[ome-users] Migrating from 3.1.x to 4.1.0
Chris Allan
callan at blackcat.ca
Fri Nov 6 12:48:54 GMT 2009
On 5 Nov 2009, at 21:12, Kent Nasveschuk wrote:
> 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?
It needs 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
Looks good.
> ...
>
> 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'
That's an authentication failure quite simply. Is this still using the
upgrade? Are you logging in using a user that exists in OMERO?
> ...
>
> Any ideas? Anywhere else I can look?
>
> Kent
-Chris
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