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https://github.com/sbesson/omero-server-jep403

A minimal OMERO.server running on strongly encapsulated JDK
https://github.com/sbesson/omero-server-jep403

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A minimal OMERO.server running on strongly encapsulated JDK

Host: GitHub
URL: https://github.com/sbesson/omero-server-jep403
Owner: sbesson
Created: 2024-04-29T11:30:59.000Z (7 months ago)
Default Branch: main
Last Pushed: 2024-04-30T07:40:12.000Z (7 months ago)
Last Synced: 2024-04-30T12:42:56.750Z (7 months ago)
Language: Dockerfile
Homepage:
Size: 5.86 KB
Stars: 0
Watchers: 1
Forks: 0
Open Issues: 0
Metadata Files:
- Readme: README.md

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README

OMERO.server on JDK 17+
=======================

This repository is a minimal Docker-based example of the issues
associated with running OMERO.server up to 5.6.10 against JDK 17
LTS and later.

The Docker compose defines 4 containers: a PSQL database container
and 3 containers with OMERO.server running on Java 11, 17 and 21.
These containers can be built and started using the standard
``docker compose`` commands:

docker compose build
docker compose up -d

Within each container, the ``init.sh`` script will initialize the database
and sets a minimal OMERO configuration including self-signed certificates.

Java 11
-------

On the Java 11 container, it should be possible to start OMERO.server
immediately after running the initialization script

docker compose exec jdk11 bash
(OMERO.venv) omero@e85df0ecd93b:~$ ./init.sh
...
UPDATE 1
COMMIT
OpenSSL 3.0.2 15 Mar 2022 (Library: OpenSSL 3.0.2 15 Mar 2022)
certificates created: /OMERO/certs/server.key /OMERO/certs/server.pem /OMERO/certs/server.p12
(OMERO.venv) omero@e85df0ecd93b:~$ omero admin start
WARNING: Your server has not been configured for production use.
See https://docs.openmicroscopy.org/omero/latest/sysadmins/server-performance.html?highlight=poolsize
for more information.
Creating /opt/omero/OMERO.current/var/master
Initializing /opt/omero/OMERO.current/var/log
Creating /opt/omero/OMERO.current/var/registry
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit

Java 17+
--------

On the Java 17 and 21 container, running `omero admin start` immediately
after running the initialization script will lead to a startup failure due
to the strong encapsulation enforcement in Java 17 and later
A workaround is to set ``--add-opens`` and ``--add-exports`` using the
``omero.jvmcfg.append`` configuration:

docker compose exec jdk17 bash
(OMERO.venv) omero@72b42ffbf2c3:~$ ./init.sh
...
UPDATE 1
COMMIT
OpenSSL 3.0.2 15 Mar 2022 (Library: OpenSSL 3.0.2 15 Mar 2022)
certificates created: /OMERO/certs/server.key /OMERO/certs/server.pem /OMERO/certs/server.p12
(OMERO.venv) omero@72b42ffbf2c3:~$ omero config set omero.jvmcfg.append '--add-opens java.base/java.lang=ALL-UNNAMED --add-exports java.naming/com.sun.jndi.ldap=ALL-UNNAMED'
(OMERO.venv) omero@72b42ffbf2c3:~$ omero admin start
WARNING: Your server has not been configured for production use.
See https://docs.openmicroscopy.org/omero/latest/sysadmins/server-performance.html?highlight=poolsize
for more information.
Creating /opt/omero/OMERO.current/var/master
Initializing /opt/omero/OMERO.current/var/log
Creating /opt/omero/OMERO.current/var/registry
No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit
(OMERO.venv) omero@72b42ffbf2c3:~$

References
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