MCP not working

[Leonel Peña]

I was testing the MCP server in HAPI using the following configuration, but I’m getting a “not found” error. Is there any additional configuration I need to do?

spring:
  ai:
    mcp:
      server:
        name: FHIR MCP Server
        version: 1.0.0
        instructions: "This server provides access to a FHIR RESTful API. You can use it to query FHIR resources, perform operations, and retrieve data in a structured format."
        enabled: true
        streamable-http:
          mcp-endpoint: /mcp/messages

[herb...@gmail.com]

As far as I know, HAPI-FHIR does not support the MCP protocol. The docs (https://hapifhir.io/hapi-fhir/docs/) do not list this feature and if I'am not wrong neither HL7 FHIR (https://hl7.org/fhir/index.html) has any description of it.

Maybe you had to put a additional layer to enable the MCP protocol on a HAPI-FHIR server.

Try this: https://medium.com/@itsarmanpani/talking-to-your-fhir-server-how-mcp-turns-llms-into-healthcare-assistants-65f866ba192e

[Leonel Peña]

 I took this configuration from the project’s GitHub repository  https://github.com/hapifhir/hapi-fhir-jpaserver-starter?tab=readme-ov-file#enable-mcp, but I’ll take a look at what you sent.  

[Rob Ferguson]

It works for me :)


See: https://rob-ferguson.me/hapi-fhir-mcp-server/

[Leonel Peña]

Hi, what configuration do you use in the application.yaml in fhir server and what version are you testing on. If you access de url by a browser works?

[Rob Ferguson]

I have a fork of the HAPI FHIR JPA Server Starter Project which I have configured to sync with the upstream repository.

See: https://github.com/Robinyo/hapi-fhir-jpaserver-starter

Also see: https://rob-ferguson.me/tag/fhir/

The current HAPI FHIR JPA Server Starter Project version is v8.4.0-2

Note: You can also use the most recent Docker Image: hapiproject/hapi:v8.4.0-2

If you take a look at the project's `application.yml` you will see the following (default) Spring AI MCP Server configuration:

```

spring:
  ai:
    mcp:
      server:
        name: FHIR MCP Server
        version: 1.0.0
        instructions: "This server provides access to a FHIR RESTful API. You can use it to query FHIR resources, perform operations, and retrieve data in a structured format."
        enabled: true
        streamable-http:
          mcp-endpoint: /mcp/messages

```

I also updated the project's `application.yml`, to configure the Web Testpage Overlay:

```

tester:
  home:
    name: Local Tester
    server_address: 'http://localhost:8080/fhir'
    refuse_to_fetch_third_party_urls: false
    fhir_version: R4

```

Then configure your MCP client (e.g., Claude for Desktop):

```

"mcpServers": {
  "hapi": {
    "command": "npx",
      "args": [
        "mcp-remote@latest",
        "http://localhost:8080/mcp/messages"
    ]
  }

}

```

Restart Claude for Desktop and then click on the 'Search and tools' button.

You should see something like:



Also see: https://rob-ferguson.me/hapi-fhir-mcp-server/

[Leonel Peña]

I think there might be an issue with the Docker image uploaded by the HAPI project. When I change only the image in your Docker Compose file, it stops working. However, if I use your image, everything works perfectly.

  hapi-fhir:
    image: hapiproject/hapi:v8.4.0-2
    #image: robferguson/hapi-fhir-au:v8.4.0-2

2025-10-16T12:36:59.063Z WARN 1 --- [nio-8080-exec-1] o.s.web.servlet.PageNotFound : No mapping for GET /mcp/messages

2025-10-16T12:36:59.092Z WARN 1 --- [nio-8080-exec-1] o.s.web.servlet.PageNotFound : No endpoint GET /mcp/messages.

[Rob Ferguson]

I have created this issue: https://github.com/hapifhir/hapi-fhir-jpaserver-starter/issues/873