Open Microscopy Environment

Hello everyone,

At work, we are running Omero for a couple of month now, and it was time for us to think about continuous integration.

Omero is available on docker (https://hub.docker.com/r/openmicroscopy/omero-server/), so we installed it. I also installed another Omero Cli container to connect to the server container where I downloaded our internal code as well. Both are using the latest 5.4.7 Omero version.

I can use the omero command line from the omero-server container.
On the client side, I use Ubuntu 18. I have installed Omero Server as described https://docs.openmicroscopy.org/omero/5.4.3/sysadmins/unix/server-ubuntu-ice36.html (with very minor changes due to the OS version difference).

I have both containers running on the same docker network.

When I test the remote CLI (from the ubuntu container), I get an SSL error:

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$ /opt/omero/OMERO.server/bin/omero group add -s omero-server -u root -w omero-root-password --type read-write test
WARNING:omero.client:..Ignoring error in client.__del__:<class 'Ice.ProtocolException'>
InternalException: Failed to connect: exception ::Ice::ProtocolException
{
    reason = SSL error occurred for new outgoing connection:
remote address = 172.18.0.3:4064
no ciphers available
}


I think it could make sense since I have not registered any certificate. But, I don't know how to fix this and I don't think I have any log to troubleshoot. I have read this page https://docs.openmicroscopy.org/omero/5.4.7/users/cli/installation.html, but there is nothing about SSL... I would appreciate any hint, guidance or documentation regarding fixing that issue.

Thank you for your time,

Etienne

Ubuntu installation script:

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#!/bin/bash
set -x
OMERO_OPT_DIR=/opt/omero
apt-get update

# installed for convenience
apt-get -y install unzip wget bc

# install Java
apt-get -y install software-properties-common
add-apt-repository -y ppa:openjdk-r/ppa
apt-get update
apt-get -y install openjdk-8-jre

# install dependencies
apt-get update
apt-get -y install \
   unzip \
   wget \
   python-{pip,tables,virtualenv,yaml,jinja2}

# Omero Core
apt-get -y install zlib1g-dev
apt-get -y install python-{pillow,numpy}

# Install Ice
export DEBIAN_FRONTEND=noninteractive
apt-get -y install db5.3-util
apt-get -y install libssl-dev libbz2-dev libmcpp-dev libdb++-dev libdb-dev

apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 5E6DA83306132997
apt-add-repository "deb http://zeroc.com/download/apt/ubuntu`lsb_release -rs` stable main"
apt-get update
apt-get -y install zeroc-ice-all-runtime zeroc-ice-all-dev

pip install "zeroc-ice>3.5,<3.7"

# install Postgres
apt-get -y install apt-transport-https
add-apt-repository -y "deb https://apt.postgresql.org/pub/repos/apt/ xenial-pgdg main 9.6"
wget --quiet -O - https://www.postgresql.org/media/keys/ACCC4CF8.asc | apt-key add -
apt-get update
apt-get -y install postgresql-9.6

mkdir -p "$OMERO_OPT_DIR"
cd $OMERO_OPT_DIR
SERVER=https://downloads.openmicroscopy.org/latest/omero5/server-ice36.zip
wget $SERVER -O OMERO.server-ice36.zip
unzip -q OMERO.server*

ln -s OMERO.server-*/ OMERO.server


Dear Etienne,

Could it be that you are running into the issue described at https://docs.openmicroscopy.org/latest/ ... sl-version?

Cheers,
Mark

Hi Mark,

Thank you for your reply. After executing the sed and the python line, it fails on the server side now:

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$ ./OMERO.server/bin/omero group add -s localhost -u root -w omero-root-password --type read-write phenomic
InternalException: Failed to connect: exception ::Ice::PluginInitializationException
{
    reason = IceSSL: unable to set ciphers using `ADH:@SECLEVEL=0':
invalid command
}


Hi Etienne,

I've been struggling with the same issue in several of my PRs:

• https://github.com/openmicroscopy/openm ... 773be762fd
• https://github.com/openmicroscopy/omero ... b04f0f49cd

So far, I haven't found anything that will work in all combination. In order to try to reproduce what you are seeing, can you share your entire CLI Dockerfile with me?

Thanks,
~Josh

Hi Josh,

Please find my scripts attached:

1. execute bin/start-docker.sh
It will create the omero-server, phenomic and postgres containers

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$MY_FOLDER/bin/start-docker.sh


2. go into the the phenomic container and execute /code/bin/install-omerocli-ubuntu.sh

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docker exec -it phenomic /bin/bash
/code/bin/install-omerocli-ubuntu.sh


3. Login as phenomic user

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su - phenomic


4. try any omero command

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/opt/omero/OMERO.server/bin/omero group add -s omero-server -u root -w omero-root-password --type read-write phenomicai


Thank you so much for looking into this.

Etienne

Hi Etienne,

I ran the first few lines of your install script and saw OpenJDK8 being installed. Then I kicked off the full script and saw OpenJDK11 being installed!

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root@126b8c3cb7db:/code# java -version
openjdk version "11" 2018-09-25
OpenJDK Runtime Environment (build 11+24-Ubuntu-118.04)
OpenJDK 64-Bit Server VM (build 11+24-Ubuntu-118.04, mixed mode, sharing)


I haven't tracked down what flipped the Java version, but I would definitely suggest getting back JDK8 as a first step. I was using the `openjdk` docker image and it recently went from 8 to 10. I'm beginning to suspect this may have been my problem all along as well:

see https://github.com/openmicroscopy/openmicroscopy/pull/5787/commits/48fcfeea55a6a697c0ee1309f07e019f4ddf41d1

Cheers,
~Josh

Hi Josh,

Here is what I did:

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$ update-alternatives --config java
$ java -version
openjdk version "1.8.0_171"
OpenJDK Runtime Environment (build 1.8.0_171-8u171-b11-0ubuntu0.18.04.1-b11)
OpenJDK 64-Bit Server VM (build 25.171-b11, mixed mode)


Unfortunately, I still get the same error:

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$ /opt/omero/OMERO.server/bin/omero group add -s omero-server -u root -w omero-root-password --type read-write phenomicai
WARNING:omero.client:..Ignoring error in client.__del__:<class 'Ice.ProtocolException'>
InternalException: Failed to connect: exception ::Ice::ProtocolException
{
    reason = SSL error occurred for new outgoing connection:
remote address = 172.18.0.3:4064
no ciphers available
}


Thanks for checking. I'll retry tomorrow (CEST) based on an openjdk8. Just to confirm: no modifications have been applied to the server docker? ~J

No, I use the latest omero-server version available on dockerhub.

Hi everyone,

I did not have to use Ubuntu 18.04 for my use case. I just use to stick to the latest LTS.
After trying the exact same script on 16.04, it is working for me.
I can still work collaboratively to make this config work on 18.04, but this question lost its urgency for my personal case.

Thank you for looking into it!