OMERO 5.6.1 on Ubuntu 16.04 - issues with web and partial solution

To all who want to install OMERO 5.6.1 on Ubuntu 16.04:
I noticed some problems related to Python 3.5 (the standard version on Ubuntu 16.04) and omero-web, omero-iviewer, and maybe other components:

  1. see Query for DatasetImageLink ID for an issue with moving objects between Datasets. @mtbc’s PR fixes the issue but that isn’t yet in the current release.
  2. in omero-iviewer, users cannot save any ROIs applied to the image - you get an error message.
  3. in omero-iviewer, users cannot save their rendering settings - this silently fails. But using the classical viewer and the preview, one CAN save rendering settings just fine.

To resolve problems 1 and 2, I found that you can install a Python 3.6 environment in Ubuntu 16.04 and modify the installation instructions for OMERO.web (see: https://docs.openmicroscopy.org/omero/5.6.1/sysadmins/unix/install-web/walkthrough/omeroweb-install-ubuntu1604-ice3.6.html) as follows:

  1. instead of the lines:
apt-get -y install python3
apt-get -y install python3-venv

do this:

add-apt-repository ppa:deadsnakes/ppa
apt-get update
apt-get install python3.6 python3.6-venv python3.6-dev
  1. instead of these lines:
python3 -mvenv /opt/omero/web/venv3
/opt/omero/web/venv3/bin/pip install --upgrade https://github.com/ome/zeroc-ice-py-ubuntu1604/releases/download/0.2.0/zeroc_ice-3.6.5-cp35-cp35m-linux_x86_64.whl

do this:

python3.6 -mvenv /opt/omero/web/venv3
/opt/omero/web/venv3/bin/pip install zeroc-ice==3.6.5

This will take a while to compile and install.

Now your omero-web and all plugins run under Python 3.6 which resolved some of the issues I noticed but issue #3 was resolved in some circumstances but not in others. I’ll keep investigating but maybe @will-moore has an idea? Might it have something to do with log messages such as:

2020-05-07 00:48:45,893  INFO [                           omero.gateway] (proc.32371) getWindowMin():7646 getStatsInfo() is null. See #9695

Cheers,
Damir

1 Like

Thanks @dsudar
We have focused in our doc, to use the package installed by “default”
We will look into making some adjustments in the doc, so people can have both option available.

Building a wheel for Python 3.6 will definitely speed up the installation of the Ice Python bindings

Thanks for the feedback

Cheers

Jmarie

Hi Damir

I have opened a PR to install Python 3.6 on Ubuntu 16.04.
You will see that a few more dependencies needed to be installed when starting from a vanilla machine, in order to install ice 3.6.5.
see https://github.com/ome/omeroweb-install/pull/63

Cheers

Jmarie