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

Fri Nov 6 15:32:31 GMT 2009

OK I was able to login as root via admin interface. I will leave all settings related to Django pointing to sqlite3. 

Question, I noticed some stuff related to LDAP, does that mean I could tie user authentication to an OpenLDAP directory? If so, can local authentication coexist with LDAP? Also, I'm assuming I would have to create the user in Omero first, then some how point authentication to LDAP. 

Thanks for your help. 

Kent 

----- Original Message ----- 
From: "Chris Allan" <callan at lifesci.dundee.ac.uk> 
To: "Kent Nasveschuk" <knasveschuk at mbl.edu> 
Cc: "Bernhard Holländer" <bernhard.voigt at gmail.com> 
Sent: Friday, November 6, 2009 9:59:10 AM GMT -05:00 US/Canada Eastern 
Subject: Re: [ome-users] Migrating from 3.1.x to 4.1.0 

On 6 Nov 2009, at 14:45, Kent Nasveschuk wrote: 

> 
> 
> Kent 
> 
> ----- Original Message ----- 
> From: "Chris Allan" <callan at lifesci.dundee.ac.uk> 
> To: "Kent Nasveschuk" <knasveschuk at mbl.edu> 
> Cc: "Bernhard Holländer" <bernhard.voigt at gmail.com> 
> Sent: Friday, November 6, 2009 7:52:15 AM GMT -05:00 US/Canada Eastern 
> Subject: Re: [ome-users] Migrating from 3.1.x to 4.1.0 
> 
> 
> 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? 
> 
> I'm logging in with the "webadmin" user I created with: 
> bin/omero web superuser 

That's just a superuser for administering the Django settings, it does 
not apply to general logins. You'll need to login with whatever 
username and password is in your OMERO database (root most likely at 
this point). 

> 
> I'm trying to login to the web: 
> http://omero.mbl.edu/webadmin/login/?url=/Webadmin/ 
> 
> This is the upgraded database being used by the Beta4.1.0 version 
> 
> Here is more confusion on my part. 
> /data/omero-Beta4.1.0/lib/python/omeroweb/settings.py 
> 
> contains database settings for sqlite3, should that be pointing to 
> postgresql_psycopg2 and the omero database on postgres? 

No, they have nothing to do with each other. The sqlite3 database is 
strictly used for the configuration settings of OMERO.web. 

> 
> > ... 
> > 
> > Any ideas? Anywhere else I can look? 
> > 
> > Kent 
> 
> -Chris 

-Chris 

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