Open Microscopy Environment

Hi,

We recently had a server trouble. We fixed it, and OMERO is seemingly working well now. However, when I tried to access through MATLAB toolbox (via Java API), I realized that I cannot create a session any longer (I was able to do so on Friday).

I've tested that the username and password are correct for OMERO.web.

Any ideas about how to solve this issue?

Code: Select all

>> client = loadOmero('xxxxxx.xx.xx', 4064);
>> session = client.createSession('hoo', 'bar');
-! 10/12/18 10:59:05:284 warning: main: null - createSession retry: 1

-! 10/12/18 10:59:10:288 warning: main: null - createSession retry: 2

Java exception occurred:
omero.ClientError: Obtained null object proxy

   at omero.client.createSession(client.java:750)

Best,
Kouichi

Hi Kouichi,

sorry to hear you're having troubles. Let's start with the basics and get your diagnostics output:

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bin/omero admin diagnostics


See https://docs.openmicroscopy.org/omero/5.4.9/sysadmins/unix/server-installation.html#omero-diagnostics for an example. A next step will be to review any errors in your logs.

~Josh

Hi Josh,

I work with Kouichi, and the output of the diagnostics is:

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================================================================================
OMERO Diagnostics (admin) 5.4.9-ice36-b101
================================================================================

Commands:   java -version                  1.8.0     (/bin/java)
Commands:   python -V                      2.7.5     (/opt/omero/web/venv/bin/py                                                     thon -- 2 others)
Commands:   icegridnode --version          3.6.4     (/bin/icegridnode)
Commands:   icegridadmin --version         3.6.4     (/bin/icegridadmin)
Commands:   psql --version                 9.4.20    (/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 7693, enabled)
Server:     DropBox                        active (pid = 8585, enabled)
Server:     FileServer                     active (pid = 8595, enabled)
Server:     Indexer-0                      active (pid = 8601, enabled)
Server:     MonitorServer                  active (pid = 8607, enabled)
Server:     OMERO.Glacier2                 active (pid = 8644, enabled)
Server:     OMERO.IceStorm                 active (pid = 8612, enabled)
Server:     PixelData-0                    active (pid = 8620, enabled)
Server:     Processor-0                    active (pid = 8621, enabled)
Server:     Tables-0                       active (pid = 8636, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /opt/omero/web/OMERO.py-5.4.9-ice36-b101/var/log exists
Log files:  Blitz-0.log                    n/a
Log files:  DropBox.log                    n/a
Log files:  FileServer.log                 n/a
Log files:  Indexer-0.log                  n/a
Log files:  MonitorServer.log              n/a
Log files:  OMEROweb.lock                  0.0 KB
Log files:  OMEROweb.log                   21.0 MB       errors=556  warnings=64                                                     176
Log files:  Processor-0.log                n/a
Log files:  Tables-0.log                   n/a
Log files:  TestDropBox.log                n/a
Log files:  Total size                     21.92 MB

Error while parsing logs

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=(unset)
Environment:PATH=/opt/omero/web/venv/bin:/sbin:/bin:/usr/sbin:/usr/bin
Environment:PYTHONPATH=(unset)
Environment:ICE_HOME=(unset)
Environment:LD_LIBRARY_PATH=(unset)
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO SSL port:4064
OMERO TCP port:4063
OMERO data dir:'/OMERO'                       Exists? False     Is writable? Fal                                                     se
OMERO temp dir:'/opt/omero/web/omero/tmp'     Exists? True      Is writable? Tru                                                     e   (Size: 0)

JVM settings: Blitz-${index}                -Xmx600m -XX:MaxPermSize=256m -XX:+I                                                     gnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx400m -XX:MaxPermSize=256m -XX:+I                                                     gnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx600m -XX:MaxPermSize=256m -XX:+I                                                     gnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx400m -XX:MaxPermSize=256m -XX:+I                                                     gnoreUnrecognizedVMOptions


An additional symptom is we cannot log in via OMERO.insight! Via web using same user/pass is fine.

Hi Ben,

This is the diagnostics output for OMERO.web, which looks good. There will be another directory, likely under /opt/omero/server for the main application, which will provide you similar output. However, if you are able to login via web, then there's likely nothing wrong with the server. Is it possible that the main ports were firewalled off?

~Josh

Hi Josh, sorry, Yes, you're right, it was the firewall. I'm not familar with CentOS, the firewall rule I added was not persistent after restart as I hadn't added the --permanent option. OMERO.insight access restored, hopefull Kouichi's Java API will be accessible too.

Whew. Thanks for letting us know!

All the best,
~Josh