Open Microscopy Environment

Hi list,
NOTE: I am a biologist, so please forgive my relative computing ignorance...
My OMERO server works fine through Insight. But I have been fighting with my OMERO.web access for a while, in vain. It started when upgrading from 5.0 to 5.1 I think. I just did the last upgrade available, which went fine, but web access is still out.
I followed the instruction on:
https://www.openmicroscopy.org/site/sup ... pache.html

I got stuck with what I am supposed to do with the output of:
$ bin/omero web config apache

Through OMERO.server$ bin/omero admin diagnostics I got:

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================================================================================
OMERO Diagnostics 5.2.2-ice35-b17
================================================================================
       
Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.11    (/usr/bin/python)
Commands:   icegridnode --version          3.5.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.5.2     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2360, enabled)
Server:     DropBox                        active (pid = 2402, enabled)
Server:     FileServer                     active (pid = 2410, enabled)
Server:     Indexer-0                      active (pid = 2411, enabled)
Server:     MonitorServer                  active (pid = 2412, enabled)
Server:     OMERO.Glacier2                 active (pid = 2427, enabled)
Server:     OMERO.IceStorm                 active (pid = 2445, enabled)
Server:     PixelData-0                    active (pid = 2414, enabled)
Server:     Processor-0                    active (pid = 2438, enabled)
Server:     Tables-0                       active (pid = 2425, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omero/OMERO.server-5.2.2-ice35-b17/var/log exists
Log files:  Blitz-0.log                    6.0 MB        errors=69   warnings=8   
Log files:  DropBox.log                    8.0 KB        errors=0    warnings=3   
Log files:  FileServer.log                 1.0 KB       
Log files:  Indexer-0.log                  12.0 KB     
Log files:  MonitorServer.log              5.0 KB       
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   5.0 KB        errors=0    warnings=18 
Log files:  OMEROweb_brokenrequest.lock    0.0 KB       
Log files:  OMEROweb_brokenrequest.log     0.0 KB       
Log files:  PixelData-0.log                13.0 KB     
Log files:  Processor-0.log                235.0 KB      errors=68   warnings=2   
Log files:  Tables-0.log                   6.0 KB        errors=0    warnings=2   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     4.0 KB        errors=0    warnings=8   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     6.95 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
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? True   Is writable? True
OMERO temp dir:'/home/omero/omero/tmp'        Exists? True   Is writable? True   (Size: 816)

JVM settings: Blitz-${index}                -Xmx5052m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx3368m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx5052m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx3368m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... You are deploying OMERO.web using apache and mod_wsgi. Cannot check status.
Django version: 1.8.12

Any advice to have the web access restored would be greeeeatly appreciated.

Philippe

Hi,

The step you refer to is the creation of configuration for the web server which hosts OMERO.web.

We have a couple of walkthroughs which show how to do this for Ubuntu and CentOS:

https://www.openmicroscopy.org/site/sup ... index.html

If your'e still having problems after looking at those walkthroughs, please let us know.

Cheers,

Kenny

Thanks for your quick feedback!
I also followed that tutorial.
$ OMERO.server/bin/omero web start
gave me:

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Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'

0 static files copied to '/home/omero/OMERO.server/lib/python/omeroweb/static', 618 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time... [OK]
You are deploying OMERO.web using apache and mod_wsgi. Generate apache config using 'omero web config apache' and reload web server.


I guess the problem is that I don't know what to do with the Apache cfg I got earlier, which is:

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<VirtualHost _default_:80>

  WSGIDaemonProcess omeroweb processes=5 threads=1 maximum-requests=0 display-name=%{GROUP} user=omero python-path=/usr/lib/python2.7/dist-packages:/home/omero/OMERO.server-5.2.2-ice35-b17/lib/python:/home/omero/OMERO.server-5.2.2-ice35-b17/lib/fallback:/home/omero/OMERO.server-5.2.2-ice35-b17/lib/python/omeroweb

  WSGIScriptAlias / /home/omero/OMERO.server-5.2.2-ice35-b17/lib/python/omeroweb/wsgi.py process-group=omeroweb

  <Directory "/home/omero/OMERO.server-5.2.2-ice35-b17/lib/python/omeroweb">
    WSGIProcessGroup omeroweb
    WSGIApplicationGroup %{GLOBAL}
    Order allow,deny
    Allow from all
  </Directory>

  Alias /static /home/omero/OMERO.server-5.2.2-ice35-b17/lib/python/omeroweb/static
  <Directory "/home/omero/OMERO.server-5.2.2-ice35-b17/lib/python/omeroweb/static">
      Options -Indexes FollowSymLinks
      Order allow,deny
      Allow from all
  </Directory>

</VirtualHost>

# see https://code.google.com/p/modwsgi/wiki/ConfigurationIssues
WSGISocketPrefix run/wsgi
# Use this on Ubuntu/Debian/MacOSX systems:
# WSGISocketPrefix /var/run/wsgi


Should I create a file with that (under what name?) and copy it somewhere (where?)? I could not find information on what to do with that file.

PhilippeP wrote:Thanks for your quick feedback!

Should I create a file with that (under what name?) and copy it somewhere (where?)? I could not find information on what to do with that file.

Hi,

You're welcome.

That file really needs to be given to the web server, which can be Apache, or Nginx, for example.

The server installation walkthrough has steps to create the file, and copy it to the correct location, which varies depending the path you've chosen to install.

* What version of linux are you using?
* Which of the walkthroughs did you follow to create your installation?
* What version of Apache are you using / do you have installed?

If you could get back to us with these, it will help us all work out how to redeploy web.

Thanks,

Kenny

* What version of linux are you using?

Ubuntu server 16.04

* Which of the walkthroughs did you follow to create your installation?

http://www.openmicroscopy.org/site/supp ... rough.html
AND when things were not working I tried (or the other way around)
http://www.openmicroscopy.org/site/supp ... tml#apache
Both walkthroughs are identical, right?
I must say I installed both Apache and Nginx. May not be the smartest thing I've done...

* What version of Apache are you using / do you have installed?

Server version: Apache/2.4.18 (Ubuntu)

EDIT: I just uninstalled Nginx, and reinstalled Apache following the walkthrough.
But I again get the same request for apache config file (see below in "code" frame), which is supposed to have been copied during the OMERO.web install walkthrough with:
cp ~omero/OMERO.server/apache.conf.tmp /etc/apache2/sites-available/omero-web.conf

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omero@pc5944:~$ OMERO.server/bin/omero web start
Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'

0 static files copied to '/home/omero/OMERO.server/lib/python/omeroweb/static', 618 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time... [OK]
You are deploying OMERO.web using apache and mod_wsgi. Generate apache config using 'omero web config apache' and reload web server.


Hi Philippe,

PhilippeP wrote:

* Which of the walkthroughs did you follow to create your installation?

http://www.openmicroscopy.org/site/supp ... rough.html
AND when things were not working I tried (or the other way around)
http://www.openmicroscopy.org/site/supp ... tml#apache
Both walkthroughs are identical, right?

This is the same page, did you intend to point to different pages?

PhilippeP wrote:I must say I installed both Apache and Nginx. May not be the smartest thing I've done...

* What version of Apache are you using / do you have installed?

Server version: Apache/2.4.18 (Ubuntu)

You do not need both as they will clash on the same port. I would recommend you first stop both Apache and nginx, then uninstall one of them and keep only that one you feel more familiar with.
Lets say you kept nginx,

Follow instruction on Nginx section only as stated in http://www.openmicroscopy.org/site/supp ... html#nginx

Once you successfully started nginx go to http://localhost OMERO.web should be up and running

I hope it will help.

Can I ask what is the purpose of running the server? Do you know that we offer demo server for testing? To get account follow http://qa.openmicroscopy.org.uk/registry/demo_account/


Ola

Hi Ola,

This is the same page, did you intend to point to different pages?

I meant:
https://www.openmicroscopy.org/site/sup ... pache.html

I guess I was editing the post while you were answering it, and as I mentioned in the "Edit", I went on removing one server. I left Apache, and followed the instruction found on:
http://www.openmicroscopy.org/site/supp ... tml#apache
But as shown in my "Edit", still no luck.

This server is used by 5 labs working a common project, and we upload and exchange on it thousands of images from HCS acquisitions. This is why we needed our own, after being convinced with the Demo server I tried a few months ago that OMERO was what we needed for this type of collaborative work.

Philippe

Hi,

PhilippeP wrote:I guess I was editing the post while you were answering it, and as I mentioned in the "Edit", I went on removing one server. I left Apache, and followed the instruction found on:
http://www.openmicroscopy.org/site/supp ... tml#apache
But as shown in my "Edit", still no luck.

Could you be more explicit what is not working? What is the error? Which url are you trying?
Could you also give an output of

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bin/omero admin diagnostics

and

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bin/omero config get --hide-password

and send all logs from OMERO.server/var/log/ and apache error logs

Ola

Could you be more explicit what is not working? What is the error? Which url are you trying?

Connection fails when going on:
http://pc5944.unice.fr/
with 503 error message:
Service Unavailable
The server is temporarily unable to service your request due to maintenance downtime or capacity problems. Please try again later.
Apache/2.4.18 (Ubuntu) Server at pc5944.unice.fr Port 80

Could you also give an output of... bin/omero admin diagnostics

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omero@pc5944:~/OMERO.server$ bin/omero admin diagnostics

================================================================================
OMERO Diagnostics 5.2.2-ice35-b17
================================================================================
       
Commands:   java -version                  1.8.0     (/usr/bin/java)
Commands:   python -V                      2.7.11    (/usr/bin/python)
Commands:   icegridnode --version          3.5.1     (/usr/bin/icegridnode)
Commands:   icegridadmin --version         3.5.1     (/usr/bin/icegridadmin)
Commands:   psql --version                 9.5.2     (/usr/bin/psql)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 2360, enabled)
Server:     DropBox                        active (pid = 2402, enabled)
Server:     FileServer                     active (pid = 2410, enabled)
Server:     Indexer-0                      active (pid = 2411, enabled)
Server:     MonitorServer                  active (pid = 2412, enabled)
Server:     OMERO.Glacier2                 active (pid = 2427, enabled)
Server:     OMERO.IceStorm                 active (pid = 2445, enabled)
Server:     PixelData-0                    active (pid = 2414, enabled)
Server:     Processor-0                    active (pid = 2438, enabled)
Server:     Tables-0                       active (pid = 2425, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /home/omero/OMERO.server-5.2.2-ice35-b17/var/log exists
Log files:  Blitz-0.log                    96.0 MB       errors=103  warnings=51 
Log files:  DropBox.log                    8.0 KB        errors=0    warnings=3   
Log files:  FileServer.log                 1.0 KB       
Log files:  Indexer-0.log                  41.0 KB       errors=0    warnings=1   
Log files:  MonitorServer.log              5.0 KB       
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   6.0 KB        errors=0    warnings=24 
Log files:  OMEROweb_brokenrequest.lock    0.0 KB       
Log files:  OMEROweb_brokenrequest.log     0.0 KB       
Log files:  PixelData-0.log                21.0 KB     
Log files:  Processor-0.log                294.0 KB      errors=85   warnings=2   
Log files:  Tables-0.log                   6.0 KB        errors=0    warnings=2   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     4.0 KB        errors=0    warnings=8   
Log files:  master.out                     0.0 KB       
Log files:  Total size                     97.29 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=(unset)           
Environment:PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games
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? True   Is writable? True
OMERO temp dir:'/home/omero/omero/tmp'        Exists? True   Is writable? True   (Size: 816)

JVM settings: Blitz-${index}                -Xmx5052m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx3368m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx5052m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx3368m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... You are deploying OMERO.web using apache and mod_wsgi. Cannot check status.
Django version: 1.8.12
omero@pc5944:~/OMERO.server$

and... bin/omero config get --hide-password

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omero@pc5944:~/OMERO.server$ bin/omero config get --hide-password
omero.data.dir=/OMERO
omero.db.name=tiro_database
omero.db.pass=********
omero.db.user=tiro
omero.web.application_server=wsgi
omero.web.wsgi_args= --error-logfile=/home/omero/OMERO.server/var/log/error.log
omero@pc5944:~/OMERO.server$

logs are attached are a compressed file, except for Blitz-0.log which is too big and I guess is irrelevant?.

Thanks for your help!
Philippe

Sorry forgot to ask you about apache.conf.tmp config as well, but my guess is that you are missing:

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The default value set for the WSGISocketPrefix directive in apache.conf.tmp needs to be modified:

#see https://code.google.com/p/modwsgi/wiki/ConfigurationIssues
WSGISocketPrefix run/wsgi
# Use this on Ubuntu/Debian systems:
# WSGISocketPrefix /var/run/wsgi


if the above doesn't work try

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WSGISocketPrefix /var/run/apache2/wsgi

Ola