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Using Automappa on a remote server

Follow these steps if you would like to run Automappa on a remote server but view the output on your local machine.

  1. ssh tunnel at remote server login (ssh -L localport:localhost:remoteport)
  2. Configure server host and port in .env
  3. Expose configured port in docker-compose.yml
  4. Start Automappa services

remote server login with ssh tunnel

you first need to login to the remote server with a tunnel, e.g. ssh -L localport:localhost:serverport user@hostaddress.

#ssh -L localport:127.0.0.1:serverport user@kwan-bioinformatics.pharmacy.wisc.edu
#example
ssh -L 8855:127.0.0.1:8050 sam@kwan-bioinformatics.pharmacy.wisc.edu

Configure server host and port

Once you are on the server, simply start the Automappa server (with the appropriate port from the ssh tunnel).

To set the serverport to correspond to the port defined in the ssh tunnel, edit the .env file:

# Note these values in .env
SERVER_HOST="0.0.0.0"
SERVER_PORT=8050

This means the server port (on the remote server) will be 8050

Expose configured port in docker-compose.yml

The port exposed in the web service defined in docker-compose.yml must also be changed to correspond to the user's values.

The SERVER_PORT in .env should match the exposed port for Automappa's web service (i.e. the web service in the docker-compose.yml file).

# Contents of docker-compose.yml
# ... more services above hidden ...
# Find this section
web:
    build:
      context: .
      dockerfile: Dockerfile
    restart: always
    mem_limit: 4GB
    command: python -m automappa.__main__
    user: automappa
    volumes:
      - .:/usr/src/app
    ports:
      - "8050:8050" # edit this line to match SERVER_PORT specified in .env
    # - "remoteport:SERVER_PORT"
    depends_on:
      - postgres
      - queue

Start Automappa services

After configuring the server and host port to match the forwarded ssh tunnel's remote port start Automappa's services.

  1. (local machine) ssh tunnel @ login with forwarding port: ssh -L localport:remoteport
  2. (remote server) edit SERVER_PORT in .env to whatever you prefer
  3. (remote server) edit ports: "remoteport:SERVER_PORT" in docker-compose.yml
  4. (remote server) start Automappa services: make up

i.e. in the previous example, these steps would look like this:

  1. (local machine) ssh -L 8855:8050 user@remote-server
  2. (remote server) edit .env with changes: SERVER_PORT = 8050
  3. (remote server) edit web service port in docker-compose.yml: ports: 8050:8050
  4. (remote server) start Automappa services: make up
cd Automappa
make up

NOTE: This will build Automappa and serve using SERVER_HOST and SERVER_PORT from the configuration in .env above.

Once all of the services are up and running you can navigate to the app view in your browser.

This will correspond to the localport that was passed in upon login to the remote server.

From the login example above we would navigate to localhost:8855.

Here is an illustration of the network communication.

Network communication illustration

graph LR
    A[LocalMachine]<-- localport:remoteport -->B(RemoteServer)
    B(RemoteServer)<-. remoteport:exposeport .->C(DockerContainer)
    C(DockerContainer)<-- `exposeport:SERVER_PORT` -->D[AutomappaServer]
Loading

Example network communication illustration

I've numbered the ports here to help illustrate an example network configuration.

graph LR
    A[LocalMachine]<-- 8855:8050 -->B(RemoteServer)
    B(RemoteServer)<-. 8050:8050 .->C(DockerContainer)
    C(DockerContainer)<-- 8050:8050 -->D[AutomappaServer]
Loading

Note

  • You may change any of these values as long as you change the respective value.
  • This may be useful if multiple users will need to use the app.
Bridge Port Bridge Communication Context
localport:remoteport 8855:8050 local:remote
remoteport:containerport 8050:8050 remote:docker
containerport:serverport 8050:8050 docker:server