MRE for https://forum.image.sc/t/omero-data-dir-not-respected-with-read-only-omero-rw-db/61644

.gitignore

*.sql
*.p12
*.key
*.pem
*.crt
*.jks
.env

README.md

RO OMERO ignored data.dir change

These instructions create an OMERO instance, then demonstrate how data.dir is ignored when starting up in RO data directory mode.

Note: Initially I was dumping the database before shutting down the stack, then loading it again in during database initialisation, but this proved to be irrelevant so I have simplified the example to remove these steps.

Initialise the OMERO instance and import an image for good measure

# New instance initalised 
docker-compose up -d

# Import an image
docker exec -it omero-docker_omeroserver_1 /omero-import-example.sh WwDgVUQ489LnPF

# Shutdown the stack
docker-compose down

Modify the compose

Modify the Docker compose file to replace all references to /OMERO.old with /OMERO.new.

Switch to OMERO RO data directory mode by commenting in these lines:

      CONFIG_omero_cluster_read__only.db: "false"
      CONFIG_omero_cluster_read__only.repo: "true"
      CONFIG_omero_pixeldata_memoizer_dir_local: "/tmp/BioFormatsCache"

Examine the result

# Start up the stack
docker-compose up -d

# Examine the repos
docker exec -it omero-docker_omeroserver_1 \
    /opt/omero/server/OMERO.server/bin/omero \
    -s localhost -u root -w WwDgVUQ489LnPF fs repos

The data.dir setting is not respected and remains /OMERO.old.

Created session for root@localhost:4064. Idle timeout: 10 min. Current group: system
 # | Id | UUID                                 | Type    | Path
---+----+--------------------------------------+---------+-------------------------------------------------------------
 0 | 58 | 46033d9c-bc2b-44d1-93a9-ab87b398bce2 | Public  | /OMERO.old
 1 | 59 | ScriptRepo                           | Script  | /opt/omero/server/OMERO.server-5.6.3-ice36-b228/lib/scripts
 2 | 60 | 335c6801-381e-4bc7-8c0d-177e55d23f7e | Managed | /OMERO.old/ManagedRepositor

This is in contrast to if the data.dir setting is changed, but RO mode is not set; in that scenario, the repo correctly updates.

docker-compose.yml

version: "3.2"

services:

  database:
    image: "postgres:11"
    environment:
      POSTGRES_PASSWORD: FHfrByL5rXH7ZT
      POSTGRES_OMERO_PASSWORD: tyg9woVsv75F9M
    networks:
      - omero
    volumes:
      - "database:/var/lib/postgresql/data"
      - "./init-omero-db.sh:/docker-entrypoint-initdb.d/init-user-db.sh:ro"

  # It is necessart to intialise the var volume to be owned by 9798:9798 or
  # else it is not writeable in the omeroserver container
  omeroserver-init:
      image: ubuntu
      command: sh -c "chown 9798:9798 /omero_var && chown 9798:9798 /OMERO.old"
      volumes:
        - "omeroserver_var:/omero_var"
        - "omero:/OMERO.old"

  omeroserver:
    # Use a build to align the omero-server user with the omero network user
    build:
      context: .
      args:                                                                      
        OMERO_UID: 9798
        OMERO_GID: 9798

    environment:
      ROOTPASS: WwDgVUQ489LnPF
      CONFIG_omero_db_host: database
      CONFIG_omero_db_name: omerodb

      # Workaround problem with /omero/tmp not being write-lockable ?
      # TODO Is this read-only OMERO specific?
      OMERO_TMPDIR: /tmp

      # RW Database
      CONFIG_omero_db_user: omerouser
      CONFIG_omero_db_pass: tyg9woVsv75F9M

      # Repository management
      CONFIG_omero_data_dir: "/OMERO.old"

      # Read-only configuration
      # CONFIG_omero_cluster_read__only.db: "false"
      # CONFIG_omero_cluster_read__only.repo: "true"
      # CONFIG_omero_pixeldata_memoizer_dir_local: "/tmp/BioFormatsCache"

    networks:
      - omero
    ports:
      - "4063:4063"
      - "4064:4064"
    volumes:
      - "omero:/OMERO.old"

      # OMERO var must be mounted as the original Dockerfile specified this as a volume
      # when the USER was omero-server with the old uid/gid, which are then inherited
      # by this var. If it isn't mounted, then there is no way to chown it as root
      # using an init container.
      - "omeroserver_var:/opt/omero/server/OMERO.server/var"

      # Example image to import
      - "./example.png:/example.png:ro"
      - "./omero-import-example.sh:/omero-import-example.sh:ro"

    depends_on:
      omeroserver-init:
        condition: service_completed_successfully

    healthcheck:
      test: ["CMD-SHELL", "/opt/omero/server/OMERO.server/bin/omero node status || exit 1"]
      interval: 30s
      timeout: 10s
      retries: 3
      start_period: 15s

  omeroweb:
    # This container uses the tag for the latest web release of OMERO 5
    # To upgrade to the next major release, increment the major version number
    image: "openmicroscopy/omero-web-standalone:5"
    environment:
      CONFIG_omero_web_server__list: '[["omeroserver", 4064, "omero"]]'
    networks:
      - omero
    ports:
      - "4080:4080"

    depends_on:
      omeroserver:
        condition: service_healthy

networks:
  omero:

volumes:
  database:
  omeroserver_var:
  omero:

  

Dockerfile

FROM openmicroscopy/omero-server:5
USER root
ARG OMERO_UID
ARG OMERO_GID
COPY fix-perms /usr/bin/fix-perms
RUN fix-perms
USER omero-server

example.png

fix-perms

#!/usr/bin/env bash

set -ex

OLD_UID=$(getent passwd omero-server | cut -f3 -d:)
OLD_GID=$(getent group omero-server | cut -f3 -d:)
usermod -u "${OMERO_UID}" omero-server
groupmod -g "${OMERO_GID}" omero-server
find / -xdev -user ${OLD_UID} -print -exec chown "${OMERO_UID}" -h {} \;
find / -xdev -group "${OLD_GID}" -print -exec chgrp "${OMERO_GID}" -h {} \;

init-omero-db.sh

#!/usr/bin/env bash

set -ex

# Create omerodb and omerouser
psql -v ON_ERROR_STOP=1 --username postgres <<-EOSQL
    CREATE DATABASE omerodb;
    CREATE USER omerouser WITH PASSWORD '${POSTGRES_OMERO_PASSWORD}';
    GRANT ALL PRIVILEGES ON DATABASE omerodb TO omerouser;
EOSQL

omero-import-example.sh

#!/usr/bin/env bash

OMERO="/opt/omero/server/OMERO.server/bin/omero"
${OMERO} -s localhost -u root -w ${1} import /example.png