[ome-users] Migrating from 3.1.x to 4.1.0

Thu Nov 5 21:12:23 GMT 2009

OK, I'm a little farther but can't login to that admin interface. I set the web admin user using: 

bin/omero web superuser 
answering questions. 

Here is the output of bin/omero admin diagnostics 
bash-3.2$ bin/omero admin diagnostics 

================================================================================ 
OMERO Diagnostics Beta-4.1.0-r5585-b12 
================================================================================ 

Commands: java -version 1.6.0 (/opt/jdk1.6.0_07/bin/java -- 2 others) 
Commands: python -V 2.4 (/usr/bin/python) 
Commands: icegridnode --version 3.3 (/usr/bin/icegridnode) 
Commands: icegridadmin --version 3.3 (/usr/bin/icegridadmin) 
Commands: psql --version 8.1.11 (/usr/bin/psql) 

Server: icegridnode running 
Server: Blitz-0 active (pid = 31983, enabled) 
Server: DropBox inactive (disabled) 
Server: FSServer inactive (disabled) 
Server: Indexer-0 active (pid = 31994, enabled) 
Server: OMERO.Glacier2 active (pid = 31996, enabled) 
Server: OMERO.IceStorm active (pid = 31997, enabled) 
Server: Processor-0 active (pid = 32004, enabled) 
Server: Tables-0 inactive (disabled) 
Server: TestDropBox inactive (enabled) 
Server: Web inactive (enabled) 

Log dir: /data/omero-Beta4.1.0/var/log exists 

Log files: Blitz-0.log 73.0 KB errors=0 warnings=4 
Log files: DropBox.log 3.0 KB errors=4 warnings=0 
Log files: FSServer.log 1.0 KB errors=2 warnings=0 
Log files: Indexer-0.log 3.0 KB errors=0 warnings=2 
Log files: OMEROweb.log n/a 
Log files: Processor-0.log 2.0 KB errors=0 warnings=1 
Log files: Tables-0.log n/a 
Log files: TestDropBox.log n/a 
Log files: master.err 1.0 KB errors=0 warnings=4 
Log files: master.out 0.0 KB 
Log files: Total size 0.09 MB 

output of bin/omero config get 
-bash-3.2$ bin/omero config get 
omero.data.dir=/data/OMERO 
omero.db.name=omero3 
omero.db.pass=<secret> 
omero.db.user=omero 

Tested my connection to postgres running on localhost with username and password. That works 

Using mod_python and virtualhost on apache2 which works fine. I can get to the webadmin and webadmin login. 

What's a little confusing is the omero.server an on demand daemon or does it need to be running when apache is running? 

I started with bin/omero admin start 

ps ax 
... 
31948 ? Sl 0:00 icegridnode --daemon --pidfile /data/omero-Beta4.1.0/var/master/master.pid --nochdir --Ice.Config=/data/omero-Beta4.1.0/etc/internal.cfg,/data/omero-Beta4.1.0/etc/master. 
31983 ? Sl 0:29 java -Xmx512M -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=Blitz-0 -jar lib/server/blitz.jar --Ice. 
31994 ? Sl 0:35 java -Xmx256M -Djava.awt.headless=true -Dlog4j.configuration=etc/log4j-indexing.xml -Domero.logfile=var/log/${omero.name}.log -Domero.name=Indexer-0 -jar lib/server/blitz 
31996 ? Sl 0:00 glacier2router --Ice.Config=/data/omero-Beta4.1.0/var/master/servers/OMERO.Glacier2/config/config 
31997 ? Sl 0:00 icebox --Ice.Config=/data/omero-Beta4.1.0/var/master/servers/OMERO.IceStorm/config/config 
32004 ? Sl 0:00 python lib/python/runProcessor.py --Ice.Config=/data/omero-Beta4.1.0/var/master/servers/Processor-0/config/config 
32095 ? S 0:03 postgres: omero omero3 127.0.0.1(52367) idle 
... 

The only thing I see in the weblog is: 
... 
2009-11-05 20:32:05,491 blitz_gateway: INFO first create session had errors, hold off 10 secs and retry (but only once) 
2009-11-05 20:32:05,509 blitz_gateway: INFO (3) calling createSession() 
2009-11-05 20:32:05,563 webgateway : ERROR Critical error during connect, retrying after _purge 
2009-11-05 20:32:05,592 blitz_gateway: INFO host: localhost, port: 4063 
2009-11-05 20:32:05,620 blitz_gateway: INFO (1) calling createSession() 
2009-11-05 20:32:05,648 blitz_gateway: INFO BlitzGateway.connect().createSession(): Traceback (most recent call last): 
File "/data/omero-Beta4.1.0/lib/python/omero/gateway/__init__.py", line 423, in connect 
self._createSession() 
File "/data/omero-Beta4.1.0/lib/python/omero/gateway/__init__.py", line 315, in _createSession 
self._ic_props[omero.constants.PASSWORD]) 
File "/data/omero-Beta4.1.0/lib/python/omero/clients.py", line 376, in createSession 
prx = self.getRouter(self.__ic).createSession(username, password) 
File "/usr/lib/python2.4/site-packages/Ice/Glacier2_Router_ice.py", line 107, in createSession 
return _M_Glacier2.Router._op_createSession.invoke(self, ((userId, password), _ctx)) 
PermissionDeniedException: exception ::Glacier2::PermissionDeniedException 
{ 
reason = permission denied 
} 

2009-11-05 20:32:05,687 blitz_gateway: INFO first create session had errors, hold off 10 secs and retry (but only once) 
2009-11-05 20:32:05,706 blitz_gateway: INFO (3) calling createSession() 
2009-11-05 20:32:06,034 views-web : INFO INIT '32218' 
... 

Any ideas? Anywhere else I can look? 

Kent 

----- Original Message ----- 
From: "Bernhard Holländer" <bernhard.voigt at gmail.com> 
To: "Kent Nasveschuk" <knasveschuk at mbl.edu> 
Cc: "Open Microscopy" <ome-users at lists.openmicroscopy.org.uk> 
Sent: Thursday, November 5, 2009 3:02:50 AM GMT -05:00 US/Canada Eastern 
Subject: Re: [ome-users] Migrating from 3.1.x to 4.1.0 

Good morning! 

The settings.py file is the configuration file for Omero.Web and 
you're right, that's only relevant if you have been running Omero4.0 
before. 

Here's the migration path I took: 

0. stopped Omero3.x 
1. made a dump of the Omer3.x db 
2. created new Omero4 db (only the createdb and createlang steps) 
3. restored the Omero3.x dump into the newly created Omero4 db 
4. ran all the sql upgrade scripts on the Omero4 db 
5. configured Omero4 to use the omero4 db and the existing file 
repository from the Omero3 installation 
6. started Omero4 

Cheers! Bernhard 

On Wed, Nov 4, 2009 at 8:29 PM, Kent Nasveschuk <knasveschuk at mbl.edu> wrote: 
> Hello, 
> I'm trying to migrate from a Beta3.1.1 installation to Beta4.1.0. I have 
> gone from 3.1.1 to 3.2, then upgraded the postgresql database to 4.0.0. It 
> says in the upgrade documentation 
> (http://www.openmicroscopy.org/site/support/omero4/server/upgrade) to copy 
> setting.py from your 4.0.0 installation to 4.1.0. Settings.py is I guess 
> unique to the 4.x version and hasn't been configure yet. 
> 
> Any help would be appreciated. 
> 
> Kent 
> 
> _______________________________________________ 
> ome-users mailing list 
> ome-users at lists.openmicroscopy.org.uk 
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users 
> 
> 
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