Modify docker-compose to match a real-life setup

Overview

Teaching: 20 min
Exercises: 20 min

Questions

• How can I mount local folder e.g. local storage for in-place import

Objectives

• Import an image using in-place import

This lesson was prepared using an Ubuntu Virtual Machine.

For didactic purposes only, we will mount the /tmp folder. Usually you will mount a directory corresponding to your data storage. You can set the permissions when mounting the volume e.g. mount as read-only. We will create a folder in the Virtual Machine that we will map to the /OMERO folder in the virtual machine.

First we need to stop the server.

docker compose -f docker-compose.yml down

Let’s create a folder omero in /home/ubuntu. You will usually install it in a more permanent location e.g. /

Now we mount the folder /tmp in the Virtual Machine to the /tmp folder in the container. and mount the folder ./omero in the Virtual Machine to the /OMERO folder in the container.

services:

  database:
    image: "postgres:16"
    environment:
      - POSTGRES_USER=omero
      - POSTGRES_DB=omero
      - POSTGRES_PASSWORD=SeCrEtPaSsWoRd
      - POSTGRES_HOST_AUTH_METHOD=trust
    networks:
      - omero-network
    ports:
      - "5432:5432"
    volumes:
      - ./pgdata:/var/lib/postgresql/data

  omeroserver:
    # This container uses the tag for the latest omero server release of OMERO 5
    # We mount the local ``/tmp`` folder into the ``/tmp`` folder in container
    image: "openmicroscopy/omero-server:5"
    environment:
      - CONFIG_omero_db_host=database
      - CONFIG_omero_db_name=omero
      - ROOTPASS=omero
    networks:
      - omero-network
    ports:
      - "4063:4063"
      - "4064:4064"
    volumes:
      - ./omero:/OMERO
      - /tmp:/tmp

  omeroweb:
    # This container uses the tag for the latest web release of OMERO 5
    image: "openmicroscopy/omero-web-standalone:5"
    environment:
      - OMEROHOST=omeroserver
      - CONFIG_omero_web_csrf__trusted__origins=["http://localhost:8080"]
    networks:
      - omero-network

  nginx:
    image: library/nginx:1.26
    networks:
      - omero-network
    ports:
      - "8080:80"
      - "8443:443"
    volumes:
      - ./nginx/log:/var/log/nginx
      - ./nginx/default.conf:/etc/nginx/conf.d/default.conf:ro${VOLOPTS-}
      - ./nginx/nginx.conf:/etc/nginx/nginx.conf:ro${VOLOPTS-}
      #- "./certs:/etc/nginx/ssl:ro${VOLOPTS-}"


networks:
  omero-network:
    # If it fails and your network has a non-standard MTU this may
    # need to be set if auto-detection fails
    driver_opts:
        com.docker.network.driver.mtu: 1450

Run in detach mode i.e. you will be able to close the terminal and disconnect and the server will still be running.

docker compose -f docker-compose.yml up -d

We now want to import an image. OMERO offers several import options:

• Import by moving an image from one location to the server where OMERO is running. This is commonly done by users using a Desktop client, typically OMERO.insight.
• Import “in-place”. This means that a symbolic link between OMERO and the image’s location is created i.e. the image is neither moved nor copied.

For more details please visit import scenarios

We will focus on the “in-place” import option, this will match a real-life setup commonly implemented in imaging facilities i.e. an OMERO server running on a machine with a storage mounted. In our case, we are using an Ubuntu Virtual Machine (VM) with OMERO running using Docker and the mounted storage being /tmp.

First we download a sample PNG image into the /tmp folder of the VM.

wget https://downloads.openmicroscopy.org/images/PNG/will/WesternBlots/Hela-frctns-DM1a-5.12.png -O /tmp/Hela-frctns-DM1a-5.12.png

Since we have mounted the /tmp folder of the VM into the /tmp folder of the Docker container, the image will be also visible from inside the container.

The OMERO.server runs as the omero-server user within the Docker container. We need to access the container as that user

Check the name(s) of the containers:

docker ps

Use the name of the Docker container running the OMERO.server e.g. ubuntu-omeroserver-1.

We will now perform an “in-place” import as the newly created OMERO user named user1. user1 only exists within OMERO. The omero-server user is created when building the Docker image, it exists at the level of Docker as an Operating System user but it is not an OMERO user and is not an Operating System user on the VM.

docker exec -ti -u omero-server  ubuntu-omeroserver-1 /opt/omero/server/venv3/bin/omero import --transfer=ln_s -s localhost -u user1 /tmp/Hela-frctns-DM1a-5.12.png

Key Points