Hi Philippe,
It seems you've found a bug in our documentation deployment. That text should read along the lines of "If upgrading from a 5.4.0 server, you do not need to upgrade the database".
Very sorry about that confusion.
The OME community
by kennethgillen » Fri Dec 08, 2017 1:51 pm
by phm » Fri Dec 08, 2017 2:19 pm
omero@omero:~/OMERO.server-5.4.1-ice36-b75$>psql -h localhost -U db_omero omero_database < sql/psql/OMERO5.4__0/OMERO5.3__0.sql
Mot de passe pour l'utilisateur db_omero :
BEGIN
CREATE FUNCTION
omero_assert_db_version
-------------------------
(1 ligne)
DROP FUNCTION
CREATE FUNCTION
CREATE FUNCTION
assert_db_server_prerequisites
--------------------------------
(1 ligne)
DROP FUNCTION
DROP FUNCTION
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
INSERT 0 1
CREATE TABLE
INSERT 0 1
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE TRIGGER
CREATE TABLE
CREATE INDEX
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE FUNCTION
CREATE TRIGGER
CREATE TRIGGER
CREATE TRIGGER
CREATE TRIGGER
CREATE FUNCTION
CREATE FUNCTION
CREATE TRIGGER
CREATE TRIGGER
CREATE INDEX
DROP TABLE
CREATE TABLE
CREATE INDEX
CREATE FUNCTION
DROP INDEX
CREATE INDEX
UPDATE 1
status
---------------------------------------------------------------------
+
+
+
YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.4__0+
+
+
(1 ligne)
COMMIT
omero@omero:~$>omero admin diagnostics
================================================================================
OMERO Diagnostics (admin) 5.4.1-ice36-b75
================================================================================
Commands: java -version 1.8.0 (/usr/bin/java)
Commands: python -V 2.7.5 (/usr/bin/python)
Commands: icegridnode --version 3.6.4 (/usr/bin/icegridnode)
Commands: icegridadmin --version 3.6.4 (/usr/bin/icegridadmin)
Commands: psql --version 9.6.5 (/usr/bin/psql)
Server: icegridnode running
Server: Blitz-0 active (pid = 31849, enabled)
Server: DropBox active (pid = 31871, enabled)
Server: FileServer active (pid = 31875, enabled)
Server: Indexer-0 active (pid = 31879, enabled)
Server: MonitorServer active (pid = 31881, enabled)
Server: OMERO.Glacier2 active (pid = 31883, enabled)
Server: OMERO.IceStorm active (pid = 31894, enabled)
Server: PixelData-0 active (pid = 31895, enabled)
Server: Processor-0 active (pid = 31896, enabled)
Server: Tables-0 active (pid = 31907, enabled)
Server: TestDropBox inactive (enabled)
Log dir: /home/omero/OMERO.server/var/log exists
Log files: Blitz-0.log 827.0 KB errors=2 warnings=1
Log files: Blitz-0.log.gz 2.0 KB
Log files: DropBox.log 7.0 KB errors=8 warnings=4
Log files: FileServer.log 1.0 KB
Log files: Indexer-0.log 64.0 KB errors=4 warnings=0
Log files: MonitorServer.log 2.0 KB
Log files: OMEROweb.lock 0.0 KB
Log files: OMEROweb.log 0.0 KB
Log files: PixelData-0.log 65.0 KB errors=4 warnings=0
Log files: Processor-0.log 3.0 MB errors=859 warnings=1718
Log files: Tables-0.log 3.0 MB errors=859 warnings=1718
Log files: TestDropBox.log n/a
Log files: master.err 3.0 KB errors=4 warnings=7
Log files: master.out 0.0 KB
Log files: Total size 7.13 MB
Environment:OMERO_HOME=(unset)
Environment:OMERO_NODE=(unset)
Environment:OMERO_MASTER=(unset)
Environment:OMERO_USERDIR=(unset)
Environment:OMERO_TMPDIR=/tmp
Environment:PATH=/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/dell/srvadmin/bin:/home/omero/OMERO.server/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? True Is writable? True
OMERO temp dir:'/tmp' Exists? True Is writable? True (Size: 488275)
JVM settings: Blitz-${index} -Xmx5027m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Indexer-${index} -Xmx3351m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: PixelData-${index} -Xmx5027m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
JVM settings: Repository-${index} -Xmx3351m -XX:MaxPermSize=1g -XX:+IgnoreUnrecognizedVMOptions
omero@omero:~$>ls -l
total 32
drwx------. 4 omero omero 4096 23 août 17:54 omero
drwxrwxr-x 9 omero omero 4096 21 sept. 17:36 Omero_Backup
-rwxrw-r-- 1 omero omero 745 6 oct. 09:16 omero_clean_and_backup.sh
lrwxrwxrwx 1 omero omero 24 8 déc. 15:05 OMERO.py -> OMERO.py-5.4.1-ice36-b75
drwxr-xr-x 8 omero omero 4096 18 août 14:29 OMERO.py-5.3.3-ice36-b63
drwxr-xr-x 8 omero omero 4096 8 déc. 15:07 OMERO.py-5.4.1-ice36-b75
lrwxrwxrwx 1 omero omero 24 18 août 14:21 OMERO.py-old -> OMERO.py-5.3.3-ice36-b63
lrwxrwxrwx 1 omero omero 28 6 déc. 15:16 OMERO.server -> OMERO.server-5.4.1-ice36-b75
drwxr-xr-x. 9 omero omero 4096 17 août 15:58 OMERO.server-5.3.3-ice36-b63
drwxr-xr-x 9 omero omero 4096 22 nov. 20:41 OMERO.server-5.4.1-ice36-b75
lrwxrwxrwx. 1 omero omero 29 17 août 15:56 OMERO.server-old -> OMERO.server-5.3.3-ice36-b63/
drwxr-xr-x 5 root root 4096 18 août 12:56 omerowebvenv
Go back to OMERO.web
Page not found. (404)
The requested object or URL was not found on this server. The link you followed is either outdated, inaccurate, or the server has been instructed not to let you have it.
by kennethgillen » Fri Dec 08, 2017 2:30 pm
by phm » Fri Dec 08, 2017 2:51 pm
kennethgillen wrote:Are you following the "web upgrade" docs at https://docs.openmicroscopy.org/omero/5 ... grade.html ?
Is there any change required to your NGINX configuration? (e.g. if you've got the old path hard-coded)
Can you:
[phm@server ~]$cat /etc/nginx/conf.d/omero-web.conf
omero@omero:~$>more /etc/nginx/conf.d/omero.conf
upstream omeroweb_omero {
server 127.0.0.1:4080 fail_timeout=0;
}
server {
listen 80;
server_name omero.college-de-france.fr;
rewrite ^ https://$server_name$request_uri? permanent;
}
server {
listen 443 default ssl;
server_name omero.college-de-france.fr;
keepalive_timeout 70;
ssl on;
ssl_certificate /etc/nginx/omero.college-de-france.fr.pem;
ssl_certificate_key /etc/nginx/omero.college-de-france.fr.key;
ssl_protocols TLSv1 TLSv1.1 TLSv1.2;
ssl_ciphers HIGH:!aNULL:!MD5;
sendfile on;
client_max_body_size 0;
send_timeout 60s;
# maintenance page serve from here
location @maintenance_omero {
root /home/omero/OMERO.py/etc/templates/error;
try_files $uri /maintainance.html =502;
}
# weblitz django apps serve media from here
location /omero/static {
alias /home/omero/OMERO.py/lib/python/omeroweb/static;
}
location @proxy_to_app_omero {
proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
proxy_set_header Host $http_host;
proxy_redirect off;
proxy_set_header X-Forwarded-Proto $scheme;
proxy_pass http://omeroweb_omero;
}
location /omero {
error_page 502 @maintenance_omero;
# checks for static file, if not found proxy to app
try_files $uri @proxy_to_app_omero;
}
}
omero@omero:~$>omero config set omero.web.session_expire_at_browser_close "True"
omero@omero:~$>omero config set omero.web.session_cookie_age 86400
omero@omero:~$>omero web clearsessions
Clearing expired sessions. This may take some time... Traceback (most recent call last):
File "manage.py", line 56, in <module>
execute_from_command_line(sys.argv)
File "/usr/lib/python2.7/site-packages/django/core/management/__init__.py", line 399, in execute_from_command_line
utility.execute()
File "/usr/lib/python2.7/site-packages/django/core/management/__init__.py", line 392, in execute
self.fetch_command(subcommand).run_from_argv(self.argv)
File "/usr/lib/python2.7/site-packages/django/core/management/base.py", line 242, in run_from_argv
self.execute(*args, **options.__dict__)
File "/usr/lib/python2.7/site-packages/django/core/management/base.py", line 280, in execute
translation.activate('en-us')
File "/usr/lib/python2.7/site-packages/django/utils/translation/__init__.py", line 130, in activate
return _trans.activate(language)
File "/usr/lib/python2.7/site-packages/django/utils/translation/trans_real.py", line 188, in activate
_active.value = translation(language)
File "/usr/lib/python2.7/site-packages/django/utils/translation/trans_real.py", line 177, in translation
default_translation = _fetch(settings.LANGUAGE_CODE)
File "/usr/lib/python2.7/site-packages/django/utils/translation/trans_real.py", line 159, in _fetch
app = import_module(appname)
File "/usr/lib/python2.7/site-packages/django/utils/importlib.py", line 40, in import_module
__import__(name)
ImportError: No module named pipeline
by kennethgillen » Mon Dec 11, 2017 10:07 am
by phm » Mon Dec 11, 2017 8:15 pm
kennethgillen wrote:Can I again double-check that since I see omerowebvenv in the directory listing, when you're trying to start OMERO.web, are you activating the virtualenv?
Also - the OMERO.web dependency upgrade will need to be performed also inside the virtualenv.
https://docs.openmicroscopy.org/omero/5 ... pendencies
Best,
Kenny
by kennethgillen » Tue Dec 12, 2017 11:18 am
by phm » Tue Dec 12, 2017 1:26 pm
kennethgillen wrote:Hi Philippe,
We're going to need some more logs to help us get an understanding of what's going on.
We appreciate that you've sent us a few of these in the past, but it'll help us to see the current version of all of them.
- Output of OMERO.server bin/omero config get --hide-password (Blank out any passwords)
- Output of OMERO.web|.py bin/omero config get --hide-password (Blank out any passwords)
- OMERO.server logs: ${OMERO_SERVER}/var/log
- OMERO.web|.py logs: ${OMERO_WEB|PY}/var/log
- System nginx logs (CentOS/RHEL e.g.) /var/log/nginx/{access.log,error.log}
- Nginx configuration files (CentOS/RHEL e.g.) /etc/nginx/ (Including subdirectories, omit any SSL certificates)
As before, you are welcome to zip them all up and submit via our QA system at http://qa.openmicroscopy.org.uk/qa/upload/
by kennethgillen » Tue Dec 12, 2017 2:08 pm
@proxy_to_app {
.... other settings
proxy_buffering off;by phm » Tue Dec 12, 2017 2:55 pm
kennethgillen wrote:Hi Philippe,
I notice you've an old version of the NGINX configuration.
Our docs recommend regenerating this every time you upgrade OMERO.web, as we make changes to this file as OMERO.web develops.
From location @proxy_to_app {
you are missing
- Code: Select all
@proxy_to_app {
.... other settings
proxy_buffering off;
See the "upgrading OMERO.web" documentation for more: https://docs.openmicroscopy.org/omero/5 ... grade.html
Best,
Kenny
omero.college-de-france.fr does not allow connection.
omero@omero:~$>sudo systemctl status omero-web.service
● omero-web.service - OMERO.web
Loaded: loaded (/etc/systemd/system/omero-web.service; enabled; vendor preset: disabled)
Active: active (running) since mar. 2017-12-12 15:47:58 CET; 31s ago
Process: 8281 ExecStop=/home/omero/omerowebvenv/bin/python /home/omero/OMERO.py/bin/omero web stop (code=exited, status=0/SUCCESS)
Process: 3564 ExecStart=/home/omero/omerowebvenv/bin/python /home/omero/OMERO.py/bin/omero web start (code=exited, status=0/SUCCESS)
Main PID: 3610 (gunicorn)
CGroup: /system.slice/omero-web.service
├─3610 /home/omero/omerowebvenv/bin/python2 /home/omero/omerowebvenv/bin/gunicorn -D -p /home/omero/OMERO.py/var/django.pid --bind 127.0.0.1:40...
├─3615 /home/omero/omerowebvenv/bin/python2 /home/omero/omerowebvenv/bin/gunicorn -D -p /home/omero/OMERO.py/var/django.pid --bind 127.0.0.1:40...
├─3616 /home/omero/omerowebvenv/bin/python2 /home/omero/omerowebvenv/bin/gunicorn -D -p /home/omero/OMERO.py/var/django.pid --bind 127.0.0.1:40...
├─3617 /home/omero/omerowebvenv/bin/python2 /home/omero/omerowebvenv/bin/gunicorn -D -p /home/omero/OMERO.py/var/django.pid --bind 127.0.0.1:40...
├─3630 /home/omero/omerowebvenv/bin/python2 /home/omero/omerowebvenv/bin/gunicorn -D -p /home/omero/OMERO.py/var/django.pid --bind 127.0.0.1:40...
└─3631 /home/omero/omerowebvenv/bin/python2 /home/omero/omerowebvenv/bin/gunicorn -D -p /home/omero/OMERO.py/var/django.pid --bind 127.0.0.1:40...
déc. 12 15:47:55 omero systemd[1]: Starting OMERO.web...
déc. 12 15:47:57 omero python[3564]: Post-processed 'omeroweb.viewer.min.css' as 'omeroweb.viewer.min.css'
déc. 12 15:47:57 omero python[3564]: Post-processed 'omeroweb.viewer.min.js' as 'omeroweb.viewer.min.js'
déc. 12 15:47:57 omero python[3564]: 0 static files copied to '/home/omero/OMERO.py/lib/python/omeroweb/static', 604 unmodified, 2 post-processed.
déc. 12 15:47:57 omero python[3564]: Clearing expired sessions. This may take some time... [OK]
déc. 12 15:47:57 omero python[3564]: Starting OMERO.web... [OK]
déc. 12 15:47:57 omero systemd[1]: PID file /home/omero/OMERO.py/var/django.pid not readable (yet?) after start.
déc. 12 15:47:58 omero systemd[1]: Started OMERO.web.
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