Figure and PDF export

[kennethgillen]

You may need to try Ola's command as root, rather than as the OMERO user.

[phm]

You may need to try Ola's command as root, rather than as the OMERO user.

Hi Kenneth,
I did as Ola under root

Code: Select all


[root@omero omero]# source /opt/rh/python27/enable
[root@omero omero]# pip install reportlab markdown
Collecting reportlab
/opt/rh/python27/root/usr/lib/python2.7/site-packages/pip-7.1.2-py2.7.egg/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
  Using cached reportlab-3.3.0.tar.gz
Collecting markdown
  Using cached Markdown-2.6.6.zip
Requirement already satisfied (use --upgrade to upgrade): pillow>=2.4.0 in /opt/rh/python27/root/usr/lib64/python2.7/site-packages (from reportlab)
Requirement already satisfied (use --upgrade to upgrade): pip>=1.4.1 in /opt/rh/python27/root/usr/lib/python2.7/site-packages/pip-7.1.2-py2.7.egg (from reportlab)
Collecting setuptools>=2.2 (from reportlab)
  Downloading setuptools-25.1.4-py2.py3-none-any.whl (443kB)
    100% |████████████████████████████████| 446kB 429kB/s
Installing collected packages: setuptools, reportlab, markdown
  Found existing installation: setuptools 0.9.8
    Uninstalling setuptools-0.9.8:
      Successfully uninstalled setuptools-0.9.8
  Running setup.py install for reportlab
  Running setup.py install for markdown
Successfully installed markdown-2.6.6 reportlab-3.3.0 setuptools-25.1.4
/opt/rh/python27/root/usr/lib/python2.7/site-packages/pip-7.1.2-py2.7.egg/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
You are using pip version 7.1.2, however version 8.1.2 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
[root@omero omero]# pip install --upgrade pip
/opt/rh/python27/root/usr/lib/python2.7/site-packages/pip-7.1.2-py2.7.egg/pip/_vendor/requests/packages/urllib3/util/ssl_.py:90: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
  InsecurePlatformWarning
Collecting pip
  Using cached pip-8.1.2-py2.py3-none-any.whl
Installing collected packages: pip
  Found existing installation: pip 7.1.2
    Uninstalling pip-7.1.2:
      Successfully uninstalled pip-7.1.2
Successfully installed pip-8.1.2
[root@omero omero]# pip install reportlab markdown
Requirement already satisfied (use --upgrade to upgrade): reportlab in /opt/rh/python27/root/usr/lib64/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): markdown in /opt/rh/python27/root/usr/lib/python2.7/site-packages
Requirement already satisfied (use --upgrade to upgrade): pillow>=2.4.0 in /opt/rh/python27/root/usr/lib64/python2.7/site-packages (from reportlab)
Requirement already satisfied (use --upgrade to upgrade): pip>=1.4.1 in /opt/rh/python27/root/usr/lib/python2.7/site-packages (from reportlab)
Requirement already satisfied (use --upgrade to upgrade): setuptools>=2.2 in /opt/rh/python27/root/usr/lib/python2.7/site-packages (from reportlab)


Anyway I have the same error message concerning PDF export, should I do restart the web or omero server?
Philippe

[kennethgillen]

Fantastic news!

Just restart OMERO.web, see if that has any effect.

[phm]

Fantastic news!

Just restart OMERO.web, see if that has any effect.

I reboot the server and now omero server is working (Insight) but omero web display 404 not found
That I don't understand is the line OMERO.web status... [NOT STARTED] when I run omero admin diagnostics while

Code: Select all

[omero@omero log]$ omero web restart
Stopping OMERO.web... [FAILED]
OMERO.web WSGI workers (PID 13372) not started?
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', 718 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time...
[OK]
Starting OMERO.web... [OK]


Philippe

[kennethgillen]

If you could please send us the following:

* OMERO.server logs: ${OMERO_SERVER}/var/log
* System nginx logs (CentOS/RHEL) /var/log/nginx/{access.log,error.log}

Thanks

Kenny

[atarkowska]

Philippe did you souce scl python and export all relevant variables like in https://github.com/ome/omero-install/bl ... s6py27.env

You have to do it anytime you open your terminal and want to start/stop/restart omero server and web.

Before you start

Code: Select all

ps -ef | grep gunicorn

and check if any of OMERO.web processes are still running. If so kill them by hand

Ola

[phm]

Philippe did you souce scl python and export all relevant variables like in https://github.com/ome/omero-install/bl ... s6py27.env

You have to do it anytime you open your terminal and want to start/stop/restart omero server and web.

Before you start

Code: Select all

ps -ef | grep gunicorn

and check if any of OMERO.web processes are still running. If so kill them by hand

Ola

Hi Ola

[omero@omero ~]$ more .bashrc

Code: Select all

# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
   . /etc/bashrc
fi

# User specific aliases and functions
source /opt/rh/python27/enable
ICE_HOME=/opt/Ice-3.5.1
PATH="${ICE_HOME}/bin:$PATH"
export LD_LIBRARY_PATH="${ICE_HOME}/lib64:${ICE_HOME}/lib:$LD_LIBRARY_PATH"
export PYTHONPATH="${ICE_HOME}/python:$PYTHONPATH"
export SLICEPATH="${ICE_HOME}/slice"


[omero@omero ~]$ ps -ef | grep gunicorn

Code: Select all

omero    11907     1  0 Aug05 ?        00:00:37 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    11912 11907  0 Aug05 ?        00:00:04 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    11913 11907  0 Aug05 ?        00:00:04 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    11914 11907  0 Aug05 ?        00:00:04 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    11915 11907  0 Aug05 ?        00:00:04 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    11916 11907  0 Aug05 ?        00:00:05 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    30712 30539  0 10:07 pts/0    00:00:00 grep gunicorn


[omero@omero ~]$ kill -9 11907 11912 11913 11914 11915 11916

[omero@omero ~]$ omero admin restart

Code: Select all

Waiting on shutdown. Use CTRL-C to exit
.No descriptor given. Using etc/grid/default.xml
Waiting on startup. Use CTRL-C to exit


[omero@omero ~]$ omero web restart

Code: Select all

Stopping OMERO.web... [FAILED]
OMERO.web WSGI workers (PID 15043) not started?
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', 718 unmodified, 2 post-processed.
Clearing expired sessions. This may take some time...
[OK]
Starting OMERO.web... [OK]


I have always the 404 not found web page

Code: Select all


[omero@omero ~]$ omero admin diagnostics

================================================================================
OMERO Diagnostics 5.2.0-ice35-b12
================================================================================
       
Commands:   java -version                  1.7.0     (/usr/java/latest/bin/java)
Commands:   python -V                      2.7.5     (/opt/rh/python27/root/usr/bin/python -- 3 others)
Commands:   icegridnode --version          3.5.1     (/opt/Ice-3.5.1/bin/icegridnode -- 2 others)
Commands:   icegridadmin --version         3.5.1     (/opt/Ice-3.5.1/bin/icegridadmin -- 2 others)
Commands:   psql --version                 9.4.8     (/usr/pgsql-9.4/bin/psql -- 2 others)

Server:     icegridnode                    running
Server:     Blitz-0                        active (pid = 30847, enabled)
Server:     DropBox                        active (pid = 30867, enabled)
Server:     FileServer                     active (pid = 30869, enabled)
Server:     Indexer-0                      active (pid = 30872, enabled)
Server:     MonitorServer                  active (pid = 30889, enabled)
Server:     OMERO.Glacier2                 active (pid = 30873, enabled)
Server:     OMERO.IceStorm                 active (pid = 30877, enabled)
Server:     PixelData-0                    active (pid = 30887, enabled)
Server:     Processor-0                    active (pid = 30891, enabled)
Server:     Tables-0                       active (pid = 30907, enabled)
Server:     TestDropBox                    inactive (enabled)

Log dir:    /opt/OMERO.server/var/log      exists
Log files:  Blitz-0.log                    15.0 MB       errors=85   warnings=6   
Log files:  DropBox.log                    3.0 KB        errors=0    warnings=1   
Log files:  FileServer.log                 0.0 KB       
Log files:  Indexer-0.log                  74.0 KB     
Log files:  MonitorServer.log              2.0 KB       
Log files:  OMEROweb.lock                  0.0 KB       
Log files:  OMEROweb.log                   2.0 KB        errors=0    warnings=13 
Log files:  OMEROweb_brokenrequest.lock    0.0 KB       
Log files:  OMEROweb_brokenrequest.log     0.0 KB       
Log files:  PixelData-0.log                28.0 KB     
Log files:  Processor-0.log                326.0 KB      errors=85   warnings=1   
Log files:  Tables-0.log                   2.0 KB        errors=0    warnings=1   
Log files:  TestDropBox.log                n/a
Log files:  master.err                     0.0 KB       
Log files:  master.out                     0.0 KB       
Log files:  Total size                     15.49 MB


Environment:OMERO_HOME=(unset)             
Environment:OMERO_NODE=(unset)             
Environment:OMERO_MASTER=(unset)           
Environment:OMERO_USERDIR=(unset)         
Environment:OMERO_TMPDIR=/tmp             
Environment:PATH=/opt/Ice-3.5.1/bin:/opt/rh/python27/root/usr/bin:/usr/pgsql-9.4/bin/:/usr/lib64/qt-3.3/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/opt/dell/srvadmin/bin:/opt/OMERO.server/bin:/opt/dell/srvadmin/sbin:/usr/java/latest/bin
Environment:PYTHONPATH=/opt/Ice-3.5.1/python:
Environment:ICE_HOME=(unset)               
Environment:LD_LIBRARY_PATH=/opt/Ice-3.5.1/lib64:/opt/Ice-3.5.1/lib:/opt/rh/python27/root/usr/lib64
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:'/tmp'                         Exists? True   Is writable? True   (Size: 513832)

JVM settings: Blitz-${index}                -Xmx6400m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index}              -Xmx3200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index}            -Xmx4800m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index}           -Xmx3200m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions

OMERO.web status... [RUNNING] (PID 31874)
Django version: 1.8.6


[omero@omero ~]$ tail /opt/OMERO.server/var/log/Blitz-0.log

Code: Select all

2016-08-08 10:21:37,748 INFO  [ome.services.sessions.SessionManagerImpl] (.Server-15) closeSession called but doesn't exist: 3586d8a1-27e6-4d06-9e0e-d12e9e65e590
2016-08-08 10:21:37,751 INFO  [                      omero.cmd.SessionI] (.Server-11) Session already removed. Cleaning up blitz state.
2016-08-08 10:21:37,751 INFO  [                      omero.cmd.SessionI] (.Server-11) doDestroy(ServiceFactoryI(session-d126f436-fc01-4d49-bc0e-5b7342f33936/62a675df-cda2-439c-a27b-dc07e441a0ac))
2016-08-08 10:21:37,751 INFO  [                      omero.cmd.SessionI] (.Server-11) Unregistered servant:62a675df-cda2-439c-a27b-dc07e441a0ac/d126f436-fc01-4d49-bc0e-5b7342f33936omero.api.ISession(omero.api._ISessionTie@f428251a)
2016-08-08 10:21:37,751 INFO  [                      omero.cmd.SessionI] (.Server-11) Removed servant from adapter: d126f436-fc01-4d49-bc0e-5b7342f33936omero.api.ISession
2016-08-08 10:21:37,752 INFO  [ome.services.sessions.SessionManagerImpl] (.Server-11) closeSession called but doesn't exist: 62a675df-cda2-439c-a27b-dc07e441a0ac
2016-08-08 10:22:05,729 INFO  [        ome.services.util.ServiceHandler] (l.Server-3)  Meth:   interface ome.api.ISession.getSession
2016-08-08 10:22:05,730 INFO  [        ome.services.util.ServiceHandler] (l.Server-3)  Args:   [dd3b9451-21af-4f74-976f-9b8b5e2eb310]
2016-08-08 10:22:05,730 INFO  [                 org.perf4j.TimingLogger] (l.Server-3) start[1470644525730] time[0] tag[omero.call.success.ome.services.sessions.SessionBean.getSession]
2016-08-08 10:22:05,730 INFO  [        ome.services.util.ServiceHandler] (l.Server-3)  Rslt:   ome.model.meta.Session:Id_67599


[omero@omero ~]$ tail /opt/OMERO.server/var/log/OMEROweb.log

Code: Select all

  from django.utils import importlib

2016-08-05 15:28:15,849 WARNI [       django.security.SuspiciousSession] (proc.15034) decode:108 Session data corrupted
2016-08-05 15:28:15,849 WARNI [       django.security.SuspiciousSession] (proc.15034) decode:108 Session data corrupted
2016-08-06 02:29:31,708 WARNI [       django.security.SuspiciousSession] (proc.34109) decode:108 Session data corrupted
2016-08-06 02:29:31,708 WARNI [       django.security.SuspiciousSession] (proc.34109) decode:108 Session data corrupted
2016-08-07 02:37:06,625 WARNI [       django.security.SuspiciousSession] (proc.26951) decode:108 Session data corrupted
2016-08-08 09:11:52,255 WARNI [                             py.warnings] (proc.31822) <module>:9 /opt/OMERO.server/lib/python/pipeline/utils.py:11: RemovedInDjango19Warning: django.utils.importlib will be removed in Django 1.9.
  from django.utils import importlib


Philippe

[atarkowska]

Hi Philippe

This looks correct now. Could you check again

Code: Select all

ps -ef | grep gunicorn

and see if root process pid is 31874. Could you also check in nginx logs (access.log and error.log) why you are getting 404?

Ola

[atarkowska]

Could you also tell which 404 we are talking about exactly? Is that omero.web grey page?

What is the output of

Code: Select all

curl -I https://omero.college-de-france.fr/omero

Ola

[phm]

Hi Philippe

This looks correct now. Could you check again

Code: Select all

ps -ef | grep gunicorn

and see if root process pid is 31874. Could you also check in nginx logs (access.log and error.log) why you are getting 404?

Ola

Hi Ola

Code: Select all

[root@omero omero]# ps -ef | grep gunicorn
omero    31874     1  0 10:11 ?        00:00:01 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    31879 31874  0 10:11 ?        00:00:01 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    31880 31874  0 10:11 ?        00:00:01 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    31881 31874  0 10:11 ?        00:00:01 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    31882 31874  0 10:11 ?        00:00:01 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
omero    31891 31874  0 10:11 ?        00:00:01 /opt/rh/python27/root/usr/bin/python2 /opt/rh/python27/root/usr/bin/gunicorn -D -p /opt/OMERO.server/var/django.pid --bind 127.0.0.1:4080 --workers 5 --worker-connections 1000 --max-requests 0 omeroweb.wsgi:application
root     37934 32695  0 11:48 pts/0    00:00:00 grep gunicorn


The nginx log files are empty ??

Code: Select all

[root@omero omero]# ls -l /var/log/nginx/
total 212
-rw-r-----. 1 nginx adm      0  6 août  03:29 access.log
-rw-r-----. 1 nginx adm 207421  5 août  12:28 access.log-20160806
-rw-r-----. 1 nginx adm      0  6 août  03:29 error.log
-rw-r-----. 1 nginx adm   2802  5 août  12:32 error.log-20160806
[root@omero omero]#


Philippe