Support request #694

fail to connect omero server

Added by Anonymous 26 days ago. Updated 15 days ago.

Status:Resolved - Test / MergeStart date:2020-07-10
Priority:NormalDue date:
Assignee:Niko% Done:

0%

Category:-
Target version:-

Description

Hello,

I tried to connect my HRM server to a fresh install of OMERO (on another server)
All network access are open between both servers.

I've enable the omero connector and install omero prerequisites.
When i open Raw images, click on omero icon, i've the logon screen, enter correct id & password but when i click on submit, i've a blank page with address "http://my-hrm-server/file_management.php?folder=src"

What can be the problem and how can i solve this problem ?
Thanks in advance.

History

#1 Updated by Daniel 26 days ago

Hi,

Are there any errors logged in /var/log/hrm ? can you access the remote omero server by using an omero client in the HRM machine (without using HRM).

Best,
Daniel

#2 Updated by Niko 26 days ago

Daniel, do you know by chance who reported this?

How do we deal with people creating anonymous tickets here? I'd like to contact them back on the OMERO connector issue, but I simply can't for the lack of contact details...

#3 Updated by Jeremy 26 days ago

My apologies, I did not create an account before posting my ticket.
Now you can identify me.

However, I confirm that I can access on my OMERO server from my hrm / huygens server with either omero.web or omero.insight.

Logs /var/log/hrm/error_log.txt or hrm.log or log.txt don't help me more...

Thanks
Jeremy

#4 Updated by Daniel 23 days ago

Hello Jeremy,

A few questions in order to debug the issue.

Did you set the file permissions of the HRM folder as in https://huygens-remote-manager.readthedocs.io/en/latest/admin/hrm_user_group_perm.html

What's the output of 'ls -la' in the HRM files folder? Besides the file permissions I'm also curious whether HRM failed to create one or more of the user and installation folders.

Best,
Daniel

#5 Updated by Niko 22 days ago

  • Status changed from New to In Progress
  • Assignee set to Niko

Hi Jeremy,

would it be possible to get an extract of your "hrm.log" from an attempt to run the OMERO connector? That would be very helpful in debugging what's going on.

Cheers,
Niko

#6 Updated by Jeremy 22 days ago

Hi Daniel, Niko,

Thanks for your suggestion, you're right, i don't knhow why, apache was not in hrm group... I made modification (and restart apache) but now i have a more verbose message in hrm.log : (and regarding your request Niko)

[2020-07-14 13:06:06] hrm.WARNING: OMERO connector: > bin/ome_hrm.py --user 'jmaton' --password [********] 'checkCredentials'
[2020-07-14 13:06:06] hrm.WARNING: OMERO connector: ERROR: checkCredentials(): ERROR importing the OMERO Python bindings: No module named omero.gateway
    Current PYTHONPATH:
        ['/opt/OMERO/OMERO.server-5.6.1-ice36-b225/lib/python',
         '/var/www/html/hrm/bin',
         '/usr/lib/python2.7',
         '/usr/lib/python2.7/plat-x86_64-linux-gnu',
         '/usr/lib/python2.7/lib-tk',
         '/usr/lib/python2.7/lib-old',
         '/usr/lib/python2.7/lib-dynload',
         '/usr/local/lib/python2.7/dist-packages',
         '/usr/lib/python2.7/dist-packages']

Where can i found this py module ?
Thanks
Jeremy

#7 Updated by Niko 22 days ago

  • Status changed from In Progress to Wait For Feedback

Hi Jeremy,

the steps for installing those are described here:

https://huygens-remote-manager.readthedocs.io/en/latest/admin/prerequisites.html#optional-omero-support

Please make sure to adapt them so they're matching your OMERO version, as the ones in the documentation are only showing the concept and are using an old (5.0.3) OMERO version!

Let us know if that helps,
~Niko

#8 Updated by Jeremy 22 days ago

Niko,

Thanks for the link that i've already followed (and adapt to my omero version)

I did not be able to install libicessl34 (or 36 corresponding to my omero package). I did'nt find how to install it on my hrm server (itself on Ubuntu 18.04 LTS). I don't know if the problem can come from that.

Under HRM raw images upload page, after trying to log myself on omero server, i have the message "Logging into OMERO failed, please try again!". And, in hrm.log, i have the error message that i posted before.

Thx.
Jeremy

#9 Updated by Niko 22 days ago

Hi Jeremy,

I'm confused now, in your initial report you wrote that all prerequisites were installed. Does this now mean there is a matching libecessl or not?

You're writing the HRM is running on Ubuntu 18.04, can you let us know on which OS your OMERO is installed?

Cheers,
Niko

#10 Updated by Niko 22 days ago

From the error message above, I'm assuming your OMERO version is 5.6.1 - correct?

Checking the OMERO 5.6.1 installation documentation for Ubuntu 18.04 I found the instructions for installing the correct Ice version (look for the section "To install Ice 3.6.5"):

apt-get update && \
apt-get install -y -q \
build-essential \
db5.3-util \
libbz2-dev \
libdb++-dev \
libdb-dev \
libexpat-dev \
libmcpp-dev \
libssl-dev \
mcpp \
zlib1g-dev

cd /tmp
wget -q https://github.com/ome/zeroc-ice-ubuntu1804/releases/download/0.3.0/ice-3.6.5-0.3.0-ubuntu1804-amd64.tar.gz
tar xf ice-3.6.5-0.3.0-ubuntu1804-amd64.tar.gz
mv ice-3.6.5-0.3.0 /opt
echo /opt/ice-3.6.5-0.3.0/lib/x86_64-linux-gnu > /etc/ld.so.conf.d/ice-x86_64.conf
ldconfig

To make Ice available to all users and activate the virtual environment, set the following in /etc/profile:

# Environment file for OMERO        

export ICE_HOME=/opt/ice-3.6.5-0.3.0        
export PATH="$ICE_HOME/bin:$PATH"        
#Remove commented out export below if Ice is not set globally accessible        
#export LD_LIBRARY_PATH="$ICE_HOME/lib64:$ICE_HOME/lib:$LD_LIBRARY_PATH"        
export SLICEPATH="$ICE_HOME/slice" 

Could you try these and then REBOOT the HRM server please?

Cheers,
Niko

#11 Updated by Jeremy 21 days ago

Hi Niko,

My both servers are on ubuntu 18.04 LTS (v4) and work separatly for the moment. On my HRM server, i've also huygens installed and it's work fine (according my scientists collegues). The next step is to connect each other.

I installed what i thought to be correct for my configuration (without libicessl34 library because there isn't a matching one) https://huygens-remote-manager.readthedocs.io/en/latest/admin/prerequisites.html#prerequisites-omero

I made modification in link to correspond to my omero server:

wget http://downloads.openmicroscopy.org/omero/5.6.1/artifacts/OMERO.server-5.6.1-ice36-b225.zip

and followed the installation tasks.

I've also follow the ice installation instructions you send me, reboot server, but unfortunatly it doesn't work :

[2020-07-15 07:16:17] hrm.INFO: Initialized logging.
[2020-07-15 07:16:17] hrm.INFO: OMERO connector: attempting to log on to OMERO.
[2020-07-15 07:16:17] hrm.WARNING: OMERO connector: > bin/ome_hrm.py --user 'jmaton' --password [********] 'checkCredentials'
[2020-07-15 07:16:17] hrm.WARNING: OMERO connector: ERROR: checkCredentials(): ERROR importing the OMERO Python bindings: No module named omero.gateway
    Current PYTHONPATH:
        ['/opt/OMERO/OMERO.server-5.6.1-ice36-b225/lib/python',
         '/var/www/html/hrm/bin',
         '/usr/lib/python2.7',
         '/usr/lib/python2.7/plat-x86_64-linux-gnu',
         '/usr/lib/python2.7/lib-tk',
         '/usr/lib/python2.7/lib-old',
         '/usr/lib/python2.7/lib-dynload',
         '/usr/local/lib/python2.7/dist-packages',
         '/usr/lib/python2.7/dist-packages']
[2020-07-15 07:16:17] hrm.INFO: OMERO connector: ERROR connecting to OMERO!

I'm not familiar with python but shouldn't find a file called omero.gateway on my server ? isnt'it ?

Something else, ice version in ubuntu18.04 repositories is 3.7. May the error can come from that? not sure but... ?

Thanks so much for your help.
Jeremy

#12 Updated by Daniel 16 days ago

Hello Jeremy,

Could this link be helpful? https://docs.openmicroscopy.org/omero/5.6.0/developers/Python.html

Supposedly, this should install the Python client libraries and let you import the Omero gateway.

Best,
Daniel

#13 Updated by Niko 16 days ago

Hi Jeremy,

sorry but I am confused again. In your last message you're writing

I've also follow the ice installation instructions you send me, reboot server, but unfortunatly it doesn't work :

followed by this one further down:

Something else, ice version in ubuntu18.04 repositories is 3.7. May the error can come from that? not sure but... ?

Now the question is, did you install the Ice libs following the instructions from the OMERO documentation, or did you install them from the Ubuntu repositories?

If you installed them as described in the documentation, the version in Ubuntu doesn't matter as you're not using that one. Could you report the result of running this command on the server please?

dpkg --get-selections | grep -i ice | sort

Cheers,
Niko

#14 Updated by Jeremy 15 days ago

Hi Daniel & Niko,

I followed instructions provided by Daniel concerning Python, i followed this link to correspond to my omero version :
https://docs.openmicroscopy.org/omero/5.6.1/developers/Python.html

Then i created a symbolic link

cd /opt/omero/server/OMERO.server/lib
ln -s /opt/omero/server/venv3/lib/python3.6/site-packages python

At this point HRM didn't ask for omero.gateway module in the hrm.log but connection failed with a "checkCredentials()" error message.

[2020-07-20 11:21:21] hrm.INFO: Initialized logging.
[2020-07-20 11:21:21] hrm.INFO: OMERO connector: attempting to log on to OMERO.
[2020-07-20 11:21:21] hrm.WARNING: OMERO connector: > bin/ome_hrm.py --user 'jmaton' --password [****] 'checkCredentials'
[2020-07-20 11:21:21] hrm.WARNING: OMERO connector: ERROR: checkCredentials():
[2020-07-20 11:21:21] hrm.INFO: OMERO connector: ERROR connecting to OMERO!

So I looked in the PYTHONPATH and it was configured to use Python 2.7 which tend to be replace by v3.

I replaced also in /var/www/html/hrm/bin/ome_hrm.py and /var/www/html/hrm/bin/hrm_config.py at 1st line #!/usr/bin/env python by #!/usr/bin/env python3

That's all folks ! ;-)
Now it's ok all is works fine (import an re-import after deconvolution)

Thanks for your help.
Best regards.
Jeremy

#15 Updated by Niko 15 days ago

  • Status changed from Wait For Feedback to Resolved - Test / Merge

Hi Jeremy,

glad to hear it's sorted and working for you.

Actually I am a bit surprised that it does, since I didn't have a minute yet to make that stuff Python 3 ready - it's one of the things I have on my list as we need to migrate as well.

Don't hesitate to come back if you experience issues with the connector!

Cheers,
Niko

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