,8 @@ +{ + "extends": "@ai-rxos/typescript-config/base.json", + "compilerOptions": { + "outDir": "dist", + "rootDir": "src" + }, + "include": ["src"] +} diff --git a/packages/types/.eslintrc.js b/packages/types/.eslintrc.js new file mode 100644 index 0000000..75a60d0 --- /dev/null +++ b/packages/types/.eslintrc.js @@ -0,0 +1 @@ +module.exports = { root: true, extends: ["@ai-rxos/eslint-config"] }; diff --git a/packages/types/package.json b/packages/types/package.json new file mode 100644 index 0000000..f4907c4 --- /dev/null +++ b/packages/types/package.json @@ -0,0 +1,33 @@ +{ + "name": "@ai-rxos/types", + "version": "0.1.0", + "private": true, + "main": "./dist/index.js", + "module": "./dist/index.mjs", + "types": "./dist/index.d.ts", + "exports": { + ".": { + "types": "./dist/index.d.ts", + "import": "./dist/index.mjs", + "require": "./dist/index.js" + } + }, + "scripts": { + "build": "tsup src/index.ts --format esm,cjs --dts", + "dev": "tsup src/index.ts --format esm,cjs --dts --watch", + "lint": "eslint src --max-warnings 0", + "typecheck": "tsc --noEmit", + "clean": "rimraf dist .turbo" + }, + "dependencies": { + "zod": "^3.24.1" + }, + "devDependencies": { + "@ai-rxos/eslint-config": "workspace:*", + "@ai-rxos/typescript-config": "workspace:*", + "eslint": "^8.57.1", + "rimraf": "^6.0.1", + "tsup": "^8.3.5", + "typescript": "^5.7.2" + } +} diff --git a/packages/types/src/index.ts b/packages/types/src/index.ts new file mode 100644 index 0000000..8c8a74e --- /dev/null +++ b/packages/types/src/index.ts @@ -0,0 +1,99 @@ +import { z } from "zod"; + +/** Shared domain types for the AI-RxOS platform. Mirrors architecture/03-api-contracts.md. */ + +export const UserSchema = z.object({ + id: z.string().uuid(), + email: z.string().email(), + displayName: z.string(), + organizationId: z.string().uuid(), + roles: z.array(z.string()), + createdAt: z.string().datetime(), +}); +export type User = z.infer; + +export const OrganizationSchema = z.object({ + id: z.string().uuid(), + name: z.string(), + slug: z.string(), + plan: z.enum(["free", "team", "enterprise"]), +}); +export type Organization = z.infer; + +export const PaperSchema = z.object({ + id: z.string().uuid(), + title: z.string(), + abstract: z.string().optional(), + source: z.enum(["pubmed", "biorxiv", "medrxiv", "patent", "conference"]), + doi: z.string().optional(), + publishedAt: z.string().datetime().optional(), + citationCount: z.number().int().nonnegative().default(0), +}); +export type Paper = z.infer; + +export const GraphEntitySchema = z.object({ + id: z.string(), + label: z.string(), + type: z.enum(["gene", "protein", "disease", "drug", "pathway", "compound"]), + properties: z.record(z.string(), z.unknown()).default({}), +}); +export type GraphEntity = z.infer; + +export const MoleculeSchema = z.object({ + id: z.string().uuid(), + smiles: z.string(), + name: z.string().optional(), + molecularWeight: z.number().optional(), + logP: z.number().optional(), +}); +export type Molecule = z.infer; + +export const DockingResultSchema = z.object({ + id: z.string().uuid(), + moleculeId: z.string().uuid(), + targetId: z.string(), + bindingAffinity: z.number(), + pose: z.string().optional(), + status: z.enum(["queued", "running", "completed", "failed"]), +}); +export type DockingResult = z.infer; + +export const AgentTaskSchema = z.object({ + id: z.string().uuid(), + agentType: z.string(), + input: z.record(z.string(), z.unknown()), + status: z.enum(["pending", "running", "succeeded", "failed"]), + result: z.record(z.string(), z.unknown()).optional(), +}); +export type AgentTask = z.infer; + +export const SearchResultSchema = z.object({ + id: z.string(), + score: z.number(), + source: z.enum(["opensearch", "pgvector", "graph"]), + title: z.string(), + snippet: z.string().optional(), +}); +export type SearchResult = z.infer; + +export const ReportSchema = z.object({ + id: z.string().uuid(), + title: z.string(), + type: z.enum(["scientific", "competitive", "due-diligence", "executive"]), + status: z.enum(["draft", "generating", "ready", "failed"]), + createdAt: z.string().datetime(), +}); +export type Report = z.infer; + +export interface Paginated { + items: T[]; + total: number; + page: number; + pageSize: number; +} + +export interface ApiError { + code: string; + message: string; + details?: Record; +} diff --git a/packages/types/tsconfig.json b/packages/types/tsconfig.json new file mode 100644 index 0000000..932c2c0 --- /dev/null +++ b/packages/types/tsconfig.json @@ -0,0 +1,8 @@ +{ + "extends": "@ai-rxos/typescript-config/base.json", + "compilerOptions": { + "outDir": "dist", + "rootDir": "src" + }, + "include": ["src"] +} diff --git a/packages/ui/.eslintrc.js b/packages/ui/.eslintrc.js new file mode 100644 index 0000000..5ade715 --- /dev/null +++ b/packages/ui/.eslintrc.js @@ -0,0 +1 @@ +module.exports = { root: true, extends: ["@ai-rxos/eslint-config/react-library.js"] }; diff --git a/packages/ui/package.json b/packages/ui/package.json new file mode 100644 index 0000000..a9b035c --- /dev/null +++ b/packages/ui/package.json @@ -0,0 +1,39 @@ +{ + "name": "@ai-rxos/ui", + "version": "0.1.0", + "private": true, + "main": "./dist/index.js", + "module": "./dist/index.mjs", + "types": "./dist/index.d.ts", + "exports": { + ".": { + "types": "./dist/index.d.ts", + "import": "./dist/index.mjs", + "require": "./dist/index.js" + }, + "./styles.css": "./dist/styles.css" + }, + "scripts": { + "build": "tsup src/index.ts --format esm,cjs --dts --external react", + "dev": "tsup src/index.ts --format esm,cjs --dts --external react --watch", + "lint": "eslint src --max-warnings 0", + "typecheck": "tsc --noEmit", + "clean": "rimraf dist .turbo" + }, + "peerDependencies": { + "react": "^18.3.1", + "react-dom": "^18.3.1" + }, + "devDependencies": { + "@ai-rxos/eslint-config": "workspace:*", + "@ai-rxos/typescript-config": "workspace:*", + "@types/react": "^18.3.18", + "@types/react-dom": "^18.3.5", + "eslint": "^8.57.1", + "react": "^18.3.1", + "react-dom": "^18.3.1", + "rimraf": "^6.0.1", + "tsup": "^8.3.5", + "typescript": "^5.7.2" + } +} diff --git a/packages/ui/src/Badge.tsx b/packages/ui/src/Badge.tsx new file mode 100644 index 0000000..6f9ceee --- /dev/null +++ b/packages/ui/src/Badge.tsx @@ -0,0 +1,18 @@ +import * as React from "react"; + +export interface BadgeProps extends React.HTMLAttributes { + tone?: "neutral" | "success" | "warning" | "danger" | "info"; +} + +const TONE_CLASS: Record, string> = { + neutral: "rxos-badge-neutral", + success: "rxos-badge-success", + warning: "rxos-badge-warning", + danger: "rxos-badge-danger", + info: "rxos-badge-info", +}; + +export function Badge({ tone = "neutral", className, ...props }: BadgeProps) { + const classes = ["rxos-badge", TONE_CLASS[tone], className].filter(Boolean).join(" "); + return ; +} diff --git a/packages/ui/src/Button.tsx b/packages/ui/src/Button.tsx new file mode 100644 index 0000000..927b2e5 --- /dev/null +++ b/packages/ui/src/Button.tsx @@ -0,0 +1,29 @@ +import * as React from "react"; + +export interface ButtonProps extends React.ButtonHTMLAttributes { + variant?: "primary" | "secondary" | "ghost" | "danger"; + size?: "sm" | "md" | "lg"; +} + +const VARIANT_CLASS: Record, string> = { + primary: "rxos-btn-primary", + secondary: "rxos-btn-secondary", + ghost: "rxos-btn-ghost", + danger: "rxos-btn-danger", +}; + +const SIZE_CLASS: Record, string> = { + sm: "rxos-btn-sm", + md: "rxos-btn-md", + lg: "rxos-btn-lg", +}; + +export const Button = React.forwardRef( + ({ variant = "primary", size = "md", className, ...props }, ref) => { + const classes = ["rxos-btn", VARIANT_CLASS[variant], SIZE_CLASS[size], className] + .filter(Boolean) + .join(" "); + return