feat: implement CLI entrypoints and minimize docker image size

services/fermentaladin-service/.dockerignore

@@ -0,0 +1,10 @@
+test/
+http-tests/
+*.md
+.gitignore
+.demo.env
+Makefile
+__pycache__/
+.ruff_cache/
+.git/
+.venv/

services/fermentaladin-service/Dockerfile

@@ -1,26 +1,24 @@
-FROM python:3.12-slim-trixie
-
-# The installer requires curl (and certificates) to download the release archive
-RUN apt-get update && apt-get install -y --no-install-recommends curl ca-certificates \
-    && rm -rf /var/lib/apt/lists/*
+# ---- build stage ----
+FROM python:3.12-slim-trixie AS builder
 
-# Download the latest installer
-ADD https://astral.sh/uv/install.sh /uv-installer.sh
+COPY --from=ghcr.io/astral-sh/uv:0.11.7 /uv /uvx /bin/
 
-# Run the installer then remove it
-RUN sh /uv-installer.sh && rm /uv-installer.sh
+COPY . /app
+WORKDIR /app
 
-# Ensure the installed binary is on the `PATH`
-ENV PATH="/root/.local/bin/:$PATH"
+# Sync into the project virtual environment; exclude dev dependencies
+RUN uv sync --locked --no-dev
 
-# Copy the project into the image
-COPY . /app
+# ---- runtime stage ----
+FROM python:3.12-slim-trixie
 
-# Sync the project into a new environment, asserting the lockfile is up to date
-# --no-dev: exclude dev dependencies (pytest, ruff) from the production image
+# Copy only the application code and the ready-made virtual environment
+COPY --from=builder /app /app
 WORKDIR /app
-RUN uv sync --locked --no-dev
+
+# Place the virtual-env Python first on PATH so we don't need `uv run`
+ENV PATH="/app/.venv/bin:$PATH"
 
 EXPOSE 8000
 
-CMD ["uv", "run", "uvicorn", "api:app", "--host", "0.0.0.0", "--port", "8000", "--app-dir", "src"]
+CMD ["uvicorn", "api:app", "--host", "0.0.0.0", "--port", "8000", "--app-dir", "src"]

services/fermentaladin-service/README.md

@@ -52,6 +52,24 @@ uv run src/main.py -i excel -p ./test/Bioreactor_forPy.xlsx -o df -f ausgabe.jso
 
 This reads the model parameters from file ./test/Bioreactor_forPy.xlsx and creates a file ausgabe.json in a Dataframe format
 
+### Usage inside Docker
+
+The Docker image uses a multi-stage build and does not include `uv`. Instead, the virtual environment is already activated via `PATH`, so you run `python` directly instead of `uv run`:
+
+```sh
+# local
+uv run src/main.py -i excel -p input.xlsx -o df -f ausgabe.json
+
+# inside Docker
+python src/main.py -i excel -p input.xlsx -o df -f ausgabe.json
+```
+
+Example with `docker run`:
+
+```sh
+docker run --rm fermentaladin-service python src/main.py -i file -p ./test/test_data/user_input.json -o df -f ausgabe.json
+```
+
 ## Architecture
 
 ### Input

services/graph-rewriting-service/.env.example

@@ -1,7 +1,12 @@
-# App Environment. Can be one of: development, testing, production. Defaults to "development".
-APP_ENV=development
+# Application environment. Can be one of: development, production. Defaults to "production".
+APP_ENV=production
 
-# Connection data for neo4j docker container
-NEO4J_URI=bolt://localhost:7687
+# Database backend: "memory" (default, no external DB needed) or "neo4j"
+DB_BACKEND=memory
+
+# Neo4j connection configuration (only needed when DB_BACKEND=neo4j)
+# In docker-compose, the host is 'neo4j' (the service name).
+# When running locally, typically 'localhost'.
+NEO4J_URI=bolt://neo4j:7687
 NEO4J_USERNAME=neo4j
-NEO4J_PASSWORD=
+NEO4J_PASSWORD=your-secure-password-here

services/graph-rewriting-service/Dockerfile

@@ -1,5 +1,5 @@
 # ── Stage 1: builder ─────────────────────────────────────────────────────────
-# Compiles TypeScript to JavaScript and installs production-only dependencies.
+# Bundles TypeScript to JavaScript via esbuild.
 FROM node:22-slim AS builder
 
 WORKDIR /build
@@ -8,52 +8,47 @@ WORKDIR /build
 COPY package.json package-lock.json ./
 RUN npm ci
 
-# Copy source and compile
+# Copy source and build
 COPY tsconfig.json ./
+COPY scripts/ ./scripts/
 COPY src/ ./src/
 RUN npm run build
 
-# Prune to production deps only
-RUN npm ci --omit=dev
-
 # ── Stage 2: runtime ──────────────────────────────────────────────────────────
-# Uses the official Neo4j image as base so Neo4j is available out of the box.
-# Node 22 is installed via NodeSource.
-FROM neo4j:5.25.1
-
-# Install Node.js 22 (NodeSource) and supervisord
-RUN apt-get update && \
-    apt-get install -y --no-install-recommends curl ca-certificates supervisor && \
-    curl -fsSL https://deb.nodesource.com/setup_22.x | bash - && \
-    apt-get install -y --no-install-recommends nodejs && \
-    apt-get clean && rm -rf /var/lib/apt/lists/*
-
-# Copy compiled app and production node_modules from builder
+# @grafeo-db/js ships a native Rust addon compiled against glibc (gnu).
+# Using node:22-slim (Debian/glibc) keeps the same libc as the builder so the
+# native binding works.  node:22-alpine (musl) would require the -musl variant.
+FROM node:22-slim
+
 WORKDIR /app
-COPY --from=builder /build/dist ./dist
-COPY --from=builder /build/node_modules ./node_modules
 
-# Copy process manager config and entrypoint
-COPY supervisord.conf /etc/supervisor/conf.d/supervisord.conf
-COPY scripts/entrypoint.sh /entrypoint.sh
-RUN chmod +x /entrypoint.sh
+# Copy bundled app output from builder
+COPY --from=builder /build/dist ./dist
 
-# Create log directory for supervisord
-RUN mkdir -p /var/log/supervisor
+# @grafeo-db/js ships a native Rust addon (.node file) that cannot be bundled
+# by esbuild and is therefore externalized.  Copy the packages so both the
+# in-memory and neo4j backends are available at runtime.
+COPY --from=builder /build/node_modules/@grafeo-db ./node_modules/@grafeo-db
 
 # ── Environment defaults ───────────────────────────────────────────────────────
-# NEO4J_AUTH is constructed in entrypoint.sh from USERNAME + PASSWORD.
-# NEO4J_PASSWORD has a default, but should be supplied at runtime.
+# DB_BACKEND defaults to "memory" (no external DB needed).
+# Set DB_BACKEND=neo4j to use Neo4j and supply all three NEO4J_* vars;
+# NEO4J_PASSWORD has no default and must be provided explicitly.
 ENV APP_ENV=production \
-    NEO4J_URI=bolt://localhost:7687 \
-    NEO4J_USERNAME=neo4j \
-    NEO4J_PASSWORD=graph_rewriting
+    NODE_ENV=production \
+    NEO4J_URI=bolt://neo4j:7687 \
+    NEO4J_USERNAME=neo4j
 
-
-# ── Ports ──────────────────────────────────────────────────────────────────────
+# ── Port ────────────────────────────────────────────────────────────────────────
 # 8080  – Fastify HTTP API
-# 7474  – Neo4j Browser UI
-# 7687  – Neo4j Bolt
-EXPOSE 8080 7474 7687
+EXPOSE 8080
+
+# Health check (optional)
+HEALTHCHECK --interval=30s --timeout=3s --start-period=5s --retries=3 \
+    CMD node -e "require('http').get('http://localhost:8080/health', (r) => {if (r.statusCode !== 200) throw new Error(r.statusCode)})"
+
+# CLI is also available inside the container:
+#   docker run --rm -e NEO4J_URI=... graph-rewriting-service node dist/cli.js transform /data/request.json
 
-ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]
+# Start API server by default
+CMD ["node", "dist/index.js"]

services/graph-rewriting-service/Makefile

@@ -1,4 +1,4 @@
-.PHONY: build test lint start clean compile-schemas generate-openapi docker-build
+.PHONY: build test lint start clean compile-schemas generate-openapi docker-build smoke-test
 
 prep:
 	npm i
@@ -28,3 +28,6 @@ generate-openapi:
 
 docker-build:
 	docker build -t graph-rewriting-service .
+
+smoke-test:
+	./scripts/smoke-test.sh

services/graph-rewriting-service/README.md

@@ -2,8 +2,8 @@
 
 ## Prerequisites
 
-This repository contains all files necessary to run the application in a local development environment.
-It does depend on Docker and Node.js being available on your system.
+This repository contains all files necessary to run the application in local development and production environments.
+It requires Docker and Node.js 22+ on your system.
 
 When cloning this repository and opening it through VSCode, it will ask you to install all recommended VSCode extensions.
 
@@ -15,12 +15,86 @@ In order to install and run this application in your local development environme
 
 Next an .env file should be created by copying the .env.example and setting the appropriate values.
 
-## Running the application
+### Development Environment
 
-You may start the project by running the tasks `docker compose up` and `npm run dev` in your terminal.
+The application supports two database backends:
+
+#### In-Memory (default, no Neo4j needed)
+
+Simply start the application — no external database required:
+
+```bash
+npm run dev
+```
+
+#### With Neo4j
+
+To run with Neo4j as the database backend:
+
+1. Start Neo4j container:
+    ```bash
+    docker compose -f docker-compose.dev.yml up
+    ```
+
+2. In another terminal, start the application with neo4j backend:
+    ```bash
+    DB_BACKEND=neo4j npm run dev
+    ```
 
 If using VSCode you can instead run the VSCode-Task `Start dev environment` as a shortcut.
 
+### Production Environment (Docker + Compose)
+
+To run the application in production using Docker containers:
+
+```bash
+# Set required environment variables
+export NEO4J_PASSWORD=your-secure-password
+
+# Start both Neo4j and the application service
+docker compose -f docker-compose.prod.yml up -d
+```
+
+The application will be available at `http://localhost:8080`.  
+Neo4j Browser is accessible at `http://localhost:7474`.
+
+**Note:** As of this version, the Docker image is split into two services:
+- `graph-rewriting-service`: Node.js API server (port 8080)
+- `neo4j`: Graph database (ports 7687 for Bolt, 7474 for Browser)
+
+This separation reduces image size and enables independent scaling.
+
+## Architecture
+
+### Build Pipeline
+
+- `npm run build` now bundles the service with esbuild.
+- `npm run typecheck` runs TypeScript checks without emitting files.
+- The build emits bundled artifacts to `dist/index.js` and `dist/cli.js`.
+- Static assets from `src/static` are copied to `dist/static` during the build.
+
+### Docker Images
+
+- **graph-rewriting-service**: Lightweight Node.js container based on `node:22-alpine`
+  - Runs the Fastify HTTP API
+  - Connects to Neo4j via environment variables
+  - Contains bundled runtime artifacts only (no `node_modules` in the final image)
+  - No embedded database or process manager
+
+- **neo4j** (from official image): Graph database service
+  - Provides pattern matching and graph transformation operations
+  - Can be deployed separately or in the same compose stack
+
+### Environment Variables
+
+| Variable | Default | Required | Description |
+|----------|---------|----------|-------------|
+| `APP_ENV` | `production` | No | Application environment: `development`, `production` |
+| `DB_BACKEND` | `memory` | No | Database backend: `memory` (in-memory, no external DB) or `neo4j` |
+| `NEO4J_URI` | `bolt://neo4j:7687` | No | Neo4j Bolt connection URI (only when `DB_BACKEND=neo4j`) |
+| `NEO4J_USERNAME` | `neo4j` | No | Neo4j username (only when `DB_BACKEND=neo4j`) |
+| `NEO4J_PASSWORD` | (none) | When neo4j | Neo4j password (must be set when using neo4j backend) |
+
 ## Documentation
 
 For documentation of the rewrite and instantiation rules, please refer to the [Wiki](https://github.com/sonjaka/graph-rewriting-as-a-service/wiki).
@@ -52,6 +126,48 @@ A very simple TicTacToe game againt a computer player powered by graph transform
 This testcase consists of a very basic web app built on the Vue.js Framework.
 You can install the project by first running `npm install`, then `npm run dev`.
 
+## Testing
+
+### Unit Tests
+
+```bash
+npm test
+```
+
+### Smoke Tests
+
+End-to-end smoke tests using `curl` against a running service.
+
+#### Memory backend only (no external dependencies)
+
+```bash
+make smoke-test
+```
+
+#### Memory + Neo4j backend
+
+Start a Neo4j container first, then run the smoke test with Neo4j credentials:
+
+```bash
+# Start Neo4j
+NEO4J_USERNAME=neo4j NEO4J_PASSWORD=<your-password> \
+  docker compose -f docker-compose.dev.yml up -d neo4j
+
+# Run smoke tests for both backends
+NEO4J_URI=bolt://localhost:7687 \
+NEO4J_USERNAME=neo4j \
+NEO4J_PASSWORD=<your-password> \
+  make smoke-test
+```
+
+When `NEO4J_URI` is not set, the Neo4j portion of the smoke test is skipped automatically.
+
+#### Teardown
+
+```bash
+docker compose -f docker-compose.dev.yml down
+```
+
 ## SwaggerUI / OpenAPI
 
 When the server is running, you can access the SwaggerUI / OpenAPI documentation via the following url: