Merge pull request #63 from papagala/main

Making the dockerfile and code ready for kagent.

Author: rafiattrach

Dockerfile

@@ -27,9 +27,19 @@ RUN m3 init mimic-iv-demo
 
 # Lite: SQLite only
 FROM base AS lite
+ENV MCP_TRANSPORT=http \
+    MCP_HOST=0.0.0.0 \
+    MCP_PORT=3000 \
+    MCP_PATH=/sse
+EXPOSE 3000
 CMD ["python", "-m", "m3.mcp_server"]
 
 # BigQuery: add GCP client
 FROM base AS bigquery
 RUN pip install --no-cache-dir google-cloud-bigquery
+ENV MCP_TRANSPORT=http \
+    MCP_HOST=0.0.0.0 \
+    MCP_PORT=3000 \
+    MCP_PATH=/sse
+EXPOSE 3000
 CMD ["python", "-m", "m3.mcp_server"]

Makefile

@@ -0,0 +1,58 @@
+# Makefile for M3 Docker Image Build and Push
+DOCKER ?= docker
+IMAGE_NAME := m3-mimic-demo
+IMAGE_TAG ?= 0.4.0
+
+# Prompt for registry only if not set
+ifndef DOCKER_REGISTRY
+DOCKER_REGISTRY := $(shell bash -c 'read -p "Enter Docker registry/username: " registry; echo $${registry}')
+endif
+
+DOCKER_IMAGE := $(DOCKER_REGISTRY)/$(IMAGE_NAME):$(IMAGE_TAG)
+
+DB_FILE := m3_data/databases/mimic_iv_demo.db
+
+.PHONY: help
+help: ## Show help
+	@grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "  %-20s %s\n", $$1, $$2}'
+
+.PHONY: all
+all: download-db build push ## Complete workflow: download DB, build and push
+
+.PHONY: login
+login: ## Login to Docker Hub
+	@$(DOCKER) login docker.io
+
+.PHONY: download-db
+download-db: ## Download MIMIC-IV demo database
+	@uv sync
+	@uv run m3 init mimic-iv-demo
+
+.PHONY: build
+build: ## Build Docker image (lite version)
+	@test -f $(DB_FILE) || { echo "Run 'make download-db' first"; exit 1; }
+	@$(DOCKER) build --target lite -t $(DOCKER_IMAGE) -t $(DOCKER_REGISTRY)/$(IMAGE_NAME):lite .
+
+.PHONY: build-bigquery
+build-bigquery: ## Build BigQuery version
+	@test -f $(DB_FILE) || { echo "Run 'make download-db' first"; exit 1; }
+	@$(DOCKER) build --target bigquery -t $(DOCKER_REGISTRY)/$(IMAGE_NAME):bigquery .
+
+.PHONY: push
+push: ## Push Docker image to registry (run 'make login' first)
+	@$(DOCKER) push $(DOCKER_IMAGE)
+	@$(DOCKER) push $(DOCKER_REGISTRY)/$(IMAGE_NAME):lite
+
+.PHONY: push-bigquery
+push-bigquery: ## Push BigQuery image (run 'make login' first)
+	@$(DOCKER) push $(DOCKER_REGISTRY)/$(IMAGE_NAME):bigquery
+
+.PHONY: test-image
+test-image: ## Test the built Docker image
+	@$(DOCKER) run --rm $(DOCKER_IMAGE) python -c "import m3; print(f'M3 version: {m3.__version__}')"
+
+.PHONY: clean
+clean: ## Remove database and raw files
+	@rm -rf m3_data
+
+.DEFAULT_GOAL := help

README.md

@@ -548,7 +548,23 @@ m3-mcp-server
 - 🔐 **Enhanced Security**: Role-based access control, audit logging
 - 🌐 **Multi-tenant Support**: Organization-level data isolation
 
-## Contributing
+## 🐳 Kubernetes Deployment
+
+Deploy M3 on Kubernetes using Docker images with pre-loaded MIMIC-IV demo database:
+
+```bash
+# Build and push Docker image
+make all  # Will prompt for Docker registry/username
+
+# Or specify registry directly
+make all DOCKER_REGISTRY=your-username DOCKER=podman
+```
+
+The container uses StreamableHTTP transport on port 3000 with path `/sse`. Configure your MCP client to connect to the service endpoint (e.g., `http://m3.kagent.svc.cluster.local:3000/sse` for intra-cluster access).
+
+Helm charts for deploying M3 are available in a separate repository.
+
+## 🤝 Contributing
 
 We welcome contributions! Please:
 

src/m3/mcp_server.py

@@ -682,9 +682,30 @@ def get_race_distribution(limit: int = 10) -> str:
 
 
 def main():
-    """Main entry point for MCP server."""
-    # Run the FastMCP server
-    mcp.run()
+    """Main entry point for MCP server.
+
+    Runs FastMCP server in either STDIO mode (desktop clients) or HTTP mode
+    (Kubernetes/web clients). Transport mode configured via environment variables.
+
+    Environment Variables:
+        MCP_TRANSPORT: "stdio" (default), "sse", or "http"
+        MCP_HOST: Host binding for HTTP mode (default: "0.0.0.0")
+        MCP_PORT: Port for HTTP mode (default: 3000)
+        MCP_PATH: SSE endpoint path for HTTP mode (default: "/sse")
+
+    Notes:
+        HTTP/SSE mode uses streamable-http transport for containerized deployments
+        where STDIO is unavailable. Binds to 0.0.0.0 for Kubernetes service mesh access.
+    """
+    transport = os.getenv("MCP_TRANSPORT", "stdio").lower()
+
+    if transport in ("sse", "http"):
+        host = os.getenv("MCP_HOST", "0.0.0.0")
+        port = int(os.getenv("MCP_PORT", "3000"))
+        path = os.getenv("MCP_PATH", "/sse")
+        mcp.run(transport="streamable-http", host=host, port=port, path=path)
+    else:
+        mcp.run()
 
 
 if __name__ == "__main__":