Refactor database implementation to use PostgreSQL instead of MongoDB (#289)

Fixes #228

## Motivation and Context

See #19

## How Has This Been Tested?

- Run locally
- Run in docker compose
- Run infra in minikube
- Unit and integration tests all passing :)

## Breaking Changes

Yes: users will not be able to access any data they used to have in
custom mongodb. We are accepting this breaking change, given the
registry is in experimental development status.

## Types of changes
<!-- What types of changes does your code introduce? Put an `x` in all
the boxes that apply: -->
- [ ] Bug fix (non-breaking change which fixes an issue)
- [ ] New feature (non-breaking change which adds functionality)
- [x] Breaking change (fix or feature that would cause existing
functionality to change)
- [ ] Documentation update

## Checklist
<!-- Go over all the following points, and put an `x` in all the boxes
that apply. -->
- [x] I have read the [MCP
Documentation](https://modelcontextprotocol.io)
- [x] My code follows the repository's style guidelines
- [x] New and existing tests pass locally
- [x] I have added appropriate error handling
- [x] I have added or updated documentation as needed

## Additional context

I have not implemented connection pooling support for simplicity, and
because cloudnative-pg already provides built-in connection pooling with
pgBouncer so if we want it later we can switch to this endpoint easily.

Author: domdomegg

.env.example

@@ -6,8 +6,9 @@ MCP_REGISTRY_VERSION=dev
 MCP_REGISTRY_LOG_LEVEL=info
 
 # Database configuration
-MCP_REGISTRY_DATABASE_TYPE=mongodb
-MCP_REGISTRY_DATABASE_URL=mongodb://username:password@localhost:27017
+# Supported types: postgresql, memory
+MCP_REGISTRY_DATABASE_TYPE=postgresql
+MCP_REGISTRY_DATABASE_URL=postgres://username:password@localhost:5432/mcp-registry
 MCP_REGISTRY_DATABASE_NAME=mcp-registry
 MCP_REGISTRY_COLLECTION_NAME=servers_v2
 

Makefile

@@ -57,7 +57,7 @@ check: lint validate test-all ## Run all checks (lint, validate, unit tests)
 dev-compose: ## Start development environment with Docker Compose (builds image automatically)
 	docker compose up --build
 
-dev-local: ## Run registry locally (requires MongoDB)
+dev-local: ## Run registry locally
 	go run ./cmd/registry
 
 # Cleanup

README.md

@@ -24,7 +24,7 @@ The MCP Registry service provides a centralized repository for MCP server entrie
 - Health check endpoint for service monitoring
 - Support for various environment configurations
 - Graceful shutdown handling
-- MongoDB and in-memory database support
+- PostgreSQL and in-memory database support
 - Comprehensive API documentation
 - Pagination support for listing registry entries
 - Seed data export/import composability with HTTP support
@@ -35,7 +35,7 @@ The MCP Registry service provides a centralized repository for MCP server entrie
 ### Prerequisites
 
 - Go 1.24.x (required - check with `go version`)
-- MongoDB
+- PostgreSQL
 - Docker (optional, but recommended for development)
 
 For development:
@@ -46,14 +46,13 @@ For development:
 
 ## Running
 
-The easiest way to get the registry running is uses docker compose. This will setup the MCP Registry service, import the seed data and run MongoDB in a local Docker environment.
+The easiest way to get the registry running is uses docker compose. This will setup the MCP Registry service, import the seed data and run PostgreSQL in a local Docker environment.
 
 ```bash
-# Run the registry and MongoDB with docker compose
 make dev-compose
 ```
 
-This will start the MCP Registry service and MongoDB with Docker, running at [`localhost:8080`](http://localhost:8080).
+This will start the MCP Registry service running at [`localhost:8080`](http://localhost:8080).
 
 ## Building
 
@@ -63,15 +62,15 @@ If you prefer to run the service locally without Docker, you can build and run i
 # Build a registry executable
 make build
 ```
-This will create the `registry` binary in the current directory. You'll need to have MongoDB running locally or with Docker.
+This will create the `registry` binary in the current directory.
 
 To run the service locally:
 ```bash
-# Run registry locally (requires MongoDB)
+# Run registry locally
 make dev-local
 ```
 
-By default, the service will run on [`localhost:8080`](http://localhost:8080).
+By default, the service will run on [`localhost:8080`](http://localhost:8080). You'll need to use the in-memory database or have PostgreSQL running.
 
 To build the CLI tool for publishing MCP servers to the registry:
 
@@ -95,11 +94,12 @@ Key development commands:
 ```bash
 # Development
 make dev-compose   # Start development environment with Docker Compose
-make dev-local     # Run registry locally (requires MongoDB)
+make dev-local     # Run registry locally
 
 # Build targets
 make build          # Build the registry application
 make publisher      # Build the publisher tool
+make migrate        # Build the database migration tool
 
 # Testing
 make test-unit        # Run unit tests with coverage report
@@ -156,7 +156,7 @@ This will prevent commits that fail linting or have formatting issues.
 │   ├── api/       # HTTP server and request handlers (routing)
 │   ├── auth/      # GitHub OAuth integration
 │   ├── config/    # Configuration management
-│   ├── database/  # Data persistence abstraction (MongoDB and in-memory)
+│   ├── database/  # Data persistence abstraction
 │   ├── model/     # Data models and domain structures
 │   └── service/   # Business logic implementation
 ├── pkg/           # Public libraries
@@ -175,9 +175,9 @@ This will prevent commits that fail linting or have formatting issues.
 5. JSON responses returned to clients
 
 ### Key Interfaces
-- **Database Interface** (`internal/database/database.go`) - Abstracts data persistence with MongoDB and memory implementations
+- **Database Interface** (`internal/database/database.go`) - Abstracts data persistence with PostgreSQL and in-memory implementations
 - **RegistryService** (`internal/service/service.go`) - Business logic abstraction over database
-- **Auth Service** (`internal/auth/auth.go`) - GitHub OAuth token validation
+- **Auth Service** (`internal/auth/jwt.go`) - Registry token creation and validation
 
 ### Authentication Flow
 Publishing requires GitHub OAuth validation:

cmd/registry/main.go

@@ -48,38 +48,37 @@ func main() {
 	case config.DatabaseTypeMemory:
 		db = database.NewMemoryDB(map[string]*model.Server{})
 		registryService = service.NewRegistryServiceWithDB(db)
-	case config.DatabaseTypeMongoDB:
-		// Use MongoDB for real registry service in production/other environments
-		// Create a context with timeout for MongoDB connection
+	case config.DatabaseTypePostgreSQL:
+		// Use PostgreSQL for real registry service
+		// Create a context with timeout for PostgreSQL connection
 		ctx, cancel := context.WithTimeout(context.Background(), 10*time.Second)
 		defer cancel()
 
-		// Connect to MongoDB
-		db, err = database.NewMongoDB(ctx, cfg.DatabaseURL, cfg.DatabaseName, cfg.CollectionName)
+		// Connect to PostgreSQL
+		db, err = database.NewPostgreSQL(ctx, cfg.DatabaseURL)
 		if err != nil {
-			log.Printf("Failed to connect to MongoDB: %v", err)
+			log.Printf("Failed to connect to PostgreSQL: %v", err)
 			return
 		}
 
-		// Create registry service with MongoDB
+		// Create registry service with PostgreSQL
 		registryService = service.NewRegistryServiceWithDB(db)
-		log.Printf("MongoDB database name: %s", cfg.DatabaseName)
-		log.Printf("MongoDB collection name: %s", cfg.CollectionName)
+		log.Printf("PostgreSQL database URL: %s", cfg.DatabaseURL)
 
-		// Store the MongoDB instance for later cleanup
+		// Store the PostgreSQL instance for later cleanup
 		defer func() {
 			if err := db.Close(); err != nil {
-				log.Printf("Error closing MongoDB connection: %v", err)
+				log.Printf("Error closing PostgreSQL connection: %v", err)
 			} else {
-				log.Println("MongoDB connection closed successfully")
+				log.Println("PostgreSQL connection closed successfully")
 			}
 		}()
 	default:
-		log.Printf("Invalid database type: %s; supported types: %s, %s", cfg.DatabaseType, config.DatabaseTypeMemory, config.DatabaseTypeMongoDB)
+		log.Printf("Invalid database type: %s; supported types: %s, %s", cfg.DatabaseType, config.DatabaseTypeMemory, config.DatabaseTypePostgreSQL)
 		return
 	}
 
-	// Import seed data if seed source is provided (works for both memory and MongoDB)
+	// Import seed data if seed source is provided
 	if cfg.SeedFrom != "" {
 		log.Printf("Importing data from %s...", cfg.SeedFrom)
 		ctx, cancel := context.WithTimeout(context.Background(), 5*time.Minute)

deploy/Pulumi.local.yaml

@@ -3,4 +3,5 @@ config:
   mcp-registry:provider: local
   mcp-registry:githubClientId: Iv23licy3GSiM9Km5jtd
   mcp-registry:githubClientSecret: 0e8db54879b02c29adef51795586f3c510a9341d
+  mcp-registry:jwtPrivateKey: bb2c6b424005acd5df47a9e2c87f446def86dd740c888ea3efb825b23f7ef47c
 encryptionsalt: v1:ijIHaqhbXVA=:v1:7voX1Kv+Bunz33iN:fyVHMOhlGIymzJ+ILgUBy3ExTwUUnA==

deploy/README.md

@@ -11,7 +11,7 @@ Pre-requisites:
 - Access to a Kubernetes cluster via kubeconfig. You can run a cluster locally with [minikube](https://minikube.sigs.k8s.io/docs/start/).
 
 1. Ensure your kubeconfig is configured at the cluster you want to use. For minikube, run `minikube start && minikube tunnel`.
-2. Run `make local-up` to deploy the stack. Run this again if the first attempt fails.
+2. Run `make local-up` to deploy the stack.
 3. Access the repository via the ingress load balancer. You can find its external IP with `kubectl get svc ingress-nginx-controller -n ingress-nginx`. Then run `curl -H "Host: local.registry.modelcontextprotocol.io" -k https://<EXTERNAL-IP>/v0/ping` to check that the service is up.
 
 #### To change config
@@ -103,7 +103,7 @@ Pre-requisites:
     │   ├── cert_manager.go    # SSL certificate management
     │   ├── deploy.go          # Deployment orchestration
     │   ├── ingress.go         # Ingress controller setup
-    │   ├── mongodb.go         # MongoDB deployment
+    │   ├── postgres.go        # PostgreSQL database deployment
     │   └── registry.go        # MCP Registry deployment
     └── providers/       # Kubernetes cluster providers
         ├── types.go           # Provider interface definitions
@@ -122,7 +122,7 @@ Pre-requisites:
 5. `k8s.DeployAll()` orchestrates complete deployment:
    - Certificate manager for SSL/TLS
    - Ingress controller for external access
-   - MongoDB for data persistence
+   - Database for data persistence
    - MCP Registry application
 
 ## Configuration
@@ -152,5 +152,5 @@ kubectl get svc -n ingress-nginx
 
 ```bash
 kubectl logs -l app=mcp-registry
-kubectl logs -l app=mongodb
+kubectl logs -l app=postgres
 ```

deploy/pkg/k8s/cert_manager.go

@@ -69,7 +69,7 @@ func SetupCertManager(ctx *pulumi.Context, cluster *providers.ProviderInfo) erro
 				},
 			},
 		},
-	}, pulumi.Provider(cluster.Provider), pulumi.DependsOn([]pulumi.Resource{certManager}))
+	}, pulumi.Provider(cluster.Provider), pulumi.DependsOnInputs(certManager.Ready))
 	if err != nil {
 		return err
 	}

deploy/pkg/k8s/deploy.go

@@ -16,19 +16,19 @@ func DeployAll(ctx *pulumi.Context, cluster *providers.ProviderInfo, environment
 	}
 
 	// Setup ingress controller
-	err = SetupIngressController(ctx, cluster, environment)
+	ingressNginx, err := SetupIngressController(ctx, cluster, environment)
 	if err != nil {
 		return nil, err
 	}
 
-	// Deploy MongoDB
-	err = DeployMongoDB(ctx, cluster, environment)
+	// Deploy PostgreSQL databases
+	pgCluster, err := DeployPostgresDatabases(ctx, cluster, environment)
 	if err != nil {
 		return nil, err
 	}
 
 	// Deploy MCP Registry
-	service, err = DeployMCPRegistry(ctx, cluster, environment)
+	service, err = DeployMCPRegistry(ctx, cluster, environment, ingressNginx, pgCluster)
 	if err != nil {
 		return nil, err
 	}

deploy/pkg/k8s/ingress.go

@@ -13,7 +13,7 @@ import (
 )
 
 // SetupIngressController sets up the NGINX Ingress Controller
-func SetupIngressController(ctx *pulumi.Context, cluster *providers.ProviderInfo, environment string) error {
+func SetupIngressController(ctx *pulumi.Context, cluster *providers.ProviderInfo, environment string) (*helm.Chart, error) {
 	conf := config.New(ctx, "mcp-registry")
 	provider := conf.Get("provider")
 	if provider == "" {
@@ -27,7 +27,7 @@ func SetupIngressController(ctx *pulumi.Context, cluster *providers.ProviderInfo
 		},
 	}, pulumi.Provider(cluster.Provider))
 	if err != nil {
-		return err
+		return nil, err
 	}
 
 	// Install NGINX Ingress Controller
@@ -60,7 +60,7 @@ func SetupIngressController(ctx *pulumi.Context, cluster *providers.ProviderInfo
 		},
 	}, pulumi.Provider(cluster.Provider))
 	if err != nil {
-		return err
+		return nil, err
 	}
 
 	// Extract ingress IPs from the Helm chart's controller service
@@ -90,5 +90,5 @@ func SetupIngressController(ctx *pulumi.Context, cluster *providers.ProviderInfo
 	})
 	ctx.Export("ingressIps", ingressIps)
 
-	return nil
+	return ingressNginx, nil
 }