From callan at blackcat.ca  Mon Sep  1 15:39:16 2008
From: callan at blackcat.ca (Chris Allan)
Date: Mon, 1 Sep 2008 15:39:16 +0100
Subject: [ome-users] JVM Launcher error.
In-Reply-To: <d357b5d90808301203s5dfa1f60xe563dbcc4b24a826@mail.gmail.com>
References: <d357b5d90808301203s5dfa1f60xe563dbcc4b24a826@mail.gmail.com>
Message-ID: <2B4B704B-FA43-463E-95F0-2B3CB5BBF9CE@blackcat.ca>

On 30 Aug 2008, at 20:03, Peter McKenney wrote:

> Hello again everyone,

Hi Peter.

>
>
> OMERO is up and running on our windows computer, but now when I try to
> start importer or insight I get the following error message box:
>
> Java Virtual Machine Launcher
>
> Could not find the main class. Program will exit.
>
> Does anyone have any ideas?

I assume this is also Windows you're trying? Vista perhaps? If you go  
to a command prompt and type "java -version" what's the result?

> Thanks again,
> Peter.

Thanks for the feedback.

-Chris

From rubenalves at fm.ul.pt  Mon Sep  8 16:09:30 2008
From: rubenalves at fm.ul.pt (=?ISO-8859-1?Q?=BB_Ruben_Alves?=)
Date: Mon, 08 Sep 2008 16:09:30 +0100
Subject: [ome-users] Logs in OMERO?
Message-ID: <48C5402A.50901@fm.ul.pt>

Hi,
I was tuning OMERO, and I need to output some logs in order to debug the 
application and made some stats.
Is anyway to output OMERO to a file like apache logs?

Best regards,

// Ruben Alves

-- 
Ruben Alves
USI @ Instituto de Medicina Molecular
Edif?cio Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999411 ext 47026


From smwilson at hpc.unm.edu  Tue Sep  9 20:51:54 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Tue, 9 Sep 2008 13:51:54 -0600
Subject: [ome-users] Howto change OME installation from default apache port
Message-ID: <00815B9B-77E3-4C16-A790-B4266CF72BAF@hpc.unm.edu>

Hi,

I am installing OME server on a SLES10 server.  apache is running, but  
it's default port is not 80 or 8080.  The mod_perl test keeps failing  
because it is attempting to connect to localhost on the default port  
and this will not work.  If I run curl on the mod_perl_test to  
localhost:<port> it works perfectly.  How can I change the port?  I  
apologize if this has been asked over and over, but I have not been  
able to search the list archives as a set - only one month at a time.

I have tried modifing the ApacheConfigTask.pm to include the non- 
default port in the OME-2.6.1 installation directory structure, but  
somehow the file that is installed in the /OME directory structure is  
still missing the port and the installation fails.

Thanks.
Susan

From josh.moore at gmx.de  Tue Sep  9 22:17:38 2008
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Tue, 9 Sep 2008 23:17:38 +0200
Subject: [ome-users]  Logs in OMERO?
In-Reply-To: <48C5402A.50901@fm.ul.pt>
References: <48C5402A.50901@fm.ul.pt>
Message-ID: <18630.59378.245968.832131@josh-moores-computer.local>


Hi Ruben,

JBoss' logging, which is configured in

  OMERO_HOME/server/default/conf/jboss-log4j.xml

by default logs to:

  OMERO_HOME/server/default/log/server.log

Could you let us know what exactly it is you need to log? I bet we can
work out something that will work for you.

Best wishes,
~Josh

? Ruben Alves writes:
 > I was tuning OMERO, and I need to output some logs in order to debug the 
 > application and made some stats.
 >
 > Is anyway to output OMERO to a file like apache logs?
 > 
 > Best regards,
 > // Ruben Alves

From rubenalves at fm.ul.pt  Wed Sep 10 10:00:52 2008
From: rubenalves at fm.ul.pt (=?ISO-8859-1?Q?=BB_Ruben_Alves?=)
Date: Wed, 10 Sep 2008 10:00:52 +0100
Subject: [ome-users] Logs in OMERO?
Message-ID: <48C78CC4.2030905@fm.ul.pt>

Hi Josh,
In fact, I was searching a way to produce stats from logs:

+ with Awstats (adapting OMERO logs to Apache Logs)
----+ Visitors,
----+ Bandwidth,
----+ Top 10 hosts,
----+ Top 10 users,
 
+ MRTG - I was thinking a way to write scripts in order to see how many 
simultaneous users are connected to OMERO.

In order to conclude, I was searching a way to monitor and have a better 
understanding of how OMERO works in the server.
Best Regards,

//Ruben

josh.moore at gmx.de wrote:
> Hi Ruben,
>
> JBoss' logging, which is configured in
>
>   OMERO_HOME/server/default/conf/jboss-log4j.xml
>
> by default logs to:
>
>   OMERO_HOME/server/default/log/server.log
>
> Could you let us know what exactly it is you need to log? I bet we can
> work out something that will work for you.
>
> Best wishes,
> ~Josh
>
> ? Ruben Alves writes:
>  > I was tuning OMERO, and I need to output some logs in order to debug the 
>  > application and made some stats.
>  >
>  > Is anyway to output OMERO to a file like apache logs?
>  > 
>  > Best regards,
>  > // Ruben Alves
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>   


-- 
Ruben Alves
USI @ Instituto de Medicina Molecular
Edif?cio Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999411 ext 47026



From Karl_Johnson at nrel.gov  Wed Sep 10 18:11:59 2008
From: Karl_Johnson at nrel.gov (Johnson, Karl)
Date: Wed, 10 Sep 2008 11:11:59 -0600
Subject: [ome-users] OMERO.editor
In-Reply-To: <mailman.3.1220958001.27726.ome-users@lists.openmicroscopy.org.uk>
References: <mailman.3.1220958001.27726.ome-users@lists.openmicroscopy.org.uk>
Message-ID: <94CA9432ECEFB84092222C964C32E50904CD80F4@mail-4a.nrel.gov>

Hi All,
I was using the editor to make templates for a microscopy lab.  I have
two questions.  

The first do you have an ETA for when the editor metadata will be
incorporated with the images in the database.

The second is a problem.  When I make the template, others can open the
template and save the values under a different name.  When we try to
open the edited file, using OMERO.editor the file will not open, if we
open the template first then open the edited file then we can open the
file but only the first three lines are visible.  We can see and open
the files in an XML editor with no problem and see all the lines of XML
code.

Any ideas?  

Thanks
Karl 




From will at lifesci.dundee.ac.uk  Thu Sep 11 12:48:13 2008
From: will at lifesci.dundee.ac.uk (Will Moore)
Date: Thu, 11 Sep 2008 12:48:13 +0100
Subject: [ome-users] OMERO.editor
In-Reply-To: <94CA9432ECEFB84092222C964C32E50904CD80F4@mail-4a.nrel.gov>
References: <mailman.3.1220958001.27726.ome-users@lists.openmicroscopy.org.uk>
	<94CA9432ECEFB84092222C964C32E50904CD80F4@mail-4a.nrel.gov>
Message-ID: <EC1ACACD-4A4A-4444-BC29-25F05FC6B5C1@lifesci.dundee.ac.uk>

Hi Karl,

On 10 Sep 2008, at 18:11, Johnson, Karl wrote:

> Hi All,
> I was using the editor to make templates for a microscopy lab.

Great!

> I have
> two questions.
>
> The first do you have an ETA for when the editor metadata will be
> incorporated with the images in the database.

Currently we suggest that you attach the Editor xml files to the  
Project/Dataset/Image in
OMERO using the Insight client. (At the bottom of the metadata panel  
on the right, Under the "Related Documents" header, there is an  
"upload" function for uploading local files to OMERO). This will  
attach the file to the current Project / Dataset or Image, and the  
file will be indexed to allow searching in Insight.

In the OMERO Beta 3.1 release, which should be out in the next few  
weeks, you will be able to view editor files from within Insight.
(Double-clicking on attached editor files in the metadata panel will  
launch a view of the Editor, although you will not be able to edit  
files in this way).

Before the 3.1 release, you will still be able to view attached  
Editor files by downloading them and opening the local copy with Editor.

>
> The second is a problem.  When I make the template, others can open  
> the
> template and save the values under a different name.  When we try to
> open the edited file, using OMERO.editor the file will not open, if we
> open the template first then open the edited file then we can open the
> file but only the first three lines are visible.  We can see and open
> the files in an XML editor with no problem and see all the lines of  
> XML
> code.
>
> Any ideas?

Hmm, this sounds like a bug!
It's probably something to do with the forth field (after the 3 that  
appear).
Is this a link field? Does the problem depend which computer you open  
the file on?
It may be caused by a broken link, although I have tried to address  
this issue, I may have missed something.

Let me know what this field is (the first one that fails to appear)  
and any more details you have about
what conditions it doesn't work in.
Or send me the XML fragment for this field (if you can work out which  
it is in an XML editor), or the whole XML file if
privacy is not an issue.
It's always nice to see the way that people are using Editor too!

   Many thanks for your feedback,


     Will.



>
> Thanks
> Karl
>
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

William Moore
Division of Gene Regulation and Expression
College of Life Sciences
University of Dundee
Scotland
DD1 5PH

Tel 01382 386364

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From smwilson at hpc.unm.edu  Thu Sep 11 17:14:33 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Thu, 11 Sep 2008 10:14:33 -0600
Subject: [ome-users] Package OME::Web::Login does not inherit from OME::Web
Message-ID: <68114281-703E-49A3-899A-594333953830@hpc.unm.edu>

Hi,

Has anyone seen this problem.  $pageClass->isa("OME::Web") for  
Page=OME::Web::Login fails.

Thanks.
Susan

From josh.moore at gmx.de  Thu Sep 11 21:36:37 2008
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Thu, 11 Sep 2008 22:36:37 +0200
Subject: [ome-users] Logs in OMERO?
In-Reply-To: <48C78CC4.2030905@fm.ul.pt>
References: <48C78CC4.2030905@fm.ul.pt>
Message-ID: <18633.33109.141713.61910@josh-moores-computer.local>

? Ruben Alves writes:
 > Hi Josh,

Hi, Ruben.

This is an interesting idea, but probably requires adding more log
statements into the server or other functionality to take this all the
way.

 > In fact, I was searching a way to produce stats from logs:
 > 
 > + with Awstats (adapting OMERO logs to Apache Logs)
 > ----+ Visitors,
 > ----+ Bandwidth,
 > ----+ Top 10 hosts,
 > ----+ Top 10 users,

Just some initial thoughts here, but it would be interesting to hear
what others think as well:

 * visitors/users - The "Auth: " lines logged by ServiceHandler are
   really the only form of "visitor" information. They signal that a
   user has logged in, and are printed (with the right logging)
   per method call.

 * bandwidth - really depends on how this should be measured. The
   rendering engine, I believe, has some stats which are
   printed. Chris can correct me if I'm wrong, but that would be one
   form of "through-put" that could be measured. Were you thinking of
   any others?

 * The host information in both JBoss and in the OMERO.blitz server is
   not straight-forward to come by. 

 * There is also some statistically logging that can be done via the
   com.jamonapi logger.

 > + MRTG - I was thinking a way to write scripts in order to see how many 
 > simultaneous users are connected to OMERO.

 * This information is tracked by the server but not currently
   available from the API and not explicitly logged. One possible way
   to do this would be to check for all opened sessions, but it might
   not be all that straight-forward since you would have to check for
   (possibly forgotten) calls to "close".

 > In order to conclude, I was searching a way to monitor and have a better 
 > understanding of how OMERO works in the server.

Doing this via logging is certainly valid and really quite
interesting, but I think it also makes sense to eventually add methods
like this as part of the administration functionality which the API provides.
This would allow a client in any of the languages we support (with the
proper permissions!) to ask for current statistics.

OMERO.web could then use that to display the data
graphically. Currently, WebAdmin (http://localhost:8080/WebAdmin)
provides disk usage data. Ola probably already has ideas of the next
best statistics to add.

For you, Ruben, it could be "as simple as" getting the HTML and
parsing out the bits you need, or is the awstats route more what you
are looking for?

 > Best Regards,
 > //Ruben

The same to you,
~Josh.

P.S. By the way, if you or anyone else has additions like this which
you need or even just fancy, don't hesitate to add them to our to-do
list ("trac").

Log in at:

  https://trac.openmicroscopy.org.uk/omero/login

as "omero" with password "omero". Then, click on "New Ticket". I went
ahead and added this as:

  https://trac.openmicroscopy.org.uk/omero/ticket/1095

in case anyone wants to take a look. (No need to login)

 > 
 > josh.moore at gmx.de wrote:
 > > Hi Ruben,
 > >
 > > JBoss' logging, which is configured in
 > >
 > >   OMERO_HOME/server/default/conf/jboss-log4j.xml
 > >
 > > by default logs to:
 > >
 > >   OMERO_HOME/server/default/log/server.log
 > >
 > > Could you let us know what exactly it is you need to log? I bet we can
 > > work out something that will work for you.
 > >
 > > Best wishes,
 > > ~Josh
 > >
 > > ? Ruben Alves writes:
 > >  > I was tuning OMERO, and I need to output some logs in order to debug the 
 > >  > application and made some stats.
 > >  >
 > >  > Is anyway to output OMERO to a file like apache logs?
 > >  > 
 > >  > Best regards,
 > >  > // Ruben Alves

From knasveschuk at mbl.edu  Mon Sep 15 21:29:32 2008
From: knasveschuk at mbl.edu (Kent Nasveschuk)
Date: Mon, 15 Sep 2008 16:29:32 -0400
Subject: [ome-users] install on CentOS 5
Message-ID: <1221510572.3627.13.camel@kln-laptop.mbl.edu>

Hello,
I've installed the the OME 2.6.1 version on a CentOS5 box. I haven't
seen anywhere how to create the database and tables. Just wondering if
that occurs after install.pl checks mod_perl?

Any help would be appreciated.

Kent


-- 
Kent L. Nasveschuk
Systems Administrator
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA 02543
Tel. (508) 289-7263

From knasveschuk at mbl.edu  Tue Sep 16 20:47:31 2008
From: knasveschuk at mbl.edu (Kent Nasveschuk)
Date: Tue, 16 Sep 2008 15:47:31 -0400
Subject: [ome-users] Regarding OME Server Installation
In-Reply-To: <EDC22492BE5CAF409A4166B67B1F2E9A219A6B0F@EX7SM01.ad.uky.edu>
References: <EDC22492BE5CAF409A4166B67B1F2E9A219A6B01@EX7SM01.ad.uky.edu>
	<EDC22492BE5CAF409A4166B67B1F2E9A219A6B0F@EX7SM01.ad.uky.edu>
Message-ID: <1221594451.3380.46.camel@kln-laptop.mbl.edu>

Hi Sriram,

I have no experience with FC8. I switched to CentOS which closely
follows RedHat.

Current server:
Dell PowerEdge SC1420
Cerc SATA 1.5/6 ch Adaptec Raid, (5) 250GB drives raid 5
2GB ram
Single Xeon processor 2.8Ghz
Perl rpms installed using yum and rpmforge repository (some are
dependencies):

perl-Crypt-PasswdMD5-1.3-1.2.el5.rf
perl-Jcode-2.06-1.el5.rf
perl-Net-XMPP-1.02-1.el5.rf
perl-Spreadsheet-ParseExcel-0.32-1.el5.rf
perl-Digest-MD5-File-0.06-1.el5.rf
perl-UNIVERSAL-exports-0.05-1.el5.rf
perl-DBI-1.605-1.el5.rf
perl-DBD-Pg-2.8.1-1.el5.rf
perl-Spreadsheet-WriteExcel-2.24-1.el5.rf
perl-GSSAPI-0.26-1.el5.rf
perl-Parse-RecDescent-1.94-1.el5.rf
perl-Inline-0.44-1.el5.rf
perl-Class-Accessor-0.31-1.el5.rf
perl-BSD-Resource-1.2901-1.el5.rf
perl-PlRPC-0.2020-1.el5.rf
perl-Socket6-0.20-1.el5.rf
perl-MailTools-2.03-1.el5.rf
perl-SOAP-Lite-0.710.08-1.el5.rf
perl-XML-SAX-0.16-1.el5.rf
perl-Log-Agent-0.307-1.el5.rf
perl-Crypt-DES-2.05-3.2.el5.rf
perl-Net-Daemon-0.43-1.el5.rf
perl-HTML-Parser-3.56-1.el5.rf
perl-MIME-Lite-3.021-1.el5.rf
perl-XML-Stream-1.22-1.2.el5.rf
perl-libwww-perl-5.805-1.1.1
perl-XML-Parser-2.36-1.el5.rf
perl-XML-LibXML-1.58-5
perl-Inline-Struct-0.06-1.2.el5.rf
perl-HTML-Template-2.9-1.el5.rf
perl-Exporter-Lite-0.02-1.el5.rf
perl-UNIVERSAL-require-0.11-1.el5.rf
perl-IO-Socket-SSL-1.13-1.el5.rf
perl-URI-1.35-3
perl-Net-SNMP-5.2.0-1.2.el5.rf
perl-OLE-Storage_Lite-0.17-1.el5.rf
perl-Compress-Zlib-1.42-1.fc6
perl-Unicode-Map-0.112-1.el5.rf
perl-IPC-Run-0.80-1.el5.rf
perl-String-CRC32-1.4-2.fc6
perl-Digest-HMAC-1.01-15
perl-version-0.74-1.el5.rf
perl-Net-SSLeay-1.32-1.el5.rf
perl-TimeDate-1.16-5.el5
perl-Net-Jabber-2.0-1.2.el5.rf
perl-XML-NamespaceSupport-1.09-1.2.1
perl-Carp-Assert-0.20-1.el5.rf
perl-XML-SAX-Expat-0.39-1.el5.rf
perl-Digest-SHA1-2.11-1.2.1
perl-HTML-Tagset-3.20-1.el5.rf
perl-Authen-SASL-2.11-1.el5.rf
perl-XML-LibXML-Common-0.13-8.2.2
perl-Inline-Filters-0.12-1.2.el5.rf
perl-Class-Data-Inheritable-0.08-1.el5.rf

One thing that install.pl failed to find was:
perl-XML-LibXSLT

I had to install this from the OME site.

I'm kind of stuck with how to get the database built. I don't know if
install.pl does that or not.

Good luck with your install, I'm not there yet either, but I do have a
login screen.

Kent

On Tue, 2008-09-16 at 14:09 -0400, Nandakumar, Sriramkumar wrote:
> Hi Kent,
> Good Afternoon.
> I am Sriramkumar and I am a graduate student studying at University of Kentucky.
> I came to know about you from the OME users list.
> By the way I am also involved in installation of OME Server for our research project.
> Could you please appraise me the hardware configuration required for OME Server (Processor, RAM, Hard drive details).
> We have decided to use Fedora Core 8 for OME. Whats your opinion on this?
> It could be really helpful if you can guide me in installing OME Server.
> 
> Thanks in Advance.
> 
> Thanks & Regards,
> Sriram.
-- 
Kent L. Nasveschuk
Systems Administrator
Marine Biological Laboratory
7 MBL Street
Woods Hole, MA 02543
Tel. (508) 289-7263

From callan at blackcat.ca  Wed Sep 17 15:07:35 2008
From: callan at blackcat.ca (Chris Allan)
Date: Wed, 17 Sep 2008 15:07:35 +0100
Subject: [ome-users] install on CentOS 5
In-Reply-To: <1221510572.3627.13.camel@kln-laptop.mbl.edu>
References: <1221510572.3627.13.camel@kln-laptop.mbl.edu>
Message-ID: <A30F9F0F-1EFB-45A6-BBA5-2AB630C1184B@blackcat.ca>


On 15 Sep 2008, at 21:29, Kent Nasveschuk wrote:

> Hello,
> I've installed the the OME 2.6.1 version on a CentOS5 box. I haven't
> seen anywhere how to create the database and tables. Just wondering if
> that occurs after install.pl checks mod_perl?

Creation of the database is done by install.pl, yes.

> Any help would be appreciated.
>
> Kent

Ciao.

-Chris

From knasveschuk at mbl.edu  Wed Sep 17 20:21:52 2008
From: knasveschuk at mbl.edu (Kent Nasveschuk)
Date: Wed, 17 Sep 2008 15:21:52 -0400
Subject: [ome-users] install on CentOS 5
In-Reply-To: <A30F9F0F-1EFB-45A6-BBA5-2AB630C1184B@blackcat.ca>
References: <1221510572.3627.13.camel@kln-laptop.mbl.edu>
	<A30F9F0F-1EFB-45A6-BBA5-2AB630C1184B@blackcat.ca>
Message-ID: <1221679312.3490.29.camel@kln-laptop.mbl.edu>

Hey, thanks for getting back to me. I have a couple of questions, since
the documentation seems to be scarce.

I see the ome utility seems the way to modify/add/delete/group users.
The user created at install time, is that an admin user? I've tried to
do anything with the ome utility, and it kicks me out with:

[root at ome-srv01 ~]# ome admin users list --ou <username> --opw '<pwd>'
DBI connect('dbname=ome','',...) failed: FATAL:  role "root" does not
exist at /usr/lib/perl5/site_perl/5.8.8/OME/Database/Delegate.pm line
273

Kent

On Wed, 2008-09-17 at 15:07 +0100, Chris Allan wrote:
> On 15 Sep 2008, at 21:29, Kent Nasveschuk wrote:
> 
> > Hello,
> > I've installed the the OME 2.6.1 version on a CentOS5 box. I haven't
> > seen anywhere how to create the database and tables. Just wondering if
> > that occurs after install.pl checks mod_perl?
> 
> Creation of the database is done by install.pl, yes.
> 
> > Any help would be appreciated.
> >
> > Kent
> 
> Ciao.
> 
> -Chris
> 

From smwilson at hpc.unm.edu  Thu Sep 18 19:12:48 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Thu, 18 Sep 2008 12:12:48 -0600
Subject: [ome-users] Does OME Server 2.6.1 support Web UI import?
Message-ID: <B4B9A746-8251-4FA5-9EEE-2AE75C6ADB66@hpc.unm.edu>

Hi,

Fairly simple question.  Here is the (presumably default) OMEIS  
configuration.
Thanks.
Susan

ome=# select * from repositories ;
  attribute_id | module_execution_id |              
image_server_url             | path | is_local
--------------+--------------------- 
+------------------------------------------+------+----------
             4 |                   1 | http://myserver.domain/cgi-bin/omeis 
  |      | f


From smwilson at hpc.unm.edu  Thu Sep 18 20:40:33 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Thu, 18 Sep 2008 13:40:33 -0600
Subject: [ome-users] Does OME Server 2.6.1 support Web UI import?
In-Reply-To: <B4B9A746-8251-4FA5-9EEE-2AE75C6ADB66@hpc.unm.edu>
References: <B4B9A746-8251-4FA5-9EEE-2AE75C6ADB66@hpc.unm.edu>
Message-ID: <8D2758F2-2A31-497D-8628-2EB8D5566066@hpc.unm.edu>

HI again,

I updated the repositories table:

ome=# select * from repositories ;
  attribute_id | module_execution_id |              
image_server_url             |        path        | is_local
--------------+--------------------- 
+------------------------------------------+-------------------- 
+----------
             4 |                   1 | http://delphi2.hpc.unm.edu/cgi-bin/omeis 
  | /OME/data/is_local | t
(1 row)

and bounced apache.  I still cannot import files from the Web UI.   
path exists and is updatable by ome user.

Susan

On Sep 18, 2008, at 12:12 PM, Susan Wilson wrote:

> Hi,
>
> Fairly simple question.  Here is the (presumably default) OMEIS
> configuration.
> Thanks.
> Susan
>
> ome=# select * from repositories ;
>  attribute_id | module_execution_id |
> image_server_url             | path | is_local
> --------------+---------------------
> +------------------------------------------+------+----------
>             4 |                   1 | http://myserver.domain/cgi-bin/omeis
>  |      | f
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


From smwilson at hpc.unm.edu  Mon Sep 22 20:19:55 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Mon, 22 Sep 2008 13:19:55 -0600
Subject: [ome-users] server version does not match client version
Message-ID: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>

Hi,

Installing omero-Beta3.0.1 on debian_version 4.0 with postgresql 7.4.

Installation goes well, login screen at localhost appears, but when I  
login as root/omero, I get the dreaded "Most likely....".   
WebAdmin.log has plenty of output - I set JAVA_HOME to the jdk  
location, but the result is the same.

[22-09-08 13:12:31,740] ERROR - Msg: Error during invocation. Most  
likely server version does not match client version Filename:  
LoginBean.java; Method name:  login Line number: 393
  ome.client.OutOfService: Error during invocation. Most likely server  
version does not match client version
         at ome.admin.controller.LoginBean.login(LoginBean.java:393)

Any suggestions.  I can supply server.log and/or WebAdmin.log contents.

Thanks.
Susan

From smwilson at hpc.unm.edu  Mon Sep 22 20:33:01 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Mon, 22 Sep 2008 13:33:01 -0600
Subject: [ome-users] server version does not match client version
In-Reply-To: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
References: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
Message-ID: <9CC8D572-3B8E-4431-8960-F53E7E5A22D1@hpc.unm.edu>

The first error I see in the WebAdmin log is

  [22-09-08 13:24:14,156] ERROR - Msg: Got marshalling exception,  
exiting Filename: SocketClientInvoker.java; Method name:   
handleException Line number: 109
  java.lang.ClassNotFoundException: org.hibernate.search.SearchException
         at  
org 
.jboss 
.remoting 
.serialization.ClassLoaderUtility.loadClass(ClassLoaderUtility.java:82)
         at  
org 
.jboss 
.remoting 
.loading.RemotingClassLoader.loadClass(RemotingClassLoader.java:76)
.
.
.

On Sep 22, 2008, at 1:19 PM, Susan Wilson wrote:

> Hi,
>
> Installing omero-Beta3.0.1 on debian_version 4.0 with postgresql 7.4.
>
> Installation goes well, login screen at localhost appears, but when I
> login as root/omero, I get the dreaded "Most likely....".
> WebAdmin.log has plenty of output - I set JAVA_HOME to the jdk
> location, but the result is the same.
>
> [22-09-08 13:12:31,740] ERROR - Msg: Error during invocation. Most
> likely server version does not match client version Filename:
> LoginBean.java; Method name:  login Line number: 393
>  ome.client.OutOfService: Error during invocation. Most likely server
> version does not match client version
>         at ome.admin.controller.LoginBean.login(LoginBean.java:393)
>
> Any suggestions.  I can supply server.log and/or WebAdmin.log  
> contents.
>
> Thanks.
> Susan
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


From smwilson at hpc.unm.edu  Mon Sep 22 20:40:34 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Mon, 22 Sep 2008 13:40:34 -0600
Subject: [ome-users] server version does not match client version
In-Reply-To: <9A4FA9D9-4E8F-4A35-B77B-CFA2AB7311BF@lifesci.dundee.ac.uk>
References: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
	<9CC8D572-3B8E-4431-8960-F53E7E5A22D1@hpc.unm.edu>
	<9A4FA9D9-4E8F-4A35-B77B-CFA2AB7311BF@lifesci.dundee.ac.uk>
Message-ID: <F2CFA152-8F39-4EC6-82EA-49D51BD5D3F7@hpc.unm.edu>

Thanks Jason.  Everything checks out.
Susan

On Sep 22, 2008, at 1:37 PM, Jason Swedlow wrote:

> Hi Susan-
>
> The tech side is not my forte, but just to make sure, did you read  
> and follow instructions at
>
> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroAndPostgres
>
> especially the details regarding Postgres 7.4?  (this is linked from  
> the "Prerequisites" section on the OmeroInstall page).
>
> Cheers,
>
> Jason
>
> On 22 Sep 2008, at 20:33, Susan Wilson wrote:
>
>> The first error I see in the WebAdmin log is
>>
>>  [22-09-08 13:24:14,156] ERROR - Msg: Got marshalling exception,
>> exiting Filename: SocketClientInvoker.java; Method name:
>> handleException Line number: 109
>>  java.lang.ClassNotFoundException:  
>> org.hibernate.search.SearchException
>>         at
>> org
>> .jboss
>> .remoting
>> .serialization.ClassLoaderUtility.loadClass(ClassLoaderUtility.java: 
>> 82)
>>         at
>> org
>> .jboss
>> .remoting
>> .loading.RemotingClassLoader.loadClass(RemotingClassLoader.java:76)
>> .
>> .
>> .
>>
>> On Sep 22, 2008, at 1:19 PM, Susan Wilson wrote:
>>
>>> Hi,
>>>
>>> Installing omero-Beta3.0.1 on debian_version 4.0 with postgresql  
>>> 7.4.
>>>
>>> Installation goes well, login screen at localhost appears, but  
>>> when I
>>> login as root/omero, I get the dreaded "Most likely....".
>>> WebAdmin.log has plenty of output - I set JAVA_HOME to the jdk
>>> location, but the result is the same.
>>>
>>> [22-09-08 13:12:31,740] ERROR - Msg: Error during invocation. Most
>>> likely server version does not match client version Filename:
>>> LoginBean.java; Method name:  login Line number: 393
>>> ome.client.OutOfService: Error during invocation. Most likely server
>>> version does not match client version
>>>        at ome.admin.controller.LoginBean.login(LoginBean.java:393)
>>>
>>> Any suggestions.  I can supply server.log and/or WebAdmin.log
>>> contents.
>>>
>>> Thanks.
>>> Susan
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> **************************
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> phone (01382) 385819
> Intl phone:  44 1382 385819
> FAX   (01382) 388072
> email: jason at lifesci.dundee.ac.uk
>
> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> Open Microscopy Environment: http://openmicroscopy.org
> **************************
>
> The University of Dundee is a Scottish Registered Charity, No.  
> SC015096.
>
>
>


From palmeida at igc.gulbenkian.pt  Tue Sep 23 17:01:47 2008
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Tue, 23 Sep 2008 17:01:47 +0100
Subject: [ome-users] server version does not match client version
In-Reply-To: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
References: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
Message-ID: <200809231701.47989.palmeida@igc.gulbenkian.pt>

Hi,

I'm not sure this will help, but I got that error message today, although my 
problem was postgresql 7.4 was running, instead of 8.1, which is the one I 
configured to use with Omero. Is that a newly created database? I had 
problems upgrading an old database with 7.4, which is why I switched to 8.1. 
Postgresql 8.1 is in the Debian etch (4.0) repository as well, you could give 
it a try to see if that works.

Good luck,
Paulo

On Monday 22 September 2008 20:19, Susan Wilson wrote:
> Hi,
>
> Installing omero-Beta3.0.1 on debian_version 4.0 with postgresql 7.4.
>
> Installation goes well, login screen at localhost appears, but when I
> login as root/omero, I get the dreaded "Most likely....".
> WebAdmin.log has plenty of output - I set JAVA_HOME to the jdk
> location, but the result is the same.
>
> [22-09-08 13:12:31,740] ERROR - Msg: Error during invocation. Most
> likely server version does not match client version Filename:
> LoginBean.java; Method name:  login Line number: 393
>   ome.client.OutOfService: Error during invocation. Most likely server
> version does not match client version
>          at ome.admin.controller.LoginBean.login(LoginBean.java:393)
>
> Any suggestions.  I can supply server.log and/or WebAdmin.log contents.
>
> Thanks.
> Susan
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

From smwilson at hpc.unm.edu  Tue Sep 23 17:03:50 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Tue, 23 Sep 2008 10:03:50 -0600
Subject: [ome-users] server version does not match client version
In-Reply-To: <9A4FA9D9-4E8F-4A35-B77B-CFA2AB7311BF@lifesci.dundee.ac.uk>
References: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
	<9CC8D572-3B8E-4431-8960-F53E7E5A22D1@hpc.unm.edu>
	<9A4FA9D9-4E8F-4A35-B77B-CFA2AB7311BF@lifesci.dundee.ac.uk>
Message-ID: <170B61C0-C2FF-414C-81AE-0315B2700D7C@hpc.unm.edu>

This problem manifests as errors in the run.sh session with the  
following text:

--- MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM ---

so it appears to be a jboss problem?

Susan


On Sep 22, 2008, at 1:37 PM, Jason Swedlow wrote:

> Hi Susan-
>
> The tech side is not my forte, but just to make sure, did you read  
> and follow instructions at
>
> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroAndPostgres
>
> especially the details regarding Postgres 7.4?  (this is linked from  
> the "Prerequisites" section on the OmeroInstall page).
>
> Cheers,
>
> Jason
>
> On 22 Sep 2008, at 20:33, Susan Wilson wrote:
>
>> The first error I see in the WebAdmin log is
>>
>>  [22-09-08 13:24:14,156] ERROR - Msg: Got marshalling exception,
>> exiting Filename: SocketClientInvoker.java; Method name:
>> handleException Line number: 109
>>  java.lang.ClassNotFoundException:  
>> org.hibernate.search.SearchException
>>         at
>> org
>> .jboss
>> .remoting
>> .serialization.ClassLoaderUtility.loadClass(ClassLoaderUtility.java: 
>> 82)
>>         at
>> org
>> .jboss
>> .remoting
>> .loading.RemotingClassLoader.loadClass(RemotingClassLoader.java:76)
>> .
>> .
>> .
>>
>> On Sep 22, 2008, at 1:19 PM, Susan Wilson wrote:
>>
>>> Hi,
>>>
>>> Installing omero-Beta3.0.1 on debian_version 4.0 with postgresql  
>>> 7.4.
>>>
>>> Installation goes well, login screen at localhost appears, but  
>>> when I
>>> login as root/omero, I get the dreaded "Most likely....".
>>> WebAdmin.log has plenty of output - I set JAVA_HOME to the jdk
>>> location, but the result is the same.
>>>
>>> [22-09-08 13:12:31,740] ERROR - Msg: Error during invocation. Most
>>> likely server version does not match client version Filename:
>>> LoginBean.java; Method name:  login Line number: 393
>>> ome.client.OutOfService: Error during invocation. Most likely server
>>> version does not match client version
>>>        at ome.admin.controller.LoginBean.login(LoginBean.java:393)
>>>
>>> Any suggestions.  I can supply server.log and/or WebAdmin.log
>>> contents.
>>>
>>> Thanks.
>>> Susan
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
>
> **************************
> Wellcome Trust Centre for Gene Regulation & Expression
> College of Life Sciences
> MSI/WTB/JBC Complex
> University of Dundee
> Dow Street
> Dundee  DD1 5EH
> United Kingdom
>
> phone (01382) 385819
> Intl phone:  44 1382 385819
> FAX   (01382) 388072
> email: jason at lifesci.dundee.ac.uk
>
> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> Open Microscopy Environment: http://openmicroscopy.org
> **************************
>
> The University of Dundee is a Scottish Registered Charity, No.  
> SC015096.
>
>
>


From callan at blackcat.ca  Tue Sep 23 23:07:51 2008
From: callan at blackcat.ca (Chris Allan)
Date: Tue, 23 Sep 2008 23:07:51 +0100
Subject: [ome-users] server version does not match client version
In-Reply-To: <170B61C0-C2FF-414C-81AE-0315B2700D7C@hpc.unm.edu>
References: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
	<9CC8D572-3B8E-4431-8960-F53E7E5A22D1@hpc.unm.edu>
	<9A4FA9D9-4E8F-4A35-B77B-CFA2AB7311BF@lifesci.dundee.ac.uk>
	<170B61C0-C2FF-414C-81AE-0315B2700D7C@hpc.unm.edu>
Message-ID: <92FF61EA-CCBD-4871-9AA8-F1A6390F3FA9@blackcat.ca>

Hi Susan,

Can we get a copy of your server.log (from the JBoss server/default/ 
log directory)?

As Pablo mentioned, PostgreSQL 7.4 has been problematic though we are  
confident that  those issues have been resolved.

Can you confirm that you can pull up the PostgreSQL command prompt with:

psql -h localhost -U omero omero3

and then run and give me the output of:

\l

and

\du

Should be able to get to the bottom of this, thanks for your patience.

-Chris

On 23 Sep 2008, at 17:03, Susan Wilson wrote:

> This problem manifests as errors in the run.sh session with the
> following text:
>
> --- MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM ---
>
> so it appears to be a jboss problem?
>
> Susan
>
>
> On Sep 22, 2008, at 1:37 PM, Jason Swedlow wrote:
>
>> Hi Susan-
>>
>> The tech side is not my forte, but just to make sure, did you read
>> and follow instructions at
>>
>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroAndPostgres
>>
>> especially the details regarding Postgres 7.4?  (this is linked from
>> the "Prerequisites" section on the OmeroInstall page).
>>
>> Cheers,
>>
>> Jason
>>
>> On 22 Sep 2008, at 20:33, Susan Wilson wrote:
>>
>>> The first error I see in the WebAdmin log is
>>>
>>> [22-09-08 13:24:14,156] ERROR - Msg: Got marshalling exception,
>>> exiting Filename: SocketClientInvoker.java; Method name:
>>> handleException Line number: 109
>>> java.lang.ClassNotFoundException:
>>> org.hibernate.search.SearchException
>>>        at
>>> org
>>> .jboss
>>> .remoting
>>> .serialization.ClassLoaderUtility.loadClass(ClassLoaderUtility.java:
>>> 82)
>>>        at
>>> org
>>> .jboss
>>> .remoting
>>> .loading.RemotingClassLoader.loadClass(RemotingClassLoader.java:76)
>>> .
>>> .
>>> .
>>>
>>> On Sep 22, 2008, at 1:19 PM, Susan Wilson wrote:
>>>
>>>> Hi,
>>>>
>>>> Installing omero-Beta3.0.1 on debian_version 4.0 with postgresql
>>>> 7.4.
>>>>
>>>> Installation goes well, login screen at localhost appears, but
>>>> when I
>>>> login as root/omero, I get the dreaded "Most likely....".
>>>> WebAdmin.log has plenty of output - I set JAVA_HOME to the jdk
>>>> location, but the result is the same.
>>>>
>>>> [22-09-08 13:12:31,740] ERROR - Msg: Error during invocation. Most
>>>> likely server version does not match client version Filename:
>>>> LoginBean.java; Method name:  login Line number: 393
>>>> ome.client.OutOfService: Error during invocation. Most likely  
>>>> server
>>>> version does not match client version
>>>>       at ome.admin.controller.LoginBean.login(LoginBean.java:393)
>>>>
>>>> Any suggestions.  I can supply server.log and/or WebAdmin.log
>>>> contents.
>>>>
>>>> Thanks.
>>>> Susan
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>>
>> **************************
>> Wellcome Trust Centre for Gene Regulation & Expression
>> College of Life Sciences
>> MSI/WTB/JBC Complex
>> University of Dundee
>> Dow Street
>> Dundee  DD1 5EH
>> United Kingdom
>>
>> phone (01382) 385819
>> Intl phone:  44 1382 385819
>> FAX   (01382) 388072
>> email: jason at lifesci.dundee.ac.uk
>>
>> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
>> Open Microscopy Environment: http://openmicroscopy.org
>> **************************
>>
>> The University of Dundee is a Scottish Registered Charity, No.
>> SC015096.
>>
>>
>>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


From callan at blackcat.ca  Wed Sep 24 17:09:58 2008
From: callan at blackcat.ca (Chris Allan)
Date: Wed, 24 Sep 2008 17:09:58 +0100
Subject: [ome-users] server version does not match client version
In-Reply-To: <92FF61EA-CCBD-4871-9AA8-F1A6390F3FA9@blackcat.ca>
References: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
	<9CC8D572-3B8E-4431-8960-F53E7E5A22D1@hpc.unm.edu>
	<9A4FA9D9-4E8F-4A35-B77B-CFA2AB7311BF@lifesci.dundee.ac.uk>
	<170B61C0-C2FF-414C-81AE-0315B2700D7C@hpc.unm.edu>
	<92FF61EA-CCBD-4871-9AA8-F1A6390F3FA9@blackcat.ca>
Message-ID: <D540BE6D-C6B9-475D-AFCD-1E34310A8D19@blackcat.ca>

We've resolved Susan's issue offline. For the benefit of everyone  
else on list (and those who have the issue in the future), if you're  
having "MBEAN" of "BEAN" errors spewing forth when you start up  
JBoss, please check:

  * Your PostgreSQL configuration
  * The permissions on /OMERO (the problem in Susan's particular case)

I've also updated http://trac.openmicroscopy.org.uk/omero/wiki/ 
OmeroTroubleshooting with details.

Thanks!

-Chris

On 23 Sep 2008, at 23:07, Chris Allan wrote:

> Hi Susan,
>
> Can we get a copy of your server.log (from the JBoss server/default/
> log directory)?
>
> As Pablo mentioned, PostgreSQL 7.4 has been problematic though we are
> confident that  those issues have been resolved.
>
> Can you confirm that you can pull up the PostgreSQL command prompt  
> with:
>
> psql -h localhost -U omero omero3
>
> and then run and give me the output of:
>
> \l
>
> and
>
> \du
>
> Should be able to get to the bottom of this, thanks for your patience.
>
> -Chris
>
> On 23 Sep 2008, at 17:03, Susan Wilson wrote:
>
>> This problem manifests as errors in the run.sh session with the
>> following text:
>>
>> --- MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM ---
>>
>> so it appears to be a jboss problem?
>>
>> Susan
>>
>>
>> On Sep 22, 2008, at 1:37 PM, Jason Swedlow wrote:
>>
>>> Hi Susan-
>>>
>>> The tech side is not my forte, but just to make sure, did you read
>>> and follow instructions at
>>>
>>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroAndPostgres
>>>
>>> especially the details regarding Postgres 7.4?  (this is linked from
>>> the "Prerequisites" section on the OmeroInstall page).
>>>
>>> Cheers,
>>>
>>> Jason
>>>
>>> On 22 Sep 2008, at 20:33, Susan Wilson wrote:
>>>
>>>> The first error I see in the WebAdmin log is
>>>>
>>>> [22-09-08 13:24:14,156] ERROR - Msg: Got marshalling exception,
>>>> exiting Filename: SocketClientInvoker.java; Method name:
>>>> handleException Line number: 109
>>>> java.lang.ClassNotFoundException:
>>>> org.hibernate.search.SearchException
>>>>        at
>>>> org
>>>> .jboss
>>>> .remoting
>>>> .serialization.ClassLoaderUtility.loadClass 
>>>> (ClassLoaderUtility.java:
>>>> 82)
>>>>        at
>>>> org
>>>> .jboss
>>>> .remoting
>>>> .loading.RemotingClassLoader.loadClass(RemotingClassLoader.java:76)
>>>> .
>>>> .
>>>> .
>>>>
>>>> On Sep 22, 2008, at 1:19 PM, Susan Wilson wrote:
>>>>
>>>>> Hi,
>>>>>
>>>>> Installing omero-Beta3.0.1 on debian_version 4.0 with postgresql
>>>>> 7.4.
>>>>>
>>>>> Installation goes well, login screen at localhost appears, but
>>>>> when I
>>>>> login as root/omero, I get the dreaded "Most likely....".
>>>>> WebAdmin.log has plenty of output - I set JAVA_HOME to the jdk
>>>>> location, but the result is the same.
>>>>>
>>>>> [22-09-08 13:12:31,740] ERROR - Msg: Error during invocation. Most
>>>>> likely server version does not match client version Filename:
>>>>> LoginBean.java; Method name:  login Line number: 393
>>>>> ome.client.OutOfService: Error during invocation. Most likely
>>>>> server
>>>>> version does not match client version
>>>>>       at ome.admin.controller.LoginBean.login(LoginBean.java:393)
>>>>>
>>>>> Any suggestions.  I can supply server.log and/or WebAdmin.log
>>>>> contents.
>>>>>
>>>>> Thanks.
>>>>> Susan
>>>>> _______________________________________________
>>>>> ome-users mailing list
>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>>
>>> **************************
>>> Wellcome Trust Centre for Gene Regulation & Expression
>>> College of Life Sciences
>>> MSI/WTB/JBC Complex
>>> University of Dundee
>>> Dow Street
>>> Dundee  DD1 5EH
>>> United Kingdom
>>>
>>> phone (01382) 385819
>>> Intl phone:  44 1382 385819
>>> FAX   (01382) 388072
>>> email: jason at lifesci.dundee.ac.uk
>>>
>>> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
>>> Open Microscopy Environment: http://openmicroscopy.org
>>> **************************
>>>
>>> The University of Dundee is a Scottish Registered Charity, No.
>>> SC015096.
>>>
>>>
>>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users


From palmeida at igc.gulbenkian.pt  Wed Sep 24 18:02:40 2008
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Wed, 24 Sep 2008 18:02:40 +0100
Subject: [ome-users] server version does not match client version
In-Reply-To: <D540BE6D-C6B9-475D-AFCD-1E34310A8D19@blackcat.ca>
References: <5F0679A5-320F-497F-815F-12BB3F3CEBE4@hpc.unm.edu>
	<92FF61EA-CCBD-4871-9AA8-F1A6390F3FA9@blackcat.ca>
	<D540BE6D-C6B9-475D-AFCD-1E34310A8D19@blackcat.ca>
Message-ID: <200809241802.40329.palmeida@igc.gulbenkian.pt>

Hi Chris,

Regarding /OMERO , I am using a different directory to store data 
( /srv/OMERO ) and everything on the Java clients seems to be working fine, 
but in the WebAdmin, when I go to Import, it complains that /OMERO/WebAdmin 
does not exist and cannot be created. This interface will probably be 
obsolete anyway, with the Web Client, but just saying in case it may be 
useful.

Best,
Paulo 

On Wednesday 24 September 2008 17:09, Chris Allan wrote:
> We've resolved Susan's issue offline. For the benefit of everyone
> else on list (and those who have the issue in the future), if you're
> having "MBEAN" of "BEAN" errors spewing forth when you start up
> JBoss, please check:
>
>   * Your PostgreSQL configuration
>   * The permissions on /OMERO (the problem in Susan's particular case)
>
> I've also updated http://trac.openmicroscopy.org.uk/omero/wiki/
> OmeroTroubleshooting with details.
>
> Thanks!
>
> -Chris
>
> On 23 Sep 2008, at 23:07, Chris Allan wrote:
> > Hi Susan,
> >
> > Can we get a copy of your server.log (from the JBoss server/default/
> > log directory)?
> >
> > As Pablo mentioned, PostgreSQL 7.4 has been problematic though we are
> > confident that  those issues have been resolved.
> >
> > Can you confirm that you can pull up the PostgreSQL command prompt
> > with:
> >
> > psql -h localhost -U omero omero3
> >
> > and then run and give me the output of:
> >
> > \l
> >
> > and
> >
> > \du
> >
> > Should be able to get to the bottom of this, thanks for your patience.
> >
> > -Chris
> >
> > On 23 Sep 2008, at 17:03, Susan Wilson wrote:
> >> This problem manifests as errors in the run.sh session with the
> >> following text:
> >>
> >> --- MBEANS THAT ARE THE ROOT CAUSE OF THE PROBLEM ---
> >>
> >> so it appears to be a jboss problem?
> >>
> >> Susan
> >>
> >> On Sep 22, 2008, at 1:37 PM, Jason Swedlow wrote:
> >>> Hi Susan-
> >>>
> >>> The tech side is not my forte, but just to make sure, did you read
> >>> and follow instructions at
> >>>
> >>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroAndPostgres
> >>>
> >>> especially the details regarding Postgres 7.4?  (this is linked from
> >>> the "Prerequisites" section on the OmeroInstall page).
> >>>
> >>> Cheers,
> >>>
> >>> Jason
> >>>
> >>> On 22 Sep 2008, at 20:33, Susan Wilson wrote:
> >>>> The first error I see in the WebAdmin log is
> >>>>
> >>>> [22-09-08 13:24:14,156] ERROR - Msg: Got marshalling exception,
> >>>> exiting Filename: SocketClientInvoker.java; Method name:
> >>>> handleException Line number: 109
> >>>> java.lang.ClassNotFoundException:
> >>>> org.hibernate.search.SearchException
> >>>>        at
> >>>> org
> >>>> .jboss
> >>>> .remoting
> >>>> .serialization.ClassLoaderUtility.loadClass
> >>>> (ClassLoaderUtility.java:
> >>>> 82)
> >>>>        at
> >>>> org
> >>>> .jboss
> >>>> .remoting
> >>>> .loading.RemotingClassLoader.loadClass(RemotingClassLoader.java:76)
> >>>> .
> >>>> .
> >>>> .
> >>>>
> >>>> On Sep 22, 2008, at 1:19 PM, Susan Wilson wrote:
> >>>>> Hi,
> >>>>>
> >>>>> Installing omero-Beta3.0.1 on debian_version 4.0 with postgresql
> >>>>> 7.4.
> >>>>>
> >>>>> Installation goes well, login screen at localhost appears, but
> >>>>> when I
> >>>>> login as root/omero, I get the dreaded "Most likely....".
> >>>>> WebAdmin.log has plenty of output - I set JAVA_HOME to the jdk
> >>>>> location, but the result is the same.
> >>>>>
> >>>>> [22-09-08 13:12:31,740] ERROR - Msg: Error during invocation. Most
> >>>>> likely server version does not match client version Filename:
> >>>>> LoginBean.java; Method name:  login Line number: 393
> >>>>> ome.client.OutOfService: Error during invocation. Most likely
> >>>>> server
> >>>>> version does not match client version
> >>>>>       at ome.admin.controller.LoginBean.login(LoginBean.java:393)
> >>>>>
> >>>>> Any suggestions.  I can supply server.log and/or WebAdmin.log
> >>>>> contents.
> >>>>>
> >>>>> Thanks.
> >>>>> Susan
> >>>>> _______________________________________________
> >>>>> ome-users mailing list
> >>>>> ome-users at lists.openmicroscopy.org.uk
> >>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >>>>
> >>>> _______________________________________________
> >>>> ome-users mailing list
> >>>> ome-users at lists.openmicroscopy.org.uk
> >>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >>>
> >>> **************************
> >>> Wellcome Trust Centre for Gene Regulation & Expression
> >>> College of Life Sciences
> >>> MSI/WTB/JBC Complex
> >>> University of Dundee
> >>> Dow Street
> >>> Dundee  DD1 5EH
> >>> United Kingdom
> >>>
> >>> phone (01382) 385819
> >>> Intl phone:  44 1382 385819
> >>> FAX   (01382) 388072
> >>> email: jason at lifesci.dundee.ac.uk
> >>>
> >>> Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
> >>> Open Microscopy Environment: http://openmicroscopy.org
> >>> **************************
> >>>
> >>> The University of Dundee is a Scottish Registered Charity, No.
> >>> SC015096.
> >>
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

From smwilson at hpc.unm.edu  Wed Sep 24 21:09:21 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Wed, 24 Sep 2008 14:09:21 -0600
Subject: [ome-users] NumberFormatException import .zvi file
Message-ID: <E336CA01-D406-40F2-9A57-FA274ADEC5EF@hpc.unm.edu>

Hi,

Runniing Beta3.0.1 all around.  This is the error I get when I attempt  
to import a .zvi file:

java.lang.NumberFormatException: For input string: "9/17/2008 7:05:39  
PM"
	at  
java 
.lang.NumberFormatException.forInputString(NumberFormatException.java: 
48)
	at java.lang.Long.parseLong(Long.java:412)
	at java.lang.Long.parseLong(Long.java:461)
	at loci.formats.in.ZeissZVIReader.initMetadata(ZeissZVIReader.java:623)
	at loci.formats.in.ZeissZVIReader.initFile(ZeissZVIReader.java:513)
	at loci.formats.FormatReader.setId(FormatReader.java:216)
	at loci.formats.ImageReader.setId(ImageReader.java:565)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:61)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
	at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:181)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java: 
355)
	at ome.formats.importer.ImportHandler.importImages(ImportHandler.java: 
172)
	at ome.formats.importer.ImportHandler.access$0(ImportHandler.java:106)
	at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:87)

Also, I may be crazy, but the documentation for OMERO.insight does not  
match what I am seeing.  This error is on my MAC to OMERO.server on  
debian.  I downloaded and ran both (linux) importer and insight on the  
localhost debian host and got the same importer error and the same  
insight application.  Help/About shows Beta3.0.1, which is the server  
I am running, but insight has no categories, no "Browse Button"...   
And importer won't import the zvi on either platform.

Thanks.
Susan

From ctrueden at wisc.edu  Wed Sep 24 21:20:48 2008
From: ctrueden at wisc.edu (Curtis Rueden)
Date: Wed, 24 Sep 2008 15:20:48 -0500
Subject: [ome-users] NumberFormatException import .zvi file
In-Reply-To: <0K7P00003UNRAQ00@smtp5.wiscmail.wisc.edu>
References: <0K7P00003UNRAQ00@smtp5.wiscmail.wisc.edu>
Message-ID: <857a86450809241320u7d33fc69ib53a3126eb443b56@mail.gmail.com>

Hi Susan,

That exception looks like a bug in Bio-Formats to me. Are you able to import
the ZVI file into ImageJ using the Bio-Formats Importer plugin (
http://www.loci.wisc.edu/ome/formats-imagej.html) with the latest trunk
build (http://www.loci.wisc.edu/ome/formats-download.html)?

-Curtis

On Wed, Sep 24, 2008 at 3:09 PM, Susan Wilson <smwilson at hpc.unm.edu> wrote:

> Hi,
>
> Runniing Beta3.0.1 all around.  This is the error I get when I attempt
> to import a .zvi file:
>
> java.lang.NumberFormatException: For input string: "9/17/2008 7:05:39
> PM"
>        at
> java
> .lang.NumberFormatException.forInputString(NumberFormatException.java:
> 48)
>        at java.lang.Long.parseLong(Long.java:412)
>        at java.lang.Long.parseLong(Long.java:461)
>        at
> loci.formats.in.ZeissZVIReader.initMetadata(ZeissZVIReader.java:623)
>        at loci.formats.in.ZeissZVIReader.initFile(ZeissZVIReader.java:513)
>        at loci.formats.FormatReader.setId(FormatReader.java:216)
>        at loci.formats.ImageReader.setId(ImageReader.java:565)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:61)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:181)
>        at
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:
> 355)
>        at
> ome.formats.importer.ImportHandler.importImages(ImportHandler.java:
> 172)
>        at
> ome.formats.importer.ImportHandler.access$0(ImportHandler.java:106)
>        at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:87)
>
> Also, I may be crazy, but the documentation for OMERO.insight does not
> match what I am seeing.  This error is on my MAC to OMERO.server on
> debian.  I downloaded and ran both (linux) importer and insight on the
> localhost debian host and got the same importer error and the same
> insight application.  Help/About shows Beta3.0.1, which is the server
> I am running, but insight has no categories, no "Browse Button"...
> And importer won't import the zvi on either platform.
>
> Thanks.
> Susan
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
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From j.burel at dundee.ac.uk  Wed Sep 24 21:23:51 2008
From: j.burel at dundee.ac.uk (jean-marie)
Date: Wed, 24 Sep 2008 21:23:51 +0100
Subject: [ome-users] NumberFormatException import .zvi file
In-Reply-To: <E336CA01-D406-40F2-9A57-FA274ADEC5EF@hpc.unm.edu>
References: <E336CA01-D406-40F2-9A57-FA274ADEC5EF@hpc.unm.edu>
Message-ID: <DD6250EB-D318-4D55-806B-6D5E81C7576B@dundee.ac.uk>

Hi Susan

The document of OMERO.insight and OMERO.importer are for Beta2.3 version
Unfortunately, we didn't have time to update the user guides.
Categories are no longer supported in Beta3.
The browse functionality is still available (icon  has changed),
we have tried in Beta3 to reduce the number of windows to make better  
use of the space.

When for example you browse a project, the thumbnails are displayed  
in the middle-pane (working area)

We are currently updated our website and documentation.


Thanks for your comments

Jmarie


From smwilson at hpc.unm.edu  Wed Sep 24 21:36:23 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Wed, 24 Sep 2008 14:36:23 -0600
Subject: [ome-users] NumberFormatException import .zvi file
In-Reply-To: <DD6250EB-D318-4D55-806B-6D5E81C7576B@dundee.ac.uk>
References: <E336CA01-D406-40F2-9A57-FA274ADEC5EF@hpc.unm.edu>
	<DD6250EB-D318-4D55-806B-6D5E81C7576B@dundee.ac.uk>
Message-ID: <FFADC210-9417-4276-96F3-3EC5EB64101C@hpc.unm.edu>

OK, that makes sense to me, although I cannot get the browse function  
to work at all.  I thought I could select a discrete set of images,  
hit the browse button, and see those image thumbnails in the working  
area.  This does not work for me.

Susan

On Sep 24, 2008, at 2:23 PM, jean-marie wrote:

> Hi Susan
>
> The document of OMERO.insight and OMERO.importer are for Beta2.3  
> version
> Unfortunately, we didn't have time to update the user guides.
> Categories are no longer supported in Beta3.
> The browse functionality is still available (icon  has changed),
> we have tried in Beta3 to reduce the number of windows to make  
> better use of the space.
>
> When for example you browse a project, the thumbnails are displayed  
> in the middle-pane (working area)
>
> We are currently updated our website and documentation.
>
>
> Thanks for your comments
>
> Jmarie
>


From smwilson at hpc.unm.edu  Wed Sep 24 21:41:51 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Wed, 24 Sep 2008 14:41:51 -0600
Subject: [ome-users] NumberFormatException import .zvi file
In-Reply-To: <857a86450809241320u7d33fc69ib53a3126eb443b56@mail.gmail.com>
References: <0K7P00003UNRAQ00@smtp5.wiscmail.wisc.edu>
	<857a86450809241320u7d33fc69ib53a3126eb443b56@mail.gmail.com>
Message-ID: <8FD7A00D-157C-4823-9E74-4071453E2C51@hpc.unm.edu>

Hi Curtis,

Just downloaded and ran ImageJ on my MAC.  I was able to drop the zvi  
file right into ImageJ, no problems.

Susan

On Sep 24, 2008, at 2:20 PM, Curtis Rueden wrote:

> Hi Susan,
>
> That exception looks like a bug in Bio-Formats to me. Are you able  
> to import the ZVI file into ImageJ using the Bio-Formats Importer  
> plugin (http://www.loci.wisc.edu/ome/formats-imagej.html) with the  
> latest trunk build (http://www.loci.wisc.edu/ome/formats-download.html)?
>
> -Curtis
>
> On Wed, Sep 24, 2008 at 3:09 PM, Susan Wilson <smwilson at hpc.unm.edu>  
> wrote:
> Hi,
>
> Runniing Beta3.0.1 all around.  This is the error I get when I attempt
> to import a .zvi file:
>
> java.lang.NumberFormatException: For input string: "9/17/2008 7:05:39
> PM"
>        at
> java
> .lang.NumberFormatException.forInputString(NumberFormatException.java:
> 48)
>        at java.lang.Long.parseLong(Long.java:412)
>        at java.lang.Long.parseLong(Long.java:461)
>        at  
> loci.formats.in.ZeissZVIReader.initMetadata(ZeissZVIReader.java:623)
>        at  
> loci.formats.in.ZeissZVIReader.initFile(ZeissZVIReader.java:513)
>        at loci.formats.FormatReader.setId(FormatReader.java:216)
>        at loci.formats.ImageReader.setId(ImageReader.java:565)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java: 
> 61)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java: 
> 181)
>        at  
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:
> 355)
>        at  
> ome.formats.importer.ImportHandler.importImages(ImportHandler.java:
> 172)
>        at ome.formats.importer.ImportHandler.access 
> $0(ImportHandler.java:106)
>        at ome.formats.importer.ImportHandler 
> $1.run(ImportHandler.java:87)
>
> Also, I may be crazy, but the documentation for OMERO.insight does not
> match what I am seeing.  This error is on my MAC to OMERO.server on
> debian.  I downloaded and ran both (linux) importer and insight on the
> localhost debian host and got the same importer error and the same
> insight application.  Help/About shows Beta3.0.1, which is the server
> I am running, but insight has no categories, no "Browse Button"...
> And importer won't import the zvi on either platform.
>
> Thanks.
> Susan
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>

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From smwilson at hpc.unm.edu  Wed Sep 24 21:48:45 2008
From: smwilson at hpc.unm.edu (Susan Wilson)
Date: Wed, 24 Sep 2008 14:48:45 -0600
Subject: [ome-users] NumberFormatException import .zvi file
In-Reply-To: <857a86450809241320u7d33fc69ib53a3126eb443b56@mail.gmail.com>
References: <0K7P00003UNRAQ00@smtp5.wiscmail.wisc.edu>
	<857a86450809241320u7d33fc69ib53a3126eb443b56@mail.gmail.com>
Message-ID: <7BB9D4B2-89EE-40E0-99D2-760C75DCD514@hpc.unm.edu>

Hi again,

I downloaded the latest trunk build of the loci_tools.jar and placed  
it in the plugins folder and re-ran ImageJ.  The LOCI Bioformats  
Importer gives the same error on that zvi file that OMERO.insight does.

Susan

On Sep 24, 2008, at 2:20 PM, Curtis Rueden wrote:

> Hi Susan,
>
> That exception looks like a bug in Bio-Formats to me. Are you able  
> to import the ZVI file into ImageJ using the Bio-Formats Importer  
> plugin (http://www.loci.wisc.edu/ome/formats-imagej.html) with the  
> latest trunk build (http://www.loci.wisc.edu/ome/formats-download.html)?
>
> -Curtis
>
> On Wed, Sep 24, 2008 at 3:09 PM, Susan Wilson <smwilson at hpc.unm.edu>  
> wrote:
> Hi,
>
> Runniing Beta3.0.1 all around.  This is the error I get when I attempt
> to import a .zvi file:
>
> java.lang.NumberFormatException: For input string: "9/17/2008 7:05:39
> PM"
>        at
> java
> .lang.NumberFormatException.forInputString(NumberFormatException.java:
> 48)
>        at java.lang.Long.parseLong(Long.java:412)
>        at java.lang.Long.parseLong(Long.java:461)
>        at  
> loci.formats.in.ZeissZVIReader.initMetadata(ZeissZVIReader.java:623)
>        at  
> loci.formats.in.ZeissZVIReader.initFile(ZeissZVIReader.java:513)
>        at loci.formats.FormatReader.setId(FormatReader.java:216)
>        at loci.formats.ImageReader.setId(ImageReader.java:565)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java: 
> 61)
>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java: 
> 181)
>        at  
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:
> 355)
>        at  
> ome.formats.importer.ImportHandler.importImages(ImportHandler.java:
> 172)
>        at ome.formats.importer.ImportHandler.access 
> $0(ImportHandler.java:106)
>        at ome.formats.importer.ImportHandler 
> $1.run(ImportHandler.java:87)
>
> Also, I may be crazy, but the documentation for OMERO.insight does not
> match what I am seeing.  This error is on my MAC to OMERO.server on
> debian.  I downloaded and ran both (linux) importer and insight on the
> localhost debian host and got the same importer error and the same
> insight application.  Help/About shows Beta3.0.1, which is the server
> I am running, but insight has no categories, no "Browse Button"...
> And importer won't import the zvi on either platform.
>
> Thanks.
> Susan
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>

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From ctrueden at wisc.edu  Wed Sep 24 21:54:08 2008
From: ctrueden at wisc.edu (Curtis Rueden)
Date: Wed, 24 Sep 2008 15:54:08 -0500
Subject: [ome-users] NumberFormatException import .zvi file
In-Reply-To: <7BB9D4B2-89EE-40E0-99D2-760C75DCD514@hpc.unm.edu>
References: <0K7P00003UNRAQ00@smtp5.wiscmail.wisc.edu>
	<857a86450809241320u7d33fc69ib53a3126eb443b56@mail.gmail.com>
	<7BB9D4B2-89EE-40E0-99D2-760C75DCD514@hpc.unm.edu>
Message-ID: <857a86450809241354x7bba3e7fn31a178a7eda444d0@mail.gmail.com>

Hi Susan,

I downloaded the latest trunk build of the loci_tools.jar and placed it in
> the plugins folder and re-ran ImageJ.  The LOCI Bioformats Importer gives
> the same error on that zvi file that OMERO.insight does.
>

Strange; I checked the source code and it should not be generating this
error. Would you be willing to send us the problematic file for us to use
for debugging? Once we have the problem solved in Bio-Formats, the next
version of OMERO.importer will also incorporate the fix -- or I can provide
you with instructions on how to update your existing version of
OMERO.importer if you like.

-Curtis

On Wed, Sep 24, 2008 at 3:48 PM, Susan Wilson <smwilson at hpc.unm.edu> wrote:

> Hi again,
> I downloaded the latest trunk build of the loci_tools.jar and placed it in
> the plugins folder and re-ran ImageJ.  The LOCI Bioformats Importer gives
> the same error on that zvi file that OMERO.insight does.
>
> Susan
>
> On Sep 24, 2008, at 2:20 PM, Curtis Rueden wrote:
>
> Hi Susan,
>
> That exception looks like a bug in Bio-Formats to me. Are you able to
> import the ZVI file into ImageJ using the Bio-Formats Importer plugin (
> http://www.loci.wisc.edu/ome/formats-imagej.html) with the latest trunk
> build (http://www.loci.wisc.edu/ome/formats-download.html)?
>
> -Curtis
>
> On Wed, Sep 24, 2008 at 3:09 PM, Susan Wilson <smwilson at hpc.unm.edu>wrote:
>
>> Hi,
>>
>> Runniing Beta3.0.1 all around.  This is the error I get when I attempt
>> to import a .zvi file:
>>
>> java.lang.NumberFormatException: For input string: "9/17/2008 7:05:39
>> PM"
>>        at
>> java
>> .lang.NumberFormatException.forInputString(NumberFormatException.java:
>> 48)
>>        at java.lang.Long.parseLong(Long.java:412)
>>        at java.lang.Long.parseLong(Long.java:461)
>>        at
>> loci.formats.in.ZeissZVIReader.initMetadata(ZeissZVIReader.java:623)
>>        at loci.formats.in.ZeissZVIReader.initFile(ZeissZVIReader.java:513)
>>        at loci.formats.FormatReader.setId(FormatReader.java:216)
>>        at loci.formats.ImageReader.setId(ImageReader.java:565)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:61)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:181)
>>        at
>> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:
>> 355)
>>        at
>> ome.formats.importer.ImportHandler.importImages(ImportHandler.java:
>> 172)
>>        at
>> ome.formats.importer.ImportHandler.access$0(ImportHandler.java:106)
>>        at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:87)
>>
>> Also, I may be crazy, but the documentation for OMERO.insight does not
>> match what I am seeing.  This error is on my MAC to OMERO.server on
>> debian.  I downloaded and ran both (linux) importer and insight on the
>> localhost debian host and got the same importer error and the same
>> insight application.  Help/About shows Beta3.0.1, which is the server
>> I am running, but insight has no categories, no "Browse Button"...
>> And importer won't import the zvi on either platform.
>>
>> Thanks.
>> Susan
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>
>
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From ctrueden at wisc.edu  Wed Sep 24 23:04:10 2008
From: ctrueden at wisc.edu (Curtis Rueden)
Date: Wed, 24 Sep 2008 17:04:10 -0500
Subject: [ome-users] NumberFormatException import .zvi file
In-Reply-To: <857a86450809241354x7bba3e7fn31a178a7eda444d0@mail.gmail.com>
References: <0K7P00003UNRAQ00@smtp5.wiscmail.wisc.edu>
	<857a86450809241320u7d33fc69ib53a3126eb443b56@mail.gmail.com>
	<7BB9D4B2-89EE-40E0-99D2-760C75DCD514@hpc.unm.edu>
	<857a86450809241354x7bba3e7fn31a178a7eda444d0@mail.gmail.com>
Message-ID: <857a86450809241504s34a427d8yd3691c4f91c793e6@mail.gmail.com>

Hi Susan,

Thanks for the file; the bug should be fixed in the latest trunk build of
Bio-Formats, and hence the next release of OMERO.

If you want to update your existing OMERO installation with the fix, you
will need to inject the new ZeissZVIReader into the OMERO.importer
application. Before proceeding, please note that though this procedure
should work in theory, it is untested and unsupported, and will void your
warranty. :-)

First, download loci_tools.jar to your Desktop. Assuming you have installed
OMERO.importer in your Applications folder with the default folder name
(OMERO.clients-Beta3.0.1.mac), you can then run the following commands from
the Terminal:

export SRC_JAR=~/Desktop/loci_tools.jar
export
DEST_JAR=/Applications/OMERO.clients-Beta3.0.1.mac/OMERO.importer.app/Contents/Resources/Java/jar_1.jar
jar xvf $SRC_JAR 'loci/formats/in/ZeissZVIReader.class'
jar xvf $SRC_JAR 'loci/formats/in/ZeissZVIReader$1.class'
jar uvf $DEST_JAR 'loci/formats/in/ZeissZVIReader.class'
jar uvf $DEST_JAR 'loci/formats/in/ZeissZVIReader$1.class'
rm -rf loci

This sequence of commands will update the jar_1.jar resource with the new
ZeissZVIReader code.  You may want to back up your existing jar_1.jar file
first, just in case.

-Curtis
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From jason at lifesci.dundee.ac.uk  Wed Sep 24 23:55:20 2008
From: jason at lifesci.dundee.ac.uk (Jason Swedlow)
Date: Wed, 24 Sep 2008 23:55:20 +0100
Subject: [ome-users] NumberFormatException import .zvi file
In-Reply-To: <857a86450809241354x7bba3e7fn31a178a7eda444d0@mail.gmail.com>
References: <0K7P00003UNRAQ00@smtp5.wiscmail.wisc.edu>
	<857a86450809241320u7d33fc69ib53a3126eb443b56@mail.gmail.com>
	<7BB9D4B2-89EE-40E0-99D2-760C75DCD514@hpc.unm.edu>
	<857a86450809241354x7bba3e7fn31a178a7eda444d0@mail.gmail.com>
Message-ID: <53C752B7-6280-4275-B7F1-0F7E9E2328E2@lifesci.dundee.ac.uk>

Hi Susan-

On 24 Sep 2008, at 21:54, Curtis Rueden wrote:

> Hi Susan,
>
> I downloaded the latest trunk build of the loci_tools.jar and  
> placed it in the plugins folder and re-ran ImageJ.  The LOCI  
> Bioformats Importer gives the same error on that zvi file that  
> OMERO.insight does.
>
> Strange; I checked the source code and it should not be generating  
> this error. Would you be willing to send us the problematic file  
> for us to use for debugging? Once we have the problem solved in Bio- 
> Formats, the next version of OMERO.importer will also incorporate  
> the fix -- or I can provide you with instructions on how to update  
> your existing version of OMERO.importer if you like.
>

Can you let us know which version of Zeiss software produced the  
file.  We test .zvi files before every release, but our testing is  
only as good and as up-to-date as our test files, so knowing which  
versions are giving us problems is very helpful.

Thanks!

Cheers,

Jason


> -Curtis
>
> On Wed, Sep 24, 2008 at 3:48 PM, Susan Wilson  
> <smwilson at hpc.unm.edu> wrote:
> Hi again,
>
> I downloaded the latest trunk build of the loci_tools.jar and  
> placed it in the plugins folder and re-ran ImageJ.  The LOCI  
> Bioformats Importer gives the same error on that zvi file that  
> OMERO.insight does.
>
> Susan
>
> On Sep 24, 2008, at 2:20 PM, Curtis Rueden wrote:
>
>> Hi Susan,
>>
>> That exception looks like a bug in Bio-Formats to me. Are you able  
>> to import the ZVI file into ImageJ using the Bio-Formats Importer  
>> plugin (http://www.loci.wisc.edu/ome/formats-imagej.html) with the  
>> latest trunk build (http://www.loci.wisc.edu/ome/formats- 
>> download.html)?
>>
>> -Curtis
>>
>> On Wed, Sep 24, 2008 at 3:09 PM, Susan Wilson  
>> <smwilson at hpc.unm.edu> wrote:
>> Hi,
>>
>> Runniing Beta3.0.1 all around.  This is the error I get when I  
>> attempt
>> to import a .zvi file:
>>
>> java.lang.NumberFormatException: For input string: "9/17/2008 7:05:39
>> PM"
>>        at
>> java
>> .lang.NumberFormatException.forInputString 
>> (NumberFormatException.java:
>> 48)
>>        at java.lang.Long.parseLong(Long.java:412)
>>        at java.lang.Long.parseLong(Long.java:461)
>>        at loci.formats.in.ZeissZVIReader.initMetadata 
>> (ZeissZVIReader.java:623)
>>        at loci.formats.in.ZeissZVIReader.initFile 
>> (ZeissZVIReader.java:513)
>>        at loci.formats.FormatReader.setId(FormatReader.java:216)
>>        at loci.formats.ImageReader.setId(ImageReader.java:565)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at loci.formats.ChannelFiller.setId(ChannelFiller.java:186)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at loci.formats.ChannelSeparator.setId 
>> (ChannelSeparator.java:61)
>>        at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:71)
>>        at ome.formats.importer.ImportLibrary.open 
>> (ImportLibrary.java:181)
>>        at ome.formats.importer.ImportLibrary.importImage 
>> (ImportLibrary.java:
>> 355)
>>        at ome.formats.importer.ImportHandler.importImages 
>> (ImportHandler.java:
>> 172)
>>        at ome.formats.importer.ImportHandler.access$0 
>> (ImportHandler.java:106)
>>        at ome.formats.importer.ImportHandler$1.run 
>> (ImportHandler.java:87)
>>
>> Also, I may be crazy, but the documentation for OMERO.insight does  
>> not
>> match what I am seeing.  This error is on my MAC to OMERO.server on
>> debian.  I downloaded and ran both (linux) importer and insight on  
>> the
>> localhost debian host and got the same importer error and the same
>> insight application.  Help/About shows Beta3.0.1, which is the server
>> I am running, but insight has no categories, no "Browse Button"...
>> And importer won't import the zvi on either platform.
>>
>> Thanks.
>> Susan
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users



**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.



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From cunha at caltech.edu  Thu Sep 25 02:02:24 2008
From: cunha at caltech.edu (Alexandre Cunha)
Date: Wed, 24 Sep 2008 18:02:24 -0700
Subject: [ome-users] [Newbie] Connecting problem
Message-ID: <48DAE320.3070102@caltech.edu>

Hello,

I am a newbie to OMERO and having problems to connect to the server over 
our network. I have installed the OMERO server on a linux box running 
ubuntu,

# uname -a
Linux XXX 2.6.22-15-generic #1 SMP Fri Jul 11 18:56:36 UTC 2008 x86_64 
GNU/Linux

and I was able to access XXX:8080/WebAdmin and perform tasks with no 
problem either via the server computer itself or using a OS X laptop 
hooked to a wireless network. The problem I am having is to connect via 
OMERO.insight. I have done all steps suggested in the Troubleshooting 
page, including setting TCP window scaling to none,

# cat /proc/sys/net/ipv4/tcp_window_scaling
0

but to no avail. I have restarted the server after any modification was 
made. All the necessary ports seem to be open,

sudo iptables -A INPUT -p tcp --dport 1098 -j ACCEPT
sudo iptables -A INPUT -p tcp --dport 1099 -j ACCEPT
sudo iptables -A INPUT -p tcp --dport 4444 -j ACCEPT
sudo iptables -A INPUT -p tcp --dport 3873 -j ACCEPT

on the server side but when connecting via wireless using OMERO.insigth 
on the laptop to XXX:8080 with a permitted user and password the thing 
just hangs almost forever and it doesn't offer any error message, at 
least I couldn't spot any. I can connect though running insight in the 
server computer, flawlessly, which apparently says the database and 
server are doing their job.

What am I missing ? Any suggestion is appreciated since I am running out 
of options. If necessary I can send log files (?).

Many thanks,
- Alex.



From rubenalves at fm.ul.pt  Thu Sep 25 09:11:59 2008
From: rubenalves at fm.ul.pt (=?ISO-8859-1?Q?=BB_Ruben_Alves?=)
Date: Thu, 25 Sep 2008 09:11:59 +0100
Subject: [ome-users] [Newbie] Connecting problem
In-Reply-To: <48DAE320.3070102@caltech.edu>
References: <48DAE320.3070102@caltech.edu>
Message-ID: <48DB47CF.4010502@fm.ul.pt>

Hi Alexandre, did you see your /etc/hosts file?
In the Troubleshooting page 
(http://trac.openmicroscopy.org.uk/omero/wiki/OmeroTroubleshooting), 
there is a reference of this kind of problem.
For me, I had to change this values in order to put OMERO available for 
all the network.

Cheers

//Ruben


Alexandre Cunha wrote:
> Hello,
>
> I am a newbie to OMERO and having problems to connect to the server over 
> our network. I have installed the OMERO server on a linux box running 
> ubuntu,
>
> # uname -a
> Linux XXX 2.6.22-15-generic #1 SMP Fri Jul 11 18:56:36 UTC 2008 x86_64 
> GNU/Linux
>
> and I was able to access XXX:8080/WebAdmin and perform tasks with no 
> problem either via the server computer itself or using a OS X laptop 
> hooked to a wireless network. The problem I am having is to connect via 
> OMERO.insight. I have done all steps suggested in the Troubleshooting 
> page, including setting TCP window scaling to none,
>
> # cat /proc/sys/net/ipv4/tcp_window_scaling
> 0
>
> but to no avail. I have restarted the server after any modification was 
> made. All the necessary ports seem to be open,
>
> sudo iptables -A INPUT -p tcp --dport 1098 -j ACCEPT
> sudo iptables -A INPUT -p tcp --dport 1099 -j ACCEPT
> sudo iptables -A INPUT -p tcp --dport 4444 -j ACCEPT
> sudo iptables -A INPUT -p tcp --dport 3873 -j ACCEPT
>
> on the server side but when connecting via wireless using OMERO.insigth 
> on the laptop to XXX:8080 with a permitted user and password the thing 
> just hangs almost forever and it doesn't offer any error message, at 
> least I couldn't spot any. I can connect though running insight in the 
> server computer, flawlessly, which apparently says the database and 
> server are doing their job.
>
> What am I missing ? Any suggestion is appreciated since I am running out 
> of options. If necessary I can send log files (?).
>
> Many thanks,
> - Alex.
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>   


-- 
Ruben Alves
USI @ Instituto de Medicina Molecular
Edif?cio Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999411 ext 47026


From cunha at caltech.edu  Thu Sep 25 18:51:56 2008
From: cunha at caltech.edu (Alexandre Cunha)
Date: Thu, 25 Sep 2008 10:51:56 -0700
Subject: [ome-users] [Newbie] Connecting problem
In-Reply-To: <48DB47CF.4010502@fm.ul.pt>
References: <48DAE320.3070102@caltech.edu> <48DB47CF.4010502@fm.ul.pt>
Message-ID: <48DBCFBC.70105@caltech.edu>

Hi Ruben,

Thanks for the link. Actually, I had checked and included the missing

	192.168.0.100   omero-test.openmicroscopy.org.uk omero-test

in my /etc/hosts file but that didn't help. I believe I have followed 
and done all the steps shown on the installation page but I still can't 
connect using insight. Maybe I need to consult with our network expert, 
but I would like to check first if any user had a similar problem and 
solved by editing some OMERO configuration file and such.

Thanks for the tip.
- Alex.


? Ruben Alves wrote:
> Hi Alexandre, did you see your /etc/hosts file?
> In the Troubleshooting page 
> (http://trac.openmicroscopy.org.uk/omero/wiki/OmeroTroubleshooting), 
> there is a reference of this kind of problem.
> For me, I had to change this values in order to put OMERO available for 
> all the network.
> 
> Cheers
> 
> //Ruben
> 
> 
> Alexandre Cunha wrote:
>> Hello,
>>
>> I am a newbie to OMERO and having problems to connect to the server 
>> over our network. I have installed the OMERO server on a linux box 
>> running ubuntu,
>>
>> # uname -a
>> Linux XXX 2.6.22-15-generic #1 SMP Fri Jul 11 18:56:36 UTC 2008 x86_64 
>> GNU/Linux
>>
>> and I was able to access XXX:8080/WebAdmin and perform tasks with no 
>> problem either via the server computer itself or using a OS X laptop 
>> hooked to a wireless network. The problem I am having is to connect 
>> via OMERO.insight. I have done all steps suggested in the 
>> Troubleshooting page, including setting TCP window scaling to none,
>>
>> # cat /proc/sys/net/ipv4/tcp_window_scaling
>> 0
>>
>> but to no avail. I have restarted the server after any modification 
>> was made. All the necessary ports seem to be open,
>>
>> sudo iptables -A INPUT -p tcp --dport 1098 -j ACCEPT
>> sudo iptables -A INPUT -p tcp --dport 1099 -j ACCEPT
>> sudo iptables -A INPUT -p tcp --dport 4444 -j ACCEPT
>> sudo iptables -A INPUT -p tcp --dport 3873 -j ACCEPT
>>
>> on the server side but when connecting via wireless using 
>> OMERO.insigth on the laptop to XXX:8080 with a permitted user and 
>> password the thing just hangs almost forever and it doesn't offer any 
>> error message, at least I couldn't spot any. I can connect though 
>> running insight in the server computer, flawlessly, which apparently 
>> says the database and server are doing their job.
>>
>> What am I missing ? Any suggestion is appreciated since I am running 
>> out of options. If necessary I can send log files (?).
>>
>> Many thanks,
>> - Alex.
>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>   
> 
> 

From callan at blackcat.ca  Thu Sep 25 19:20:38 2008
From: callan at blackcat.ca (Chris Allan)
Date: Thu, 25 Sep 2008 19:20:38 +0100
Subject: [ome-users] [Newbie] Connecting problem
In-Reply-To: <48DBCFBC.70105@caltech.edu>
References: <48DAE320.3070102@caltech.edu> <48DB47CF.4010502@fm.ul.pt>
	<48DBCFBC.70105@caltech.edu>
Message-ID: <B6CAD1AA-1D32-4CF9-8591-28EC0F18E9F6@blackcat.ca>


On 25 Sep 2008, at 18:51, Alexandre Cunha wrote:

> Hi Ruben,

Hi Alexandre.

> Thanks for the link. Actually, I had checked and included the missing
>
> 	192.168.0.100   omero-test.openmicroscopy.org.uk omero-test

You need to put your IP address and hostname there, not 192.168.0.100  
and "omero-test.openmicroscopy.org.uk", "omero-test".

> in my /etc/hosts file but that didn't help. I believe I have followed
> and done all the steps shown on the installation page but I still  
> can't
> connect using insight. Maybe I need to consult with our network  
> expert,
> but I would like to check first if any user had a similar problem and
> solved by editing some OMERO configuration file and such.
>
> Thanks for the tip.
> - Alex.

Let us know if that helps.

Ciao.

-Chris

From rubenalves at fm.ul.pt  Fri Sep 26 08:55:22 2008
From: rubenalves at fm.ul.pt (=?ISO-8859-1?Q?=BB_Ruben_Alves?=)
Date: Fri, 26 Sep 2008 08:55:22 +0100
Subject: [ome-users] [Newbie] Connecting problem
In-Reply-To: <48DBCFBC.70105@caltech.edu>
References: <48DAE320.3070102@caltech.edu> <48DB47CF.4010502@fm.ul.pt>
	<48DBCFBC.70105@caltech.edu>
Message-ID: <48DC956A.50200@fm.ul.pt>

Ok, the "192.168.0.100 omero-test.openmicroscopy.org.uk omero-test " was 
just to made a example. You have to put your own values.
Find the IP of your server doing: " ifconfig" should be the inet address 
for eth0 (something like 10.xxx.xxx.xxx or 168.192.xxx.xxx).
For the rest, type "hostname" on ubuntu console in order to know the 
string you have to put on your host file.
For example, imagine your Ip is 192.168.10.231, and the hostname is 
"ubuntuserver" and you subdomain is lan.caltech.edu. You should have a 
/etc/hosts file like this:

127.0.0.1       localhost
192.168.10.231  ubuntuserver ubuntuserver.lan.caltech.edu


The OMERO "HOWTO INSTALL" is very usefull and complete, if you have followed exactly, now it should work. If not, try to start OMERO in a sudo user. And if it still not work, paste you log file.


Cheers





Alexandre Cunha wrote:
> Hi Ruben,
>
> Thanks for the link. Actually, I had checked and included the missing
>
>     192.168.0.100   omero-test.openmicroscopy.org.uk omero-test
>
> in my /etc/hosts file but that didn't help. I believe I have followed 
> and done all the steps shown on the installation page but I still 
> can't connect using insight. Maybe I need to consult with our network 
> expert, but I would like to check first if any user had a similar 
> problem and solved by editing some OMERO configuration file and such.
>
> Thanks for the tip.
> - Alex.
>
>
> ? Ruben Alves wrote:
>> Hi Alexandre, did you see your /etc/hosts file?
>> In the Troubleshooting page 
>> (http://trac.openmicroscopy.org.uk/omero/wiki/OmeroTroubleshooting), 
>> there is a reference of this kind of problem.
>> For me, I had to change this values in order to put OMERO available 
>> for all the network.
>>
>> Cheers
>>
>> //Ruben
>>
>>
>> Alexandre Cunha wrote:
>>> Hello,
>>>
>>> I am a newbie to OMERO and having problems to connect to the server 
>>> over our network. I have installed the OMERO server on a linux box 
>>> running ubuntu,
>>>
>>> # uname -a
>>> Linux XXX 2.6.22-15-generic #1 SMP Fri Jul 11 18:56:36 UTC 2008 
>>> x86_64 GNU/Linux
>>>
>>> and I was able to access XXX:8080/WebAdmin and perform tasks with no 
>>> problem either via the server computer itself or using a OS X laptop 
>>> hooked to a wireless network. The problem I am having is to connect 
>>> via OMERO.insight. I have done all steps suggested in the 
>>> Troubleshooting page, including setting TCP window scaling to none,
>>>
>>> # cat /proc/sys/net/ipv4/tcp_window_scaling
>>> 0
>>>
>>> but to no avail. I have restarted the server after any modification 
>>> was made. All the necessary ports seem to be open,
>>>
>>> sudo iptables -A INPUT -p tcp --dport 1098 -j ACCEPT
>>> sudo iptables -A INPUT -p tcp --dport 1099 -j ACCEPT
>>> sudo iptables -A INPUT -p tcp --dport 4444 -j ACCEPT
>>> sudo iptables -A INPUT -p tcp --dport 3873 -j ACCEPT
>>>
>>> on the server side but when connecting via wireless using 
>>> OMERO.insigth on the laptop to XXX:8080 with a permitted user and 
>>> password the thing just hangs almost forever and it doesn't offer 
>>> any error message, at least I couldn't spot any. I can connect 
>>> though running insight in the server computer, flawlessly, which 
>>> apparently says the database and server are doing their job.
>>>
>>> What am I missing ? Any suggestion is appreciated since I am running 
>>> out of options. If necessary I can send log files (?).
>>>
>>> Many thanks,
>>> - Alex.
>>>
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>   
>>
>>


-- 
Ruben Alves
USI @ Instituto de Medicina Molecular
Edif?cio Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999411 ext 47026


From cunha at caltech.edu  Tue Sep 30 19:58:18 2008
From: cunha at caltech.edu (Alexandre Cunha)
Date: Tue, 30 Sep 2008 11:58:18 -0700
Subject: [ome-users] Insight: need to force a refresh tree to see
	modifications
Message-ID: <48E276CA.7000400@caltech.edu>

Hello,

I have just started playing with OMERO.insight before deploying it to
our community here. I have noticed that when I create a new data set for
a new project I need to explicitly "refresh current tree" to see the
proper modifications on the left and right panels. An 'Empty' icon is
all is shown under the project name/icon as I keep adding new data sets
for the same project. Also, I had to refresh the tree in order to be
able to delete a dataset. Is that what others are experiencing ? Any
configuration parameter that I need to tune ?

After deleting a dataset the project tree immediately collapses. It
would be nice if the tree is not collapsed leaving to the user to decide
if and when to collapse it once it is expanded.

Omero server and clients installed on a linux/ubuntu machine.

Cheers,
- Alex.


From j.burel at dundee.ac.uk  Tue Sep 30 20:39:31 2008
From: j.burel at dundee.ac.uk (jean-marie)
Date: Tue, 30 Sep 2008 20:39:31 +0100
Subject: [ome-users] Insight: need to force a refresh tree to see
	modifications
In-Reply-To: <48E276CA.7000400@caltech.edu>
References: <48E276CA.7000400@caltech.edu>
Message-ID: <E9229EC4-1BE0-4603-855E-A0D219A2C5B5@dundee.ac.uk>

Hello

I thought the Refresh problem was fixed.
Which version are you evaluating?
No parameters to tune, a bug in the code!

>
> After deleting a dataset the project tree immediately collapses. It
> would be nice if the tree is not collapsed leaving to the user to  
> decide
> if and when to collapse it once it is expanded.
The delete functionality has been partially implemented, so the  
behavior is not ideal
A full implementation will come in the Beta4 version we are planning  
on releasing by the end of the year

Thanks for your comments.
I will record the problems on the insight trac (http:// 
trac.openmicroscopy.org.uk/shoola)


Ciao

Jmarie


From cunha at caltech.edu  Tue Sep 30 21:00:39 2008
From: cunha at caltech.edu (Alexandre Cunha)
Date: Tue, 30 Sep 2008 13:00:39 -0700
Subject: [ome-users] Insight: need to force a refresh tree to see
	modifications
In-Reply-To: <E9229EC4-1BE0-4603-855E-A0D219A2C5B5@dundee.ac.uk>
References: <48E276CA.7000400@caltech.edu>
	<E9229EC4-1BE0-4603-855E-A0D219A2C5B5@dundee.ac.uk>
Message-ID: <48E28567.3030206@caltech.edu>

Hi,

About Omero.insight gives:

Version beta 3.0
Build: 17-06-2008

Is there a newer build with the bug fixes ?

Thanks,
- Alex.


jean-marie wrote:
> Hello
> 
> I thought the Refresh problem was fixed.
> Which version are you evaluating?
> No parameters to tune, a bug in the code!
> 
>>
>> After deleting a dataset the project tree immediately collapses. It
>> would be nice if the tree is not collapsed leaving to the user to decide
>> if and when to collapse it once it is expanded.
> The delete functionality has been partially implemented, so the behavior 
> is not ideal
> A full implementation will come in the Beta4 version we are planning on 
> releasing by the end of the year
> 
> Thanks for your comments.
> I will record the problems on the insight trac 
> (http://trac.openmicroscopy.org.uk/shoola)
> 
> 
> Ciao
> 
> Jmarie
> 

From cunha at caltech.edu  Tue Sep 30 21:04:07 2008
From: cunha at caltech.edu (Alexandre Cunha)
Date: Tue, 30 Sep 2008 13:04:07 -0700
Subject: [ome-users] Insight: removing empty orphaned datasets
In-Reply-To: <E9229EC4-1BE0-4603-855E-A0D219A2C5B5@dundee.ac.uk>
References: <48E276CA.7000400@caltech.edu>
	<E9229EC4-1BE0-4603-855E-A0D219A2C5B5@dundee.ac.uk>
Message-ID: <48E28637.90406@caltech.edu>

Hello,

Is there a (documented or not) way to remove/delete orphaned datasets ?

Thanks,
- Alex.

jean-marie wrote:
> Hello
> 
> I thought the Refresh problem was fixed.
> Which version are you evaluating?
> No parameters to tune, a bug in the code!
> 
>>
>> After deleting a dataset the project tree immediately collapses. It
>> would be nice if the tree is not collapsed leaving to the user to decide
>> if and when to collapse it once it is expanded.
> The delete functionality has been partially implemented, so the behavior 
> is not ideal
> A full implementation will come in the Beta4 version we are planning on 
> releasing by the end of the year
> 
> Thanks for your comments.
> I will record the problems on the insight trac 
> (http://trac.openmicroscopy.org.uk/shoola)
> 
> 
> Ciao
> 
> Jmarie
>