Problems with upgrading 5.1.2 to 5.2

[phm]

Yes, it sounds like an invalid config. Could you paste the output of

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omero config get --hide-password

Thanks, Simon

omero config get --hide-password
omero.data.dir=/OMERO
omero.db.name=omero_database
omero.db.pass=********
omero.db.user=db_omero
omero.jvmcfg.percent.blitz=20
omero.jvmcfg.system_memory=32000
omero.mail.config=true
omero.mail.host=smtp.college-de-france.fr
omero.mail.password=********
omero.mail.port=25
omero.mail.username=philippe.mailly@col ... -france.fr
omero.web.admins=[["Philippe Mailly", "philippe.mailly@college-de-france.fr"]]
omero.web.application_server=wsgi
omero.web.apps=["figure", "figure"]
omero.web.debug=False
omero.web.login_logo=/omero/static/webclient/image/logo_CIRB.jpg
omero.web.prefix=/omero
omero.web.public.enabled=False
omero.web.session_cookie_age=86400
omero.web.session_expire_at_browser_close=True
omero.web.static_url=/omero/static/
omero.web.ui.top_links=[["Data", "webindex", {"title": "Browse Data via Projects, Tags etc"}], ["History", "history", {"title": "History"}], ["Help", "http://help.openmicroscopy.org/", {"target": "new", "title": "Open OMERO user guide in a new tab"}], ["Figure", "figure_index", {"title": "Fast figures from your OMERO images"}]]

Thanks

Philippe

[sbesson]

Hi Philippe,

the following line

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omero.web.apps=["figure", "figure"]


might explain the duplicate warning you saw. Could you try to run:

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bin/omero config remove omero.web.apps '"figure"'


and then restart the Web?

Best,
Sebastien

[atarkowska]

Hi Philippe,

Clean web apps and then add figure again

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$OMERO_PREFIX/bin/omero config set omero.web.apps
$OMERO_PREFIX/bin/omero config append omero.web.apps '"figure"'

then restart web
Ola

[phm]

Hi Philippe,

Clean web apps and then add figure again

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$OMERO_PREFIX/bin/omero config set omero.web.apps
$OMERO_PREFIX/bin/omero config append omero.web.apps '"figure"'

then restart web
Ola

Hi Ola,

I Clean web apps and then add figure again.
When I restart omero web I got :

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 '/opt/OMERO.server/lib/python/omeroweb/static', 700 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.

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omero web config apache > web_omero.conf
cp web_omero.conf /etc/init.d/httpd/conf.d/
/etc/init.d/httpd restart
Arrêt de httpd :                                           [  OK  ]
Démarrage de httpd :                                       [  OK  ]


omero web start return same message ???
And web page not found
The requested URL /omero/webclient/login/ was not found on this server.

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more /opt/OMERO.server/var/log/OMEROweb.log

2015-11-05 14:47:32,257 WARNI [                             py.warnings] (proc.31388) <module>:9 /opt/OMERO.server/lib/python/pipeline/utils.py:11: RemovedInDjango1
9Warning: django.utils.importlib will be removed in Django 1.9.
  from django.utils import importlib

2015-11-05 14:47:33,900 WARNI [       django.security.SuspiciousSession] (proc.31395) decode:108 Session data corrupted
2015-11-05 14:47:33,901 WARNI [       django.security.SuspiciousSession] (proc.31395) decode:108 Session data corrupted
2015-11-05 14:47:33,902 WARNI [       django.security.SuspiciousSession] (proc.31395) decode:108 Session data corrupted
2015-11-05 14:56:39,105 WARNI [                             py.warnings] (proc.31746) <module>:9 /opt/OMERO.server/lib/python/pipeline/utils.py:11: RemovedInDjango1
9Warning: django.utils.importlib will be removed in Django 1.9.
  from django.utils import importlib

2015-11-05 15:04:59,029 WARNI [                             py.warnings] (proc.32301) <module>:9 /opt/OMERO.server/lib/python/pipeline/utils.py:11: RemovedInDjango1
9Warning: django.utils.importlib will be removed in Django 1.9.
  from django.utils import importlib

2015-11-05 15:06:49,935 WARNI [                             py.warnings] (proc.32399) <module>:9 /opt/OMERO.server/lib/python/pipeline/utils.py:11: RemovedInDjango1
9Warning: django.utils.importlib will be removed in Django 1.9.
  from django.utils import importlib



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tail /var/log/httpd/ssl_error_log

[Thu Nov 05 17:32:58 2015] [error] [client 192.168.111.149] Directory index forbidden by Options directive: /var/www/html/
[Thu Nov 05 17:33:28 2015] [error] [client 192.168.111.149] Directory index forbidden by Options directive: /var/www/html/
[Thu Nov 05 17:33:58 2015] [error] [client 192.168.111.149] Directory index forbidden by Options directive: /var/www/html/
[Thu Nov 05 17:34:28 2015] [error] [client 192.168.111.149] Directory index forbidden by Options directive: /var/www/html/
[Thu Nov 05 17:34:45 2015] [error] [client 192.168.188.18] File does not exist: /var/www/html/omero



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touch /var/www/html/omero
tail /var/log/httpd/ssl_error_log
[Thu Nov 05 17:51:27 2015] [error] [client 192.168.156.6] File does not exist: /var/www/html/omero/webclient/login/



Strange ???
Philippe

[atarkowska]

Hi Philippe,

If you deploy web using Apache you do not start web. When mod_wsgi is used in 'daemon' mode, UNIX sockets are used to communicate between the Apache child processes and the daemon processes which are to handle a request. The only thing what you need to do is collect statics.

Did you check https://code.google.com/p/modwsgi/wiki/ ... tionIssues

And if you use 2.4 could you try to replace:

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Order allow,deny
Allow from all

With

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Require all granted

Could you give me more details about: Apache version, how did you install mod_wsgi. Could you also paste your OMERO.web Apache config, which user runs OMERO?

Ola

[phm]

Hi Philippe,

If you deploy web using Apache you do not start web. When mod_wsgi is used in 'daemon' mode, UNIX sockets are used to communicate between the Apache child processes and the daemon processes which are to handle a request. The only thing what you need to do is collect statics.

Did you check https://code.google.com/p/modwsgi/wiki/ ... tionIssues

And if you use 2.4 could you try to replace:

Code: Select all

Order allow,deny
Allow from all

With

Code: Select all

Require all granted

Could you give me more details about: Apache version, how did you install mod_wsgi. Could you also paste your OMERO.web Apache config, which user runs OMERO?

Ola

Hi Ola,

httpd -v
Server version: Apache/2.2.15 (Unix)
Server built: Aug 24 2015 17:52:49

I installed mod_wsgi with yum install mod_wsgi
My web omero conf is :

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###
# apache config for omero
# this file should be loaded *after* ssl.conf
#
# -D options to control configurations
#  OmeroForceSSL - redirect all http requests to https

###
### Example SSL stanza for OMERO.web created 2015-11-05 16:05:55.425377
###

# Eliminate overlap warnings with the default ssl vhost
# Requires SNI (http://wiki.apache.org/httpd/NameBasedSSLVHostsWithSNI)
# support most later versions of mod_ssl and OSes will support it if you see
# "You should not use name-based virtual hosts in conjunction with SSL!!"
# or similar start apache with -D DISABLE_SNI and modify ssl.conf
#<IfDefine !DISABLE_SNI>
#  NameVirtualHost *:443
#</IfDefine>
#
## force https/ssl
#<IfDefine OmeroForceSSL>
#  RewriteEngine on
#  RewriteCond %{HTTPS} !on
#  RewriteRule (.*) https://%{HTTP_HOST}%{REQUEST_URI} [L]
#</IfDefine>
#
#<VirtualHost _default_:443>
#
#  ErrorLog logs/ssl_error_log
#  TransferLog logs/ssl_access_log
#  LogLevel warn
#
#  SSLEngine on
#  SSLProtocol all -SSLv2
#  SSLCipherSuite ALL:!ADH:!EXPORT:!SSLv2:RC4+RSA:+HIGH:+MEDIUM:+LOW
#  SSLCertificateFile /etc/pki/tls/certs/server.crt
#  SSLCertificateKeyFile /etc/pki/tls/private/server.key
#
#  # SSL Protocol Adjustments:
#  SetEnvIf User-Agent ".*MSIE.*" \
#    nokeepalive ssl-unclean-shutdown \
#    downgrade-1.0 force-response-1.0
#
#  # Per-Server Logging:
#  CustomLog logs/ssl_request_log \
#    "%t %h %{SSL_PROTOCOL}x %{SSL_CIPHER}x \"%r\" %b"
#
#</VirtualHost>

###
### Stanza for OMERO.web created 2015-11-05 16:05:55.425377
###

<VirtualHost _default_:80>

  DocumentRoot /opt/OMERO.server/lib/python/omeroweb

  WSGIDaemonProcess omeroweb_omero processes=5 threads=1 display-name=%{GROUP} user=omero python-path=/opt/Ice-3.5.1/python:/opt/OMERO.server/lib/python:/opt/OMERO.server/
lib/fallback:/opt/OMERO.server/lib/python/omeroweb
 
  WSGIProcessGroup omeroweb_omero

  WSGIScriptAlias /omero /opt/OMERO.server/lib/python/omeroweb/wsgi.py

  <Directory "/opt/OMERO.server/lib/python/omeroweb">
    #Order allow,deny
    #Allow from all
    Require all granted
  </Directory>
###

<VirtualHost _default_:80>

  DocumentRoot /opt/OMERO.server/lib/python/omeroweb

  WSGIDaemonProcess omeroweb_omero processes=5 threads=1 display-name=%{GROUP} user=omero python-path=/opt/Ice-3.5.1/python:/opt/OMERO.server/lib/python:/opt/OMERO.server/
lib/fallback:/opt/OMERO.server/lib/python/omeroweb
 
  WSGIProcessGroup omeroweb_omero

  WSGIScriptAlias /omero /opt/OMERO.server/lib/python/omeroweb/wsgi.py

  <Directory "/opt/OMERO.server/lib/python/omeroweb">
    #Order allow,deny
    #Allow from all
    Require all granted
  </Directory>

  Alias /omero/static /opt/OMERO.server/lib/python/omeroweb/static
  <Directory "/opt/OMERO.server/lib/python/omeroweb/static">
      Options -Indexes FollowSymLinks
      #Order allow,deny
      #Allow from all
      Require all granted
  </Directory>

</VirtualHost>

# see https://code.google.com/p/modwsgi/wiki/ConfigurationIssues
WSGISocketPrefix run/wsgi
# WSGISocketPrefix /var/run/wsgi


It come from omero web config apache > web_omero.conf except I replaced the lines :
Order allow,deny
Allow from all
by
Require all granted

I check the google page and the module alias (LoadModule alias_module modules/mod_alias.so in httpd.conf) is start before mod_wgsi which is started after by loading the module wgsi.conf in /etc/httpd/conf.d/

Is it the problem ??


Thanks

Philippe

[atarkowska]

Hi Philippe,

I am not sure but could you show me the output of

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ldd /etc/httpd/modules/mod_wsgi.so

Ola

[phm]

Hi Philippe,

I am not sure but could you show me the output of

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ldd /etc/httpd/modules/mod_wsgi.so

Ola

Code: Select all

ldd /etc/httpd/modules/mod_wsgi.so
   linux-vdso.so.1 =>  (0x00007ffd155fe000)
   libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007f77dfbc7000)
   libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f77df9a9000)
   libdl.so.2 => /lib64/libdl.so.2 (0x00007f77df7a5000)
   libutil.so.1 => /lib64/libutil.so.1 (0x00007f77df5a2000)
   libm.so.6 => /lib64/libm.so.6 (0x00007f77df31d000)
   libc.so.6 => /lib64/libc.so.6 (0x00007f77def89000)
   /lib64/ld-linux-x86-64.so.2 (0x0000003fe2800000)



It seems that it linked to python 2.6 and may be should be to 2.7 no ?

Philippe

[atarkowska]

I am afraid you didn't recompile it with scl python

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libpython2.6.so.1.0 => /usr/lib64/libpython2.6.so.1.0 (0x00007f77dfbc7000)


it should be :

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ldd /etc/httpd/modules/mod_wsgi.so
   libpython2.7.so.1.0 => /opt/rh/python27/root/usr/lib64/libpython2.7.so.1.0 (0x00007ff8a9063000)


Ola

[atarkowska]

Philippe, Do you have nginx available for you? it does not need to be on the same box.

Ola