Open Microscopy Environment

Hi,

I upgraded the server version to 5.0.0 (on a Debian system), following the discription on the Omero website (http://www.openmicroscopy.org/site/supp ... grade.html)

This worked well, with the exception that Omero.web is not working anymore.
The system should be configured for Apache use. I ran:
omero config set omero.web.application_server "fastcgi-tcp" to setup the fastcgi,
omero web config apache to get the stanza and
omero web start

Accessing through a browser, the message says:

Unhandled Exception
An unhandled exception was thrown by the application.


I know this is not the most informative, but I can pass you any logs you think you'll need.


Thank you in advance,

Dimitri Vanhecke

Note:
I read about the possibility that the default configuration may be incompatible with OMERO. In particular, the FastCGIWrapper option conflicts with FastCGIExternalServer required by OMERO and must be removed or commented out.
I do not understand where (which file?) I should adjust to remove the FastCGIWrapper.

Hi Dimitri

Was OMERO.web fully working before the upgrade? If so your Apache config should've continued to work without modification. Did you see anything else apart from 'Unhandled Exception An unhandled exception was thrown by the application.''?

Could you zip up the following and upload them to https://www.openmicroscopy.org/qa2/qa/upload/

• OMERO.server logs var/log
• Apache logs /var/log/apache2/{access.log,error.log}
• Output of omero admin diagnostics
• Output of omero config get (Blank out the passwords)

The FastCGIWrapper if present would be in /etc/apache2/httpd.conf or /etc/apache2/conf.d/*, though as I mentioned earlier if it was working with your previous server your configuration should be fine.

Thanks, Simon

Hi,

Thanks for the help. Yes, OMERO.web was running fine until before the update.
- Although the web was started according to omero web start, the diagnotics say something else.
- There is no var/log/apache2 folder (!), so no logs there
- I have uploaded the server logs (var/log) unsing my email address




omero web start
0 static files copied, 818 unmodified.
Starting OMERO.web... [OK]

Note: Starting the server produces the file django.pid in the var/log folder
running omero web start agains now shows:

Starting OMERO.web... Removed stale /home/imaging/apps/OMERO/OMERO.server/var/django.pid
[OK]
(but the file is still there)




omero admin diagnostics:
================================================================================
OMERO Diagnostics 5.0.0-ice34-b19
================================================================================

Commands: java -version 1.7.0 (/usr/bin/java)
Commands: python -V 2.7.3 (/usr/bin/python)
Commands: icegridnode --version 3.4.2 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.4.2 (/usr/bin/icegridadmin)
Commands: psql --version 9.1.12 (/usr/bin/psql -- 2 others)

Server: icegridnode running
Server: Blitz-0 active (pid = 6072, enabled)
Server: DropBox active (pid = 6074, enabled)
Server: FileServer active (pid = 6081, enabled)
Server: Indexer-0 active (pid = 6097, enabled)
Server: MonitorServer active (pid = 6082, enabled)
Server: OMERO.Glacier2 active (pid = 6083, enabled)
Server: OMERO.IceStorm active (pid = 6084, enabled)
Server: PixelData-0 active (pid = 6085, enabled)
Server: Processor-0 active (pid = 6090, enabled)
Server: Tables-0 active (pid = 6096, enabled)
Server: TestDropBox inactive (enabled)

OMERO: SSL port 4064
OMERO: TCP port 4063

Log dir: /home/imaging/apps/OMERO/OMERO.server/var/log exists

Log files: Blitz-0.log 80.0 MB errors=62 warnings=774
Log files: DropBox.log 3.0 KB errors=0 warnings=1
Log files: FileServer.log 0.0 KB
Log files: Indexer-0.log 13.0 MB errors=27 warnings=4
Log files: MonitorServer.log 3.0 KB
Log files: OMEROweb.log 0.0 KB
Log files: OMEROweb_request.log 0.0 KB
Log files: PixelData-0.log 26.0 KB errors=34 warnings=4
Log files: Processor-0.log 67.0 KB errors=4 warnings=0
Log files: Tables-0.log 0.0 KB
Log files: TestDropBox.log n/a
Log files: master.err 21.0 KB errors=1 warnings=6
Log files: master.out 0.0 KB
Log files: Total size 93.96 MB

Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_TEMPDIR=(unset)
Environment:PATH=/usr/local/bin:/usr/bin:/bin:/usr/local/games:/usr/games:/usr/lib/jvm/java-7-openjdk-amd64/bin:/usr/share/Ice-3.4.2:/usr/lib/postgresql/9.1/bin:/home/imaging/apps/OMERO/OMERO.server/bin
Environment:ICE_HOME=/usr/share/Ice-3.4.2
Environment:LD_LIBRARY_PATH=/usr/share/java:/usr/lib:
Environment:DYLD_LIBRARY_PATH=(unset)

OMERO data dir: '/home/imaging/apps/OMERO/OMERO.data' Exists? True Is writable? True
OMERO temp dir: '/home/imaging/omero/tmp' Exists? True Is writable? True (Size: 0)
OMERO.web status... [NOT STARTED]


omero config get:

omero.data.dir=/home/imaging/apps/OMERO/OMERO.data
omero.db.name=********
omero.db.pass=********
omero.db.user=*******
omero.web.application_server=fastcgi-tcp
omero.web.debug=False


Dimitri

- There is no var/log/apache2 folder (!), so no logs there

This may be /var/log/httpd/ if you're using RHEL or CentOS.

Best,

Kenny

Hi,

Nope, there are no folders whatsoever in var/log


Greetings,

Dimitri

Ok,

Snap! you probably meant the var/logs of the system, not the var/logs of the OMERO.server folder!
I uploaded the 2 log files to https://www.openmicroscopy.org/qa2/qa/upload/


Dimitri

Hi Dimitri

We'll take a closer look in the morning, in the meantime could you upload your Apache configuration from /etc/apache2/ in case it's useful for us. Obviously omit any SSL certificates or other private files.

Thanks

Simon

Hi,

Again, thank you very much.
I uploaded apache2.conf and ports.conf from the etc/apache2 folder using https://www.openmicroscopy.org/qa2/qa/upload/
If you need more data, please let me know.


Dimitri

Thanks for your logs - Your error.log is showing lots of ``` "NoReverseMatch: Reverse for ''waindex'' ``` - which is tricky to debug (as ticketed https://code.djangoproject.com/ticket/14343) and I can't think what is causing it to fail.

What page are you visiting when you see this error? The webadmin index 'waindex' links are only generated when the admin logs in. Can you try to go to [server]/webclient/logout/ in your browser and see if that page works?

The feedback page is generating the error, and sometimes it does this recursively since the error calls the feedback page again!

Simply try to stop and restart web and this may help.

Code: Select all

$ bin/omero web stop
$ bin/omero web start


You could also try to run OMERO.web in 'development' mode, which will remove the apache layer and let us debug a bit faster.

Code: Select all

$ bin/omero web stop
$ bin/omero config set omero.web.application_server development
$ bin/omero config set omero.web.debug True
$ bin/omero web start


Then go to localhost:4080/webclient/

Sorry I couldn't be more help. Hopefully these steps may at least give us some more clues.

Will.

Ah - this might help: http://stackoverflow.com/questions/4981 ... atch-error

Is it possible you've still got an old version of Django on your PYTHONPATH?

Try:

Code: Select all

$ python

>>> import django
>>> django.get_version()
'1.6'
>>> django.__file__
'...OMERO.5.0.0/lib/python/django/__init__.pyc'


The Django version should be 1.6 and located under your OMERO-5 path.