From kasthurisrinivasan at yahoo.com  Mon Mar  2 18:03:05 2009
From: kasthurisrinivasan at yahoo.com (Kasthuri Kannan)
Date: Mon, 2 Mar 2009 13:03:05 -0500
Subject: [ome-users] Kasthuri Kannan sent you a Friend Request on Yaari
Message-ID: <af6191392290ce1b1468d59f3b5aa823@localhost.localdomain>

Kasthuri Kannan wants you to join Yaari!

Is Kasthuri your friend?

<a href="http://yaari.com/?controller=user&action=mailregister&friend=1&sign=YaariJVI801JVT626TKN447JNU802">Yes, Kasthuri is my friend!</a> <a href="http://yaari.com/?controller=user&action=mailregister&friend=0&sign=YaariJVI801JVT626TKN447JNU802">No, Kasthuri isn't my friend.</a>

Please respond or Kasthuri may think you said no :(

Thanks,
The Yaari Team
____
If you prefer not to receive this email tell us <a href="http://yaari.com/?controller=absn&action=addoptout&email=ome-users at lists.openmicroscopy.org.uk">here</a>. If you have any concerns 
regarding the content of this message, please email abuse at yaari.com.  
Yaari LLC, 358 Angier Ave, Atlanta, GA 30312

YaariJVI801JVT626TKN447JNU802

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From kasthurisrinivasan at yahoo.com  Mon Mar  2 18:03:05 2009
From: kasthurisrinivasan at yahoo.com (Kasthuri Kannan)
Date: Mon, 2 Mar 2009 13:03:05 -0500
Subject: [ome-users] Kasthuri Kannan sent you a Friend Request on Yaari
Message-ID: <e70775573597898113cd82dafd4f4d31@localhost.localdomain>

Kasthuri Kannan wants you to join Yaari!

Is Kasthuri your friend?

<a href="http://yaari.com/?controller=user&action=mailregister&friend=1&sign=YaariQFR254JSS988FOE866TDT346">Yes, Kasthuri is my friend!</a> <a href="http://yaari.com/?controller=user&action=mailregister&friend=0&sign=YaariQFR254JSS988FOE866TDT346">No, Kasthuri isn't my friend.</a>

Please respond or Kasthuri may think you said no :(

Thanks,
The Yaari Team
____
If you prefer not to receive this email tell us <a href="http://yaari.com/?controller=absn&action=addoptout&email=ome-users at lists.openmicroscopy.org.uk">here</a>. If you have any concerns 
regarding the content of this message, please email abuse at yaari.com.  
Yaari LLC, 358 Angier Ave, Atlanta, GA 30312

YaariQFR254JSS988FOE866TDT346

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From melissa at glencoesoftware.com  Tue Mar  3 15:45:26 2009
From: melissa at glencoesoftware.com (Melissa Linkert)
Date: Tue, 03 Mar 2009 09:45:26 -0600
Subject: [ome-users] 4.0.0 release of Bio-Formats
Message-ID: <49AD5096.7090208@glencoesoftware.com>

Hi,

Today LOCI (http://loci.wisc.edu) and Glencoe Software 
(http://glencoesoftware.com) have released version 4.0.0 of Bio-Formats 
(http://loci.wisc.edu/ome/formats.html).  This release includes the 
following changes:

* Improved OME data model population for Olympus FV1000, Nikon ND2, 
Metamorph STK, Leica LEI, Leica LIF, InCell 1000 and MicroManager
* Added TestNG tests for format writers
* Added option to ImageJ plugin to specify custom colors when 
customizing channels
* Added ability to upgrade the ImageJ plugin from within ImageJ
* Fixed bugs in Nikon ND2, Leica LIF, BioRad PIC, TIFF, PSD, and OME-TIFF
* Fixed bugs in Data Browser and Exporter plugins
* Added support for Axon Raw Format (ARF), courtesy of Johannes Schindelin
* Added preliminary support for IPLab-Mac file format

You can download the latest release at:

http://loci.wisc.edu/ome/formats-download.html

Please note that we have changed the version numbering scheme in this 
release.  In the past, the release date was used as the version number; 
this release and all future releases will use three numbers separated by 
dots (e.g. 4.0.0).  This version numbering scheme corresponds to the 
scheme used by other OME products, including OMERO 
(http://trac.openmicroscopy.org.uk/omero/).

We anticipate releasing the next major version of Bio-Formats in 
mid-May.  The roadmap for this release is available at:

https://skyking.microscopy.wisc.edu/trac/java/milestone/bio-formats-4.1.0

If you have questions, comments or concerns regarding Bio-Formats, we 
would love to hear them.  Bug reports and general usage questions should 
be sent to the Bio-Formats developers at bioformats at loci.wisc.edu.  
Licensing and commercial usage questions should be sent to 
bioformats at glencoesoftware.com.

Regards,

Melissa Linkert
Glencoe Software, Inc.


From palmeida at igc.gulbenkian.pt  Fri Mar  6 16:11:45 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Fri, 6 Mar 2009 16:11:45 +0000
Subject: [ome-users] Restoring omero database with different PostgreSQL
	version
Message-ID: <200903061611.45754.palmeida@igc.gulbenkian.pt>

Hi,

I created some backups of a PostgreSQL 8.1 database and I tried restoring them 
in a 8.3 Postgre, but when I tried to login I got this error:

Cannot create session: Error during invocation. Most likely server version 
does not match client version  

Do I have to use the same version to restore, or is there something else I may 
be doing wrong?

Thanks,
Paulo


From callan at blackcat.ca  Sat Mar  7 11:17:29 2009
From: callan at blackcat.ca (Chris Allan)
Date: Sat, 7 Mar 2009 11:17:29 +0000
Subject: [ome-users] Restoring omero database with different PostgreSQL
	version
In-Reply-To: <200903061611.45754.palmeida@igc.gulbenkian.pt>
References: <200903061611.45754.palmeida@igc.gulbenkian.pt>
Message-ID: <58A38CD3-04D4-462E-AAF2-3B4B69006597@blackcat.ca>

Hi Paulo,

Shouldn't have to at all. Any errors/exceptions in the server side log?

-Chris

On 6 Mar 2009, at 16:11, Paulo Almeida wrote:

> Hi,
>
> I created some backups of a PostgreSQL 8.1 database and I tried  
> restoring them
> in a 8.3 Postgre, but when I tried to login I got this error:
>
> Cannot create session: Error during invocation. Most likely server  
> version
> does not match client version
>
> Do I have to use the same version to restore, or is there something  
> else I may
> be doing wrong?
>
> Thanks,
> Paulo
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users



From sriramkumar at uky.edu  Sat Mar  7 15:59:57 2009
From: sriramkumar at uky.edu (Nandakumar, Sriramkumar)
Date: Sat, 7 Mar 2009 10:59:57 -0500
Subject: [ome-users] Entity  - Relationship diagram for OME
Message-ID: <EDC22492BE5CAF409A4166B67B1F2E9A9F286898@EX7SM01.ad.uky.edu>

Hi all,
I am Sriram.
I am looking for Entity relationship diagram for OME.  
Do any one have that?


Thanks & Regards,
Sriram.

From palmeida at igc.gulbenkian.pt  Mon Mar  9 12:19:54 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Mon, 9 Mar 2009 12:19:54 +0000
Subject: [ome-users] Restoring omero database with different PostgreSQL
	version
In-Reply-To: <58A38CD3-04D4-462E-AAF2-3B4B69006597@blackcat.ca>
References: <200903061611.45754.palmeida@igc.gulbenkian.pt>
	<58A38CD3-04D4-462E-AAF2-3B4B69006597@blackcat.ca>
Message-ID: <200903091219.54705.palmeida@igc.gulbenkian.pt>

Hi Chris, 

I'm sending the server log in attachment. I looked at it, and there are some 
errors, but I couldn't figure out what they mean.

Thanks,
Paulo

On Saturday 07 March 2009 11:17:29 Chris Allan wrote:
> Hi Paulo,
>
> Shouldn't have to at all. Any errors/exceptions in the server side log?
>
> -Chris
>
> On 6 Mar 2009, at 16:11, Paulo Almeida wrote:
> > Hi,
> >
> > I created some backups of a PostgreSQL 8.1 database and I tried
> > restoring them
> > in a 8.3 Postgre, but when I tried to login I got this error:
> >
> > Cannot create session: Error during invocation. Most likely server
> > version
> > does not match client version
> >
> > Do I have to use the same version to restore, or is there something
> > else I may
> > be doing wrong?
> >
> > Thanks,
> > Paulo
> > _______________________________________________
> > 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 callan at blackcat.ca  Mon Mar  9 13:06:41 2009
From: callan at blackcat.ca (Chris Allan)
Date: Mon, 09 Mar 2009 13:06:41 +0000
Subject: [ome-users] Restoring omero database with different PostgreSQL
 version
In-Reply-To: <200903091219.54705.palmeida@igc.gulbenkian.pt>
References: <200903061611.45754.palmeida@igc.gulbenkian.pt>
	<58A38CD3-04D4-462E-AAF2-3B4B69006597@blackcat.ca>
	<200903091219.54705.palmeida@igc.gulbenkian.pt>
Message-ID: <1236604001.7516.2.camel@shadowblade.openmicroscopy.org.uk>

On Mon, 2009-03-09 at 12:19 +0000, Paulo Almeida wrote:
> Hi Chris, 

Hi Paulo.

> 
> I'm sending the server log in attachment. I looked at it, and there are some 
> errors, but I couldn't figure out what they mean.

The key error is:

Caused by: org.postgresql.util.PSQLException: ERROR: column "version" of
relation "session" does not exist

Something seems very odd with the database restore, can you visually
check that the session table has a "version" column?

psql omero3 -c '\d session'

> 
> Thanks,
> Paulo

-Chris



From lszabo at ms.sapientia.ro  Mon Mar  9 13:22:36 2009
From: lszabo at ms.sapientia.ro (Laszlo Szabo)
Date: Mon, 9 Mar 2009 15:22:36 +0200 (EET)
Subject: [ome-users] Entity  - Relationship diagram for OME
In-Reply-To: <EDC22492BE5CAF409A4166B67B1F2E9A9F286898@EX7SM01.ad.uky.edu>
References: <EDC22492BE5CAF409A4166B67B1F2E9A9F286898@EX7SM01.ad.uky.edu>
Message-ID: <1887.192.168.112.81.1236604956.squirrel@ms.sapientia.ro>

> Hi all,
> I am Sriram.
> I am looking for Entity relationship diagram for OME.
> Do any one have that?
>
>

Hello,

You may want to try PostgreSQL autodoc: http://www.rbt.ca/autodoc/ .
Creates HTML, Dot, Dia and DocBook XML files which describe the database.
It's not an ER diagram, but You can follow the database.

Laszlo Sz.



From m.woodbridge at imperial.ac.uk  Mon Mar  9 13:29:00 2009
From: m.woodbridge at imperial.ac.uk (Mark Woodbridge)
Date: Mon, 9 Mar 2009 13:29:00 +0000
Subject: [ome-users] Entity  - Relationship diagram for OME
In-Reply-To: <EDC22492BE5CAF409A4166B67B1F2E9A9F286898@EX7SM01.ad.uky.edu>
References: <EDC22492BE5CAF409A4166B67B1F2E9A9F286898@EX7SM01.ad.uky.edu>
Message-ID: <49B5199C.6080502@imperial.ac.uk>

Hi,

You might also find this documentation useful:

http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_OME

It describes the XML Schema representation of the OME model.

Mark.

Nandakumar, Sriramkumar wrote:
> Hi all,
> I am Sriram.
> I am looking for Entity relationship diagram for OME.  
> Do any one have that?
> 
> 
> Thanks & Regards,
> Sriram.
> _______________________________________________
> 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  Mon Mar  9 13:34:46 2009
From: callan at blackcat.ca (Chris Allan)
Date: Mon, 09 Mar 2009 13:34:46 +0000
Subject: [ome-users] Entity  - Relationship diagram for OME
In-Reply-To: <49B5199C.6080502@imperial.ac.uk>
References: <EDC22492BE5CAF409A4166B67B1F2E9A9F286898@EX7SM01.ad.uky.edu>
	<49B5199C.6080502@imperial.ac.uk>
Message-ID: <1236605686.7516.8.camel@shadowblade.openmicroscopy.org.uk>

Hi all,

Historically we've avoided diagraming every type in one diagram using ER
because of the sheer size of image that creates. Usually to the
detriment of actual model understanding.

Mark has conveniently already laid out the XML Schema representation for
which the database follows almost exclusively. Other diagrams with high
level explanations for some of the more complicated relationships, and
some rationale, are also available here:

http://www.ome-xml.org/wiki/DeveloperInfo

Ciao.

-Chris

On Mon, 2009-03-09 at 13:29 +0000, Mark Woodbridge wrote:
> Hi,
> 
> You might also find this documentation useful:
> 
> http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_OME
> 
> It describes the XML Schema representation of the OME model.
> 
> Mark.
> 
> Nandakumar, Sriramkumar wrote:
> > Hi all,
> > I am Sriram.
> > I am looking for Entity relationship diagram for OME.  
> > Do any one have that?
> > 
> > 
> > Thanks & Regards,
> > Sriram.
> > _______________________________________________
> > 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  Mon Mar  9 13:55:34 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Mon, 9 Mar 2009 13:55:34 +0000
Subject: [ome-users] Restoring omero database with different PostgreSQL
	version
In-Reply-To: <1236604001.7516.2.camel@shadowblade.openmicroscopy.org.uk>
References: <200903061611.45754.palmeida@igc.gulbenkian.pt>
	<200903091219.54705.palmeida@igc.gulbenkian.pt>
	<1236604001.7516.2.camel@shadowblade.openmicroscopy.org.uk>
Message-ID: <200903091355.35398.palmeida@igc.gulbenkian.pt>

Hi Chris,

I did that and confirmed the "version" column does not exist. When I do 
a "java omero setup-db deploy" with an empty database, that "version" column 
is created, but if I restore the database, it is not. This is the command I 
use to restore:

pg_restore -Fc -d omero 
< /home/palmeida/omero3.2009-03-06_07\:35\:11-WET.pg_dump

The original database does have the "version" column, so I don't know why it 
is being lost in the dump/restore process. I will check the dumps to see what 
the commands are in there, but in the mean time, if you see something obvious 
that I'm doing wrong, please illuminate me.

Thanks,
Paulo

On Monday 09 March 2009 13:06:41 you wrote:
> On Mon, 2009-03-09 at 12:19 +0000, Paulo Almeida wrote:
> > Hi Chris,
>
> Hi Paulo.
>
> > I'm sending the server log in attachment. I looked at it, and there are
> > some errors, but I couldn't figure out what they mean.
>
> The key error is:
>
> Caused by: org.postgresql.util.PSQLException: ERROR: column "version" of
> relation "session" does not exist
>
> Something seems very odd with the database restore, can you visually
> check that the session table has a "version" column?
>
> psql omero3 -c '\d session'
>
> > Thanks,
> > Paulo
>
> -Chris




From josh.moore at gmx.de  Mon Mar  9 14:22:18 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Mon, 9 Mar 2009 15:22:18 +0100
Subject: [ome-users] Restoring omero database with different
	PostgreSQL	version
In-Reply-To: <200903091355.35398.palmeida@igc.gulbenkian.pt>
References: <200903061611.45754.palmeida@igc.gulbenkian.pt>
	<200903091219.54705.palmeida@igc.gulbenkian.pt>
	<1236604001.7516.2.camel@shadowblade.openmicroscopy.org.uk>
	<200903091355.35398.palmeida@igc.gulbenkian.pt>
Message-ID: <18869.9754.56504.114881@echo.mac>


Hey Paulo,

Paulo Almeida writes:
 > I did that and confirmed the "version" column does not exist. When I do 
 > a "java omero setup-db deploy" with an empty database, that "version" column 
 > is created, but if I restore the database, it is not. This is the command I 
 > use to restore:

Sounding very odd. Could you possibly provide us the output from:

  select * from dbpatch;

for both the restored and the fresh databases.

 > pg_restore -Fc -d omero 
 > < /home/palmeida/omero3.2009-03-06_07\:35\:11-WET.pg_dump
 > 
 > The original database does have the "version" column, so I don't know why it 
 > is being lost in the dump/restore process. I will check the dumps to see what 
 > the commands are in there, but in the mean time, if you see something obvious 
 > that I'm doing wrong, please illuminate me.

Nothing obvious yet, but we'll get there!
~Josh.

 > Thanks,
 > Paulo
 > 
 > On Monday 09 March 2009 13:06:41 you wrote:
 > > On Mon, 2009-03-09 at 12:19 +0000, Paulo Almeida wrote:
 > > > Hi Chris,
 > >
 > > Hi Paulo.
 > >
 > > > I'm sending the server log in attachment. I looked at it, and there are
 > > > some errors, but I couldn't figure out what they mean.
 > >
 > > The key error is:
 > >
 > > Caused by: org.postgresql.util.PSQLException: ERROR: column "version" of
 > > relation "session" does not exist
 > >
 > > Something seems very odd with the database restore, can you visually
 > > check that the session table has a "version" column?
 > >
 > > psql omero3 -c '\d session'
 > >
 > > > Thanks,
 > > > Paulo
 > >
 > > -Chris


From palmeida at igc.gulbenkian.pt  Mon Mar  9 15:59:19 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Mon, 9 Mar 2009 15:59:19 +0000
Subject: [ome-users] Restoring omero database with different PostgreSQL
	version
In-Reply-To: <1236604001.7516.2.camel@shadowblade.openmicroscopy.org.uk>
References: <200903061611.45754.palmeida@igc.gulbenkian.pt>
	<200903091219.54705.palmeida@igc.gulbenkian.pt>
	<1236604001.7516.2.camel@shadowblade.openmicroscopy.org.uk>
Message-ID: <200903091559.20303.palmeida@igc.gulbenkian.pt>

Hi Chris,

The problem was the dump. I was dumping omero3, which existed but was not the 
right database. Everything seems to be ok now.

Thanks and sorry about the non-problem...
Paulo 

On Monday 09 March 2009 13:06:41 you wrote:
> On Mon, 2009-03-09 at 12:19 +0000, Paulo Almeida wrote:
> > Hi Chris,
>
> Hi Paulo.
>
> > I'm sending the server log in attachment. I looked at it, and there are
> > some errors, but I couldn't figure out what they mean.
>
> The key error is:
>
> Caused by: org.postgresql.util.PSQLException: ERROR: column "version" of
> relation "session" does not exist
>
> Something seems very odd with the database restore, can you visually
> check that the session table has a "version" column?
>
> psql omero3 -c '\d session'
>
> > Thanks,
> > Paulo
>
> -Chris




From sriramkumar at uky.edu  Mon Mar  9 18:28:39 2009
From: sriramkumar at uky.edu (Nandakumar, Sriramkumar)
Date: Mon, 9 Mar 2009 14:28:39 -0400
Subject: [ome-users] Entity  - Relationship diagram for OME
In-Reply-To: <1236605686.7516.8.camel@shadowblade.openmicroscopy.org.uk>
References: <EDC22492BE5CAF409A4166B67B1F2E9A9F286898@EX7SM01.ad.uky.edu>
	<49B5199C.6080502@imperial.ac.uk>,
	<1236605686.7516.8.camel@shadowblade.openmicroscopy.org.uk>
Message-ID: <EDC22492BE5CAF409A4166B67B1F2E9A9F28689A@EX7SM01.ad.uky.edu>

Hi,
Thanks for providing the information.

Thanks & Regards,
Sriram.
________________________________________
From: Chris Allan [callan at blackcat.ca]
Sent: Monday, March 09, 2009 9:34 AM
To: Mark Woodbridge
Cc: Nandakumar, Sriramkumar; ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] Entity  - Relationship diagram for OME

Hi all,

Historically we've avoided diagraming every type in one diagram using ER
because of the sheer size of image that creates. Usually to the
detriment of actual model understanding.

Mark has conveniently already laid out the XML Schema representation for
which the database follows almost exclusively. Other diagrams with high
level explanations for some of the more complicated relationships, and
some rationale, are also available here:

http://www.ome-xml.org/wiki/DeveloperInfo

Ciao.

-Chris

On Mon, 2009-03-09 at 13:29 +0000, Mark Woodbridge wrote:
> Hi,
>
> You might also find this documentation useful:
>
> http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_OME
>
> It describes the XML Schema representation of the OME model.
>
> Mark.
>
> Nandakumar, Sriramkumar wrote:
> > Hi all,
> > I am Sriram.
> > I am looking for Entity relationship diagram for OME.
> > Do any one have that?
> >
> >
> > Thanks & Regards,
> > Sriram.
> > _______________________________________________
> > 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 mvalle at cscs.ch  Tue Mar 10 15:11:14 2009
From: mvalle at cscs.ch (Mario Valle)
Date: Tue, 10 Mar 2009 16:11:14 +0100
Subject: [ome-users] Client issues
Message-ID: <49B68312.406@cscs.ch>

(Really I don't know if the list is the correct one, please advise)

So the Beta4 adventure started.

Built the server without big problems (almost...)

Run .insight with a retrieval error, but anyway the db is empty.

So I found a .importer zip file on Hudson and tried it. Besides saying "version 3.1.1",
it crashes importing a tif file with, seems, an out-of-memory error. Instead the messages 
on the console are much more pacific (see below).

Maybe I should calm down and wait for a RC1 also for the clients, isn't it?

Ciao!
	mario



pazzallo ~/Desktop/OMERO.importer-build1841 > ./importer-gui
Starting OMERO.importer...
Suitable java version found [java = 1.5.0_16]
Configuring environment...
Java exec found in PATH. Verifying...
Loading OMERO.importer:
java -Xmx256m -cp 
"./OmeroImporter.jar:./libs/FontBox.jar:./libs/PDFBox.jar:./libs/TableLayout.jar:./libs/activation.jar:./libs/ant.jar:./libs/asm-attrs.jar:./libs/asm.jar:./libs/backport-util-concurrent.jar:./libs/bio-formats.jar:./libs/blitz.jar:./libs/btm.jar:./libs/bufr.jar:./libs/cglib.jar:./libs/checkstyle.jar:./libs/common.jar:./libs/commons-beanutils.jar:./libs/commons-codec.jar:./libs/commons-collections.jar:./libs/commons-httpclient.jar:./libs/commons-io.jar:./libs/commons-lang.jar:./libs/commons-logging.jar:./libs/commons-pool.jar:./libs/dsl.jar:./libs/ehcache.jar:./libs/emma.jar:./libs/emma_ant.jar:./libs/freemarker.jar:./libs/geronimo-spec-jta.jar:./libs/grib.jar:./libs/hibernate-annotations.jar:./libs/hibernate-commons-annotations.jar:./libs/hibernate-search.jar:./libs/hibernate-tools.jar:./libs/hibernate-validator.jar:./libs/hsqldb.jar:./libs/ice-db.jar:./libs/ice.jar:./libs/ij.jar:./libs/importer-common.jar:./libs/importer.jar:./libs/ini4j.jar:./libs/jamon.jar:./libs/java-getop
t.jar:./libs/jsr107cache.jar:./libs/jtidy.jar:./libs/loci-common.jar:./libs/log4j.jar:./libs/lucene-core.jar:./libs/lucene-highlighter.jar:./libs/lucene-spellchecker.jar:./libs/mail.jar:./libs/model-psql.jar:./libs/netcdf.jar:./libs/ome-java.jar:./libs/ome-xml.jar:./libs/omero-clients-util.jar:./libs/omero_client.jar:./libs/persistence-api.jar:./libs/poi-loci.jar:./libs/postgresql.jar:./libs/quaqua-filechooser-only.jar:./libs/quartz.jar:./libs/rendering.jar:./libs/romio.jar:./libs/server.jar:./libs/slf4j-api.jar:./libs/slf4j-log4j12.jar:./libs/spring-ldap.jar:./libs/spring.jar:./libs/swingx.jar:./libs/velocity-tools-generic.jar:./libs/velocity.jar:./libs/xerces.jar:./libs/xml-apis.jar" 
-Djava.library.path="/Users/mvalle/Desktop/OMERO.importer-build1841" 
ome.formats.importer.Main
/Users/mvalle/omero/log
2009-03-10 15:36:22,186 0          [      main] INFO 
ome.system.UpgradeCheck  - no update needed

Warning: class ch.randelshofer.quaqua.filechooser.Files couldn't load library 
libquaqua.jnilib.
User Name: mvalle -- Password: **********
true
Creating root!
Tiff
omero.model.Image:0 == omero.model.ImageI at 15e330,omero.model.Image:0
omero.model.OriginalFile:0 == omero.model.OriginalFileI at f69ed3,omero.model.OriginalFile:0
omero.model.Pixels:0:0 == omero.model.PixelsI at 356db6,Pixels:0
omero.model.Channel:0:0 == omero.model.ChannelI at b5f36e,omero.model.Channel:0:0
omero.model.LogicalChannel:0:0 == 
omero.model.LogicalChannelI at 80ce9c,omero.model.LogicalChannel:0:0

Starting references....
Pixels:0 == omero.model.OriginalFile:0

containerCache contains 5 entries.
referenceCache contains 1 entries.
Saving pixels id: 1

-- 
Ing. Mario Valle
Data Analysis Group                              | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82


From j.burel at dundee.ac.uk  Tue Mar 10 15:19:51 2009
From: j.burel at dundee.ac.uk (jburel)
Date: Tue, 10 Mar 2009 15:19:51 +0000
Subject: [ome-users] Client issues
In-Reply-To: <49B68312.406@cscs.ch>
References: <49B68312.406@cscs.ch>
Message-ID: <D29BE5FD-3180-4E7A-809E-2328F174A8F8@dundee.ac.uk>

Hi Mario

I am currently looking at the bug you sent

Regards
Jmarie
On 10 Mar 2009, at 15:11, Mario Valle wrote:

> (Really I don't know if the list is the correct one, please advise)
>
> So the Beta4 adventure started.
>
> Built the server without big problems (almost...)
>
> Run .insight with a retrieval error, but anyway the db is empty.
>
> So I found a .importer zip file on Hudson and tried it. Besides  
> saying "version 3.1.1",
> it crashes importing a tif file with, seems, an out-of-memory error.  
> Instead the messages
> on the console are much more pacific (see below).
>
> Maybe I should calm down and wait for a RC1 also for the clients,  
> isn't it?
>
> Ciao!
> 	mario
>
>
>
> pazzallo ~/Desktop/OMERO.importer-build1841 > ./importer-gui
> Starting OMERO.importer...
> Suitable java version found [java = 1.5.0_16]
> Configuring environment...
> Java exec found in PATH. Verifying...
> Loading OMERO.importer:
> java -Xmx256m -cp
> "./OmeroImporter.jar:./libs/FontBox.jar:./libs/PDFBox.jar:./libs/ 
> TableLayout.jar:./libs/activation.jar:./libs/ant.jar:./libs/asm- 
> attrs.jar:./libs/asm.jar:./libs/backport-util-concurrent.jar:./libs/ 
> bio-formats.jar:./libs/blitz.jar:./libs/btm.jar:./libs/bufr.jar:./ 
> libs/cglib.jar:./libs/checkstyle.jar:./libs/common.jar:./libs/ 
> commons-beanutils.jar:./libs/commons-codec.jar:./libs/commons- 
> collections.jar:./libs/commons-httpclient.jar:./libs/commons- 
> io.jar:./libs/commons-lang.jar:./libs/commons-logging.jar:./libs/ 
> commons-pool.jar:./libs/dsl.jar:./libs/ehcache.jar:./libs/emma.jar:./ 
> libs/emma_ant.jar:./libs/freemarker.jar:./libs/geronimo-spec- 
> jta.jar:./libs/grib.jar:./libs/hibernate-annotations.jar:./libs/ 
> hibernate-commons-annotations.jar:./libs/hibernate-search.jar:./libs/ 
> hibernate-tools.jar:./libs/hibernate-validator.jar:./libs/ 
> hsqldb.jar:./libs/ice-db.jar:./libs/ice.jar:./libs/ij.jar:./libs/ 
> importer-common.jar:./libs/importer.jar:./libs/ini4j.jar:./libs/ 
> jamon.jar:./libs/java-getop
> t.jar:./libs/jsr107cache.jar:./libs/jtidy.jar:./libs/loci- 
> common.jar:./libs/log4j.jar:./libs/lucene-core.jar:./libs/lucene- 
> highlighter.jar:./libs/lucene-spellchecker.jar:./libs/mail.jar:./ 
> libs/model-psql.jar:./libs/netcdf.jar:./libs/ome-java.jar:./libs/ome- 
> xml.jar:./libs/omero-clients-util.jar:./libs/omero_client.jar:./libs/ 
> persistence-api.jar:./libs/poi-loci.jar:./libs/postgresql.jar:./libs/ 
> quaqua-filechooser-only.jar:./libs/quartz.jar:./libs/rendering.jar:./ 
> libs/romio.jar:./libs/server.jar:./libs/slf4j-api.jar:./libs/slf4j- 
> log4j12.jar:./libs/spring-ldap.jar:./libs/spring.jar:./libs/ 
> swingx.jar:./libs/velocity-tools-generic.jar:./libs/velocity.jar:./ 
> libs/xerces.jar:./libs/xml-apis.jar"
> -Djava.library.path="/Users/mvalle/Desktop/OMERO.importer-build1841"
> ome.formats.importer.Main
> /Users/mvalle/omero/log
> 2009-03-10 15:36:22,186 0          [      main] INFO
> ome.system.UpgradeCheck  - no update needed
>
> Warning: class ch.randelshofer.quaqua.filechooser.Files couldn't  
> load library
> libquaqua.jnilib.
> User Name: mvalle -- Password: **********
> true
> Creating root!
> Tiff
> omero.model.Image:0 == omero.model.ImageI at 15e330,omero.model.Image:0
> omero.model.OriginalFile:0 ==  
> omero.model.OriginalFileI at f69ed3,omero.model.OriginalFile:0
> omero.model.Pixels:0:0 == omero.model.PixelsI at 356db6,Pixels:0
> omero.model.Channel:0:0 ==  
> omero.model.ChannelI at b5f36e,omero.model.Channel:0:0
> omero.model.LogicalChannel:0:0 ==
> omero.model.LogicalChannelI at 80ce9c,omero.model.LogicalChannel:0:0
>
> Starting references....
> Pixels:0 == omero.model.OriginalFile:0
>
> containerCache contains 5 entries.
> referenceCache contains 1 entries.
> Saving pixels id: 1
>
> -- 
> Ing. Mario Valle
> Data Analysis Group                              | http://www.cscs.ch/~mvalle
> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)  
> 610.82.60
> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)  
> 610.82.82
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users



From brian.loranger at lifesci.dundee.ac.uk  Tue Mar 10 15:29:04 2009
From: brian.loranger at lifesci.dundee.ac.uk (Brian Loranger)
Date: Tue, 10 Mar 2009 15:29:04 +0000
Subject: [ome-users] Client issues
In-Reply-To: <49B68312.406@cscs.ch>
References: <49B68312.406@cscs.ch>
Message-ID: <30DC19DE-AE67-43CE-98C8-C110352883FC@lifesci.dundee.ac.uk>

Hi Mario,

I sent you an email about your importer error right after you sent the  
error in (not sure if you missed it).

Just guessing based on what the error you sent me, but were you trying  
to import something with a huge image plane (or perhaps you're running  
the importer directly from the command line without giving the  
application more then the default java memory allocation)?

All the clients are also in the RC1 release cycle so you should be  
able to use the importer and insight directly against the latest  
version of the server.

Cheers,

Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
(The University of Dundee is a registered Scottish charity, No:  
SC015096)



On 10 Mar 2009, at 15:11, Mario Valle wrote:

> (Really I don't know if the list is the correct one, please advise)
>
> So the Beta4 adventure started.
>
> Built the server without big problems (almost...)
>
> Run .insight with a retrieval error, but anyway the db is empty.
>
> So I found a .importer zip file on Hudson and tried it. Besides  
> saying "version 3.1.1",
> it crashes importing a tif file with, seems, an out-of-memory error.  
> Instead the messages
> on the console are much more pacific (see below).
>
> Maybe I should calm down and wait for a RC1 also for the clients,  
> isn't it?
>
> Ciao!
> 	mario
>
>
>
> pazzallo ~/Desktop/OMERO.importer-build1841 > ./importer-gui
> Starting OMERO.importer...
> Suitable java version found [java = 1.5.0_16]
> Configuring environment...
> Java exec found in PATH. Verifying...
> Loading OMERO.importer:
> java -Xmx256m -cp
> "./OmeroImporter.jar:./libs/FontBox.jar:./libs/PDFBox.jar:./libs/ 
> TableLayout.jar:./libs/activation.jar:./libs/ant.jar:./libs/asm- 
> attrs.jar:./libs/asm.jar:./libs/backport-util-concurrent.jar:./libs/ 
> bio-formats.jar:./libs/blitz.jar:./libs/btm.jar:./libs/bufr.jar:./ 
> libs/cglib.jar:./libs/checkstyle.jar:./libs/common.jar:./libs/ 
> commons-beanutils.jar:./libs/commons-codec.jar:./libs/commons- 
> collections.jar:./libs/commons-httpclient.jar:./libs/commons- 
> io.jar:./libs/commons-lang.jar:./libs/commons-logging.jar:./libs/ 
> commons-pool.jar:./libs/dsl.jar:./libs/ehcache.jar:./libs/emma.jar:./ 
> libs/emma_ant.jar:./libs/freemarker.jar:./libs/geronimo-spec- 
> jta.jar:./libs/grib.jar:./libs/hibernate-annotations.jar:./libs/ 
> hibernate-commons-annotations.jar:./libs/hibernate-search.jar:./libs/ 
> hibernate-tools.jar:./libs/hibernate-validator.jar:./libs/ 
> hsqldb.jar:./libs/ice-db.jar:./libs/ice.jar:./libs/ij.jar:./libs/ 
> importer-common.jar:./libs/importer.jar:./libs/ini4j.jar:./libs/ 
> jamon.jar:./libs/java-getop
> t.jar:./libs/jsr107cache.jar:./libs/jtidy.jar:./libs/loci- 
> common.jar:./libs/log4j.jar:./libs/lucene-core.jar:./libs/lucene- 
> highlighter.jar:./libs/lucene-spellchecker.jar:./libs/mail.jar:./ 
> libs/model-psql.jar:./libs/netcdf.jar:./libs/ome-java.jar:./libs/ome- 
> xml.jar:./libs/omero-clients-util.jar:./libs/omero_client.jar:./libs/ 
> persistence-api.jar:./libs/poi-loci.jar:./libs/postgresql.jar:./libs/ 
> quaqua-filechooser-only.jar:./libs/quartz.jar:./libs/rendering.jar:./ 
> libs/romio.jar:./libs/server.jar:./libs/slf4j-api.jar:./libs/slf4j- 
> log4j12.jar:./libs/spring-ldap.jar:./libs/spring.jar:./libs/ 
> swingx.jar:./libs/velocity-tools-generic.jar:./libs/velocity.jar:./ 
> libs/xerces.jar:./libs/xml-apis.jar"
> -Djava.library.path="/Users/mvalle/Desktop/OMERO.importer-build1841"
> ome.formats.importer.Main
> /Users/mvalle/omero/log
> 2009-03-10 15:36:22,186 0          [      main] INFO
> ome.system.UpgradeCheck  - no update needed
>
> Warning: class ch.randelshofer.quaqua.filechooser.Files couldn't  
> load library
> libquaqua.jnilib.
> User Name: mvalle -- Password: **********
> true
> Creating root!
> Tiff
> omero.model.Image:0 == omero.model.ImageI at 15e330,omero.model.Image:0
> omero.model.OriginalFile:0 ==  
> omero.model.OriginalFileI at f69ed3,omero.model.OriginalFile:0
> omero.model.Pixels:0:0 == omero.model.PixelsI at 356db6,Pixels:0
> omero.model.Channel:0:0 ==  
> omero.model.ChannelI at b5f36e,omero.model.Channel:0:0
> omero.model.LogicalChannel:0:0 ==
> omero.model.LogicalChannelI at 80ce9c,omero.model.LogicalChannel:0:0
>
> Starting references....
> Pixels:0 == omero.model.OriginalFile:0
>
> containerCache contains 5 entries.
> referenceCache contains 1 entries.
> Saving pixels id: 1
>
> -- 
> Ing. Mario Valle
> Data Analysis Group                              | http://www.cscs.ch/~mvalle
> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)  
> 610.82.60
> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)  
> 610.82.82
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

Brian Loranger
Software Developer, Open Microscopy Environment
Division of Gene Regulation and Expression
University of Dundee
(The University of Dundee is a registered Scottish charity, No:  
SC015096)



From mvalle at cscs.ch  Tue Mar 10 15:57:42 2009
From: mvalle at cscs.ch (Mario Valle)
Date: Tue, 10 Mar 2009 16:57:42 +0100
Subject: [ome-users] Client issues
In-Reply-To: <30DC19DE-AE67-43CE-98C8-C110352883FC@lifesci.dundee.ac.uk>
References: <49B68312.406@cscs.ch>
	<30DC19DE-AE67-43CE-98C8-C110352883FC@lifesci.dundee.ac.uk>
Message-ID: <49B68DF6.4010709@cscs.ch>

Tried, but the problem is in Ice.
I have set JAVA_ARGS to the same value as the beta3.2 clients (-Xms128m -Xmx512m)
With no change. The traceback is:

Ice.MemoryLimitException
     reason = (null)
	at IceInternal.BasicStream.expand(BasicStream.java:2029)
	at IceInternal.BasicStream.writeByteSeq(BasicStream.java:688)
	at Ice.ByteSeqHelper.write(ByteSeqHelper.java:19)
	at omero.api._RawPixelsStoreDelM.setPlane(_RawPixelsStoreDelM.java:1127)
	at omero.api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java:1546)
	at omero.api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java:1518)
	at ome.formats.OMEROMetadataStoreClient.setPlane(OMEROMetadataStoreClient.java:2306)
	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java:438)
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:343)
	at ome.formats.importer.ImportHandler.importImages(ImportHandler.java:181)
	at ome.formats.importer.ImportHandler.access$000(ImportHandler.java:39)
	at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:90)

BTW, in importer-gui do not put quotes around ${JAVA_ARGS} otherwise you cannot put 
multiple arguments in JAVA_ARGS.

Hope it helps
			mario




Brian Loranger wrote:
> Hi Mario,
> 
> I sent you an email about your importer error right after you sent the 
> error in (not sure if you missed it).
> 
> Just guessing based on what the error you sent me, but were you trying 
> to import something with a huge image plane (or perhaps you're running 
> the importer directly from the command line without giving the 
> application more then the default java memory allocation)?
> 
> All the clients are also in the RC1 release cycle so you should be able 
> to use the importer and insight directly against the latest version of 
> the server.
> 
> Cheers,
> 
> Brian Loranger
> Software Developer, Open Microscopy Environment
> Division of Gene Regulation and Expression
> University of Dundee
> (The University of Dundee is a registered Scottish charity, No: SC015096)
> 
> 
> 
> On 10 Mar 2009, at 15:11, Mario Valle wrote:
> 
>> (Really I don't know if the list is the correct one, please advise)
>>
>> So the Beta4 adventure started.
>>
>> Built the server without big problems (almost...)
>>
>> Run .insight with a retrieval error, but anyway the db is empty.
>>
>> So I found a .importer zip file on Hudson and tried it. Besides saying 
>> "version 3.1.1",
>> it crashes importing a tif file with, seems, an out-of-memory error. 
>> Instead the messages
>> on the console are much more pacific (see below).
>>
>> Maybe I should calm down and wait for a RC1 also for the clients, 
>> isn't it?
>>
>> Ciao!
>>     mario
>>
>>
>>
>> pazzallo ~/Desktop/OMERO.importer-build1841 > ./importer-gui
>> Starting OMERO.importer...
>> Suitable java version found [java = 1.5.0_16]
>> Configuring environment...
>> Java exec found in PATH. Verifying...
>> Loading OMERO.importer:
>> java -Xmx256m -cp
>> "./OmeroImporter.jar:./libs/FontBox.jar:./libs/PDFBox.jar:./libs/TableLayout.jar:./libs/activation.jar:./libs/ant.jar:./libs/asm-attrs.jar:./libs/asm.jar:./libs/backport-util-concurrent.jar:./libs/bio-formats.jar:./libs/blitz.jar:./libs/btm.jar:./libs/bufr.jar:./libs/cglib.jar:./libs/checkstyle.jar:./libs/common.jar:./libs/commons-beanutils.jar:./libs/commons-codec.jar:./libs/commons-collections.jar:./libs/commons-httpclient.jar:./libs/commons-io.jar:./libs/commons-lang.jar:./libs/commons-logging.jar:./libs/commons-pool.jar:./libs/dsl.jar:./libs/ehcache.jar:./libs/emma.jar:./libs/emma_ant.jar:./libs/freemarker.jar:./libs/geronimo-spec-jta.jar:./libs/grib.jar:./libs/hibernate-annotations.jar:./libs/hibernate-commons-annotations.jar:./libs/hibernate-search.jar:./libs/hibernate-tools.jar:./libs/hibernate-validator.jar:./libs/hsqldb.jar:./libs/ice-db.jar:./libs/ice.jar:./libs/ij.jar:./libs/importer-common.jar:./libs/importer.jar:./libs/ini4j.jar:./libs/jamon.jar:./libs/java-ge
top 
>>
>> t.jar:./libs/jsr107cache.jar:./libs/jtidy.jar:./libs/loci-common.jar:./libs/log4j.jar:./libs/lucene-core.jar:./libs/lucene-highlighter.jar:./libs/lucene-spellchecker.jar:./libs/mail.jar:./libs/model-psql.jar:./libs/netcdf.jar:./libs/ome-java.jar:./libs/ome-xml.jar:./libs/omero-clients-util.jar:./libs/omero_client.jar:./libs/persistence-api.jar:./libs/poi-loci.jar:./libs/postgresql.jar:./libs/quaqua-filechooser-only.jar:./libs/quartz.jar:./libs/rendering.jar:./libs/romio.jar:./libs/server.jar:./libs/slf4j-api.jar:./libs/slf4j-log4j12.jar:./libs/spring-ldap.jar:./libs/spring.jar:./libs/swingx.jar:./libs/velocity-tools-generic.jar:./libs/velocity.jar:./libs/xerces.jar:./libs/xml-apis.jar" 
>>
>> -Djava.library.path="/Users/mvalle/Desktop/OMERO.importer-build1841"
>> ome.formats.importer.Main
>> /Users/mvalle/omero/log
>> 2009-03-10 15:36:22,186 0          [      main] INFO
>> ome.system.UpgradeCheck  - no update needed
>>
>> Warning: class ch.randelshofer.quaqua.filechooser.Files couldn't load 
>> library
>> libquaqua.jnilib.
>> User Name: mvalle -- Password: **********
>> true
>> Creating root!
>> Tiff
>> omero.model.Image:0 == omero.model.ImageI at 15e330,omero.model.Image:0
>> omero.model.OriginalFile:0 == 
>> omero.model.OriginalFileI at f69ed3,omero.model.OriginalFile:0
>> omero.model.Pixels:0:0 == omero.model.PixelsI at 356db6,Pixels:0
>> omero.model.Channel:0:0 == 
>> omero.model.ChannelI at b5f36e,omero.model.Channel:0:0
>> omero.model.LogicalChannel:0:0 ==
>> omero.model.LogicalChannelI at 80ce9c,omero.model.LogicalChannel:0:0
>>
>> Starting references....
>> Pixels:0 == omero.model.OriginalFile:0
>>
>> containerCache contains 5 entries.
>> referenceCache contains 1 entries.
>> Saving pixels id: 1
>>
>> -- 
>> Ing. Mario Valle
>> Data Analysis Group                              | 
>> http://www.cscs.ch/~mvalle
>> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 
>> 610.82.60
>> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 
>> 610.82.82
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> 
> Brian Loranger
> Software Developer, Open Microscopy Environment
> Division of Gene Regulation and Expression
> University of Dundee
> (The University of Dundee is a registered Scottish charity, No: SC015096)
> 
> 

-- 
Ing. Mario Valle
Data Analysis Group                              | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82


From callan at blackcat.ca  Tue Mar 10 16:57:14 2009
From: callan at blackcat.ca (Chris Allan)
Date: Tue, 10 Mar 2009 16:57:14 +0000
Subject: [ome-users] Client issues
In-Reply-To: <49B68DF6.4010709@cscs.ch>
References: <49B68312.406@cscs.ch>
	<30DC19DE-AE67-43CE-98C8-C110352883FC@lifesci.dundee.ac.uk>
	<49B68DF6.4010709@cscs.ch>
Message-ID: <823F1C97-0691-447D-B088-EB0FE5CD9A12@blackcat.ca>

How big is this TIFF Mario? The default MemoryLimit for planes is  
64MB. :)

Ciao.

-Chris

On 10 Mar 2009, at 15:57, Mario Valle wrote:

> Tried, but the problem is in Ice.
> I have set JAVA_ARGS to the same value as the beta3.2 clients (- 
> Xms128m -Xmx512m)
> With no change. The traceback is:
>
> Ice.MemoryLimitException
>     reason = (null)
> 	at IceInternal.BasicStream.expand(BasicStream.java:2029)
> 	at IceInternal.BasicStream.writeByteSeq(BasicStream.java:688)
> 	at Ice.ByteSeqHelper.write(ByteSeqHelper.java:19)
> 	at omero.api._RawPixelsStoreDelM.setPlane(_RawPixelsStoreDelM.java: 
> 1127)
> 	at  
> omero 
> .api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java: 
> 1546)
> 	at  
> omero 
> .api.RawPixelsStorePrxHelper.setPlane(RawPixelsStorePrxHelper.java: 
> 1518)
> 	at  
> ome 
> .formats 
> .OMEROMetadataStoreClient.setPlane(OMEROMetadataStoreClient.java:2306)
> 	at ome.formats.importer.ImportLibrary.importData(ImportLibrary.java: 
> 438)
> 	at  
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:343)
> 	at  
> ome.formats.importer.ImportHandler.importImages(ImportHandler.java: 
> 181)
> 	at ome.formats.importer.ImportHandler.access$000(ImportHandler.java: 
> 39)
> 	at ome.formats.importer.ImportHandler$1.run(ImportHandler.java:90)
>
> BTW, in importer-gui do not put quotes around ${JAVA_ARGS} otherwise  
> you cannot put
> multiple arguments in JAVA_ARGS.
>
> Hope it helps
> 			mario
>
>
>
>
> Brian Loranger wrote:
>> Hi Mario,
>>
>> I sent you an email about your importer error right after you sent  
>> the
>> error in (not sure if you missed it).
>>
>> Just guessing based on what the error you sent me, but were you  
>> trying
>> to import something with a huge image plane (or perhaps you're  
>> running
>> the importer directly from the command line without giving the
>> application more then the default java memory allocation)?
>>
>> All the clients are also in the RC1 release cycle so you should be  
>> able
>> to use the importer and insight directly against the latest version  
>> of
>> the server.
>>
>> Cheers,
>>
>> Brian Loranger
>> Software Developer, Open Microscopy Environment
>> Division of Gene Regulation and Expression
>> University of Dundee
>> (The University of Dundee is a registered Scottish charity, No:  
>> SC015096)
>>
>>
>>
>> On 10 Mar 2009, at 15:11, Mario Valle wrote:
>>
>>> (Really I don't know if the list is the correct one, please advise)
>>>
>>> So the Beta4 adventure started.
>>>
>>> Built the server without big problems (almost...)
>>>
>>> Run .insight with a retrieval error, but anyway the db is empty.
>>>
>>> So I found a .importer zip file on Hudson and tried it. Besides  
>>> saying
>>> "version 3.1.1",
>>> it crashes importing a tif file with, seems, an out-of-memory error.
>>> Instead the messages
>>> on the console are much more pacific (see below).
>>>
>>> Maybe I should calm down and wait for a RC1 also for the clients,
>>> isn't it?
>>>
>>> Ciao!
>>>    mario
>>>
>>>
>>>
>>> pazzallo ~/Desktop/OMERO.importer-build1841 > ./importer-gui
>>> Starting OMERO.importer...
>>> Suitable java version found [java = 1.5.0_16]
>>> Configuring environment...
>>> Java exec found in PATH. Verifying...
>>> Loading OMERO.importer:
>>> java -Xmx256m -cp
>>> "./OmeroImporter.jar:./libs/FontBox.jar:./libs/PDFBox.jar:./libs/ 
>>> TableLayout.jar:./libs/activation.jar:./libs/ant.jar:./libs/asm- 
>>> attrs.jar:./libs/asm.jar:./libs/backport-util-concurrent.jar:./ 
>>> libs/bio-formats.jar:./libs/blitz.jar:./libs/btm.jar:./libs/ 
>>> bufr.jar:./libs/cglib.jar:./libs/checkstyle.jar:./libs/ 
>>> common.jar:./libs/commons-beanutils.jar:./libs/commons-codec.jar:./ 
>>> libs/commons-collections.jar:./libs/commons-httpclient.jar:./libs/ 
>>> commons-io.jar:./libs/commons-lang.jar:./libs/commons- 
>>> logging.jar:./libs/commons-pool.jar:./libs/dsl.jar:./libs/ 
>>> ehcache.jar:./libs/emma.jar:./libs/emma_ant.jar:./libs/ 
>>> freemarker.jar:./libs/geronimo-spec-jta.jar:./libs/grib.jar:./libs/ 
>>> hibernate-annotations.jar:./libs/hibernate-commons- 
>>> annotations.jar:./libs/hibernate-search.jar:./libs/hibernate- 
>>> tools.jar:./libs/hibernate-validator.jar:./libs/hsqldb.jar:./libs/ 
>>> ice-db.jar:./libs/ice.jar:./libs/ij.jar:./libs/importer- 
>>> common.jar:./libs/importer.jar:./libs/ini4j.jar:./libs/jamon.jar:./ 
>>> libs/java-ge
> top
>>>
>>> t.jar:./libs/jsr107cache.jar:./libs/jtidy.jar:./libs/loci- 
>>> common.jar:./libs/log4j.jar:./libs/lucene-core.jar:./libs/lucene- 
>>> highlighter.jar:./libs/lucene-spellchecker.jar:./libs/mail.jar:./ 
>>> libs/model-psql.jar:./libs/netcdf.jar:./libs/ome-java.jar:./libs/ 
>>> ome-xml.jar:./libs/omero-clients-util.jar:./libs/ 
>>> omero_client.jar:./libs/persistence-api.jar:./libs/poi-loci.jar:./ 
>>> libs/postgresql.jar:./libs/quaqua-filechooser-only.jar:./libs/ 
>>> quartz.jar:./libs/rendering.jar:./libs/romio.jar:./libs/ 
>>> server.jar:./libs/slf4j-api.jar:./libs/slf4j-log4j12.jar:./libs/ 
>>> spring-ldap.jar:./libs/spring.jar:./libs/swingx.jar:./libs/ 
>>> velocity-tools-generic.jar:./libs/velocity.jar:./libs/xerces.jar:./ 
>>> libs/xml-apis.jar"
>>>
>>> -Djava.library.path="/Users/mvalle/Desktop/OMERO.importer-build1841"
>>> ome.formats.importer.Main
>>> /Users/mvalle/omero/log
>>> 2009-03-10 15:36:22,186 0          [      main] INFO
>>> ome.system.UpgradeCheck  - no update needed
>>>
>>> Warning: class ch.randelshofer.quaqua.filechooser.Files couldn't  
>>> load
>>> library
>>> libquaqua.jnilib.
>>> User Name: mvalle -- Password: **********
>>> true
>>> Creating root!
>>> Tiff
>>> omero.model.Image:0 == omero.model.ImageI at 15e330,omero.model.Image:0
>>> omero.model.OriginalFile:0 ==
>>> omero.model.OriginalFileI at f69ed3,omero.model.OriginalFile:0
>>> omero.model.Pixels:0:0 == omero.model.PixelsI at 356db6,Pixels:0
>>> omero.model.Channel:0:0 ==
>>> omero.model.ChannelI at b5f36e,omero.model.Channel:0:0
>>> omero.model.LogicalChannel:0:0 ==
>>> omero.model.LogicalChannelI at 80ce9c,omero.model.LogicalChannel:0:0
>>>
>>> Starting references....
>>> Pixels:0 == omero.model.OriginalFile:0
>>>
>>> containerCache contains 5 entries.
>>> referenceCache contains 1 entries.
>>> Saving pixels id: 1
>>>
>>> -- 
>>> Ing. Mario Valle
>>> Data Analysis Group                              |
>>> http://www.cscs.ch/~mvalle
>>> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)
>>> 610.82.60
>>> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)
>>> 610.82.82
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>> Brian Loranger
>> Software Developer, Open Microscopy Environment
>> Division of Gene Regulation and Expression
>> University of Dundee
>> (The University of Dundee is a registered Scottish charity, No:  
>> SC015096)
>>
>>
>
> -- 
> Ing. Mario Valle
> Data Analysis Group                              | http://www.cscs.ch/~mvalle
> Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)  
> 610.82.60
> v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)  
> 610.82.82
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users



From Guenter.Giese at mpimf-heidelberg.mpg.de  Wed Mar 11 17:28:43 2009
From: Guenter.Giese at mpimf-heidelberg.mpg.de (Guenter Giese)
Date: Wed, 11 Mar 2009 18:28:43 +0100
Subject: [ome-users] comparison list of TIFF tags and OME-TIFF (XML moiety)
	tags available?
Message-ID: <49D1C9C37908463BB74C021BE851FCD5@corona>

Dear list members,

I am just starting to implement OME-TIFF/XML storage of files obtained from
a new microscope. I did not check yet if there is some overlap between TIFF
tags and OME-TIFF (XML moiety) tags (OME scheme).

Is there some overlap? If yes, is there a comparison list of general and of
microscopy-related TIFF tags and OME-TIFF tags  (stored in the XML header)
available?

Best,

Guenter

------------------------------------------
Dr. Guenter Giese
Light Microscopy Facility Manager
Dept. of Biomedical Optics
MPI fuer Medizinische Forschung Jahnstr. 29
D-69120 Heidelberg, Germany
Phone (+49) 6221-486-360 (Fax: -325)
e-mail: guenter.giese at mpimf-heidelberg.mpg.de 



From ctrueden at wisc.edu  Wed Mar 11 18:57:44 2009
From: ctrueden at wisc.edu (Curtis Rueden)
Date: Wed, 11 Mar 2009 13:57:44 -0500
Subject: [ome-users] comparison list of TIFF tags and OME-TIFF (XML
	moiety) tags available?
In-Reply-To: <49D1C9C37908463BB74C021BE851FCD5@corona>
References: <49D1C9C37908463BB74C021BE851FCD5@corona>
Message-ID: <857a86450903111157p27679ff0wc8591512cba1b240@mail.gmail.com>

Hi Guenter,

I am just starting to implement OME-TIFF/XML storage of files obtained from
> a new microscope. I did not check yet if there is some overlap between TIFF
> tags and OME-TIFF (XML moiety) tags (OME scheme).
>
> Is there some overlap? If yes, is there a comparison list of general and of
> microscopy-related TIFF tags and OME-TIFF tags  (stored in the XML header)
> available?
>

Since TIFF is a very general image format, there is not much overlap aside
from core metadata fields:

TIFF ImageWidth = OME Pixels SizeX
TIFF ImageLength = OME Pixels SizeY
TIFF endianness signature (II / MM) = OME Pixels LittleEndian
TIFF SamplesPerPixel = OME Pixels SizeC (mostly)
TIFF number of IFDs = OME Pixels SizeT
TIFF BitsPerSample maps to OME Pixels PixelType
TIFF DateTime = OME Image CreationDate
TIFF XResolution = OME Pixels PhysicalSizeX
TIFF YResolution = OME Pixels PhysicalSizeY
TIFF ImageDescription = OME Image Description

You can see these expressed in code in the Bio-Formats base TIFF reader's
initMetadataStore() method:

https://skyking.microscopy.wisc.edu/trac/java/browser/trunk/components/bio-formats/src/loci/formats/in/BaseTiffReader.java#L490

I am not sure what you mean by "microscopy-related TIFF tags." There are
many proprietary microscopy-specific variants of TIFF (e.g.: Flex, Olympus
Fluoview, Molecular Dynamics GEL, Imaris, Improvision, Metamorph, Nikon,
Image-Pro Sequence, SVS, Zeiss LSM) that contain extra information, but
these are not OME-TIFFs. However, Bio-Formats parses each format's
proprietary metadata and converts what it can into OME-XML.

For a full list of supported OME metadata fields in each file format, see
the big table on the Bio-Formats web site:
  http://www.loci.wisc.edu/ome/formats.html

For example, if you mouse over the entry for TIFF, at the bottom of the
pop-up you will see a link to "Supported metadata fields":
  https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader

-Curtis

On Wed, Mar 11, 2009 at 12:28 PM, Guenter Giese <
Guenter.Giese at mpimf-heidelberg.mpg.de> wrote:

> Dear list members,
>
> I am just starting to implement OME-TIFF/XML storage of files obtained from
> a new microscope. I did not check yet if there is some overlap between TIFF
> tags and OME-TIFF (XML moiety) tags (OME scheme).
>
> Is there some overlap? If yes, is there a comparison list of general and of
> microscopy-related TIFF tags and OME-TIFF tags  (stored in the XML header)
> available?
>
> Best,
>
> Guenter
>
> ------------------------------------------
> Dr. Guenter Giese
> Light Microscopy Facility Manager
> Dept. of Biomedical Optics
> MPI fuer Medizinische Forschung Jahnstr. 29
> D-69120 Heidelberg, Germany
> Phone (+49) 6221-486-360 (Fax: -325)
> e-mail: guenter.giese at mpimf-heidelberg.mpg.de
>
> _______________________________________________
> 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 Guenter.Giese at mpimf-heidelberg.mpg.de  Wed Mar 11 21:21:57 2009
From: Guenter.Giese at mpimf-heidelberg.mpg.de (Guenter Giese)
Date: Wed, 11 Mar 2009 22:21:57 +0100
Subject: [ome-users] comparison list of TIFF tags and OME-TIFF
 (XML	moiety) tags available?
In-Reply-To: <857a86450903111157p27679ff0wc8591512cba1b240@mail.gmail.com>
References: <49D1C9C37908463BB74C021BE851FCD5@corona>
	<857a86450903111157p27679ff0wc8591512cba1b240@mail.gmail.com>
Message-ID: <fcb6d8b97fd3.49b83985@mpimf-heidelberg.mpg.de>

Hi Curtis,

thank you for your rapid answer! It addresses my questions almost perfectly.? 

> I am not sure what you mean by "microscopy-related TIFF tags." There are many proprietary microscopy-specific variants of TIFF (e.g.: Flex, Olympus Fluoview, Molecular Dynamics GEL, Imaris, Improvision, Metamorph, Nikon, Image-Pro Sequence, SVS, Zeiss LSM) that contain extra information, but these are not OME-TIFFs. However, Bio-Formats parses each format's proprietary metadata and converts what it can into OME-XML.
 

Sorry, I should have been more precise: My microscope is a home-built light sheet microscope (optically a type of wide field microscope) with different mechanical, electronic? and optical components, controlled by a PC. Some of the components obviously are addressed neither by TIFF tags nor by OME-XML scheme tags.

Basically, I want to store as many microscope and recording parameters as possible  in appropriate TIFF tags, and additional metadata (plus copies of the TIFF tags) in a format which is not proprietary but open and expandable (OME-TIFF / XML seems quite a good candidate). 

First I want to evaluate the metadata tags already addressed by TIFF as well as by the OME XML scheme (trying to avoid "private" data tags). 

Other metadata (many still to be defined) may then in addition be stored as (preliminary) XML tags (sometimes hopefully making it into a common, open scheme, or finding their equivalent in it).


Did I miss something, or is there a better way to proceed?


> For example, if you mouse over the entry for TIFF, at the bottom of the pop-up you will see a link to "Supported metadata fields":
> ? https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader
 
Thanks, this is exactly the stuff I was looking for. I will check in more detail tomorrow.


I am not a programmer (others are in charge of this), but highly concerned about proper metadata storage handling, and retrieval of course. I have been struggling, as a microscopy facility manager, with the mess of proprietary (or simply non-existing) metadata since years. I hope an open standard (like OME-TIFF /? XML) will meet my demands. 
 

Best,

Guenter

>  ------------------------------------------
>  Dr. Guenter Giese
>  Light Microscopy Facility Manager
>  Dept. of Biomedical Optics
>  MPI fuer Medizinische Forschung Jahnstr. 29
>  D-69120 Heidelberg, Germany
>  Phone (+49) 6221-486-360 (Fax: -325)
>  e-mail: guenter.giese at mpimf-heidelberg.mpg.de
 
>  _______________________________________________
>  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
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From bernhard.voigt at gmail.com  Fri Mar 13 08:55:17 2009
From: bernhard.voigt at gmail.com (Bernhard Voigt)
Date: Fri, 13 Mar 2009 09:55:17 +0100
Subject: [ome-users] Entity - Relationship diagram for OME
In-Reply-To: <EDC22492BE5CAF409A4166B67B1F2E9A9F28689A@EX7SM01.ad.uky.edu>
References: <EDC22492BE5CAF409A4166B67B1F2E9A9F286898@EX7SM01.ad.uky.edu>
	<49B5199C.6080502@imperial.ac.uk>
	<1236605686.7516.8.camel@shadowblade.openmicroscopy.org.uk>
	<EDC22492BE5CAF409A4166B67B1F2E9A9F28689A@EX7SM01.ad.uky.edu>
Message-ID: <21a270aa0903130155h24fc6e0ew982a27cc873250f3@mail.gmail.com>

Hi Sriram,

for reverse engineering I like to have an ER diagram of small parts of
the db schema. I'm using DBVisualizer
http://www.minq.se/products/dbvis/ for this, it works nicely. You can
select one or multiple tables and get a graph of all explicit
references that are defined. See attached screen shot. This helps to
find the right node in the xml-schema docs.

Cheers! Bernhard



On Mon, Mar 9, 2009 at 7:28 PM, Nandakumar, Sriramkumar
<sriramkumar at uky.edu> wrote:
> Hi,
> Thanks for providing the information.
>
> Thanks & Regards,
> Sriram.
> ________________________________________
> From: Chris Allan [callan at blackcat.ca]
> Sent: Monday, March 09, 2009 9:34 AM
> To: Mark Woodbridge
> Cc: Nandakumar, Sriramkumar; ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Entity ?- Relationship diagram for OME
>
> Hi all,
>
> Historically we've avoided diagraming every type in one diagram using ER
> because of the sheer size of image that creates. Usually to the
> detriment of actual model understanding.
>
> Mark has conveniently already laid out the XML Schema representation for
> which the database follows almost exclusively. Other diagrams with high
> level explanations for some of the more complicated relationships, and
> some rationale, are also available here:
>
> http://www.ome-xml.org/wiki/DeveloperInfo
>
> Ciao.
>
> -Chris
>
> On Mon, 2009-03-09 at 13:29 +0000, Mark Woodbridge wrote:
>> Hi,
>>
>> You might also find this documentation useful:
>>
>> http://cvs.openmicroscopy.org.uk/svn/specification/Documentation/Generated/OME-2008-09/ome.xsd.html#element_OME
>>
>> It describes the XML Schema representation of the OME model.
>>
>> Mark.
>>
>> Nandakumar, Sriramkumar wrote:
>> > Hi all,
>> > I am Sriram.
>> > I am looking for Entity relationship diagram for OME.
>> > Do any one have that?
>> >
>> >
>> > Thanks & Regards,
>> > Sriram.
>> > _______________________________________________
>> > 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
>
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From p.schofield at dundee.ac.uk  Mon Mar 16 12:17:09 2009
From: p.schofield at dundee.ac.uk (=?ISO-8859-1?Q?Piet=E0_Schofield?=)
Date: Mon, 16 Mar 2009 12:17:09 +0000
Subject: [ome-users] Installation problem
Message-ID: <B9229075-FB92-41F9-BCEE-F53336088051@dundee.ac.uk>

Hullo

I have tried to install OMERO on a mac running Tiger 1.5 I followed  
the installation procedure installing Postgresql  etc and everything  
seemed to go well, no error messages or warnings,  but when i  
eventually try to log in to the WebAdmin client I get the following  
login failure message.

"Connection failure: Error creating bean with name 'init' defined in  
class path resource [ome/client/spring.xml]: Cannot resolve reference  
to bean 'managed-ome.api.ISession' while setting bean property  
'sessionService'; nested exception is  
org.springframework.beans.factory.BeanCreationException: Error  
creating bean with name 'managed-ome.api.ISession': FactoryBean threw  
exception on object creation; nested exception is  
ome.client.OutOfService: Cannot initialize service proxy "

Could anybody direct me to what step in the installation I messed up  
(or missed out).

Thanks

Pieta


Piet? Schofield
p.schofield at dundee.ac.uk

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





From josh.moore at gmx.de  Mon Mar 16 14:34:19 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Mon, 16 Mar 2009 15:34:19 +0100
Subject: [ome-users]  Installation problem
In-Reply-To: <B9229075-FB92-41F9-BCEE-F53336088051@dundee.ac.uk>
References: <B9229075-FB92-41F9-BCEE-F53336088051@dundee.ac.uk>
Message-ID: <18878.25451.719547.135956@echo.mac>


Hi Piet?,

the OutOfService exception means that no connection to the server is
possible whatsoever. Would it be possible to send us the entire server
log (possibly zipped)?

Thanks,
~Josh.

Piet? Schofield writes:
 > Hullo
 > 
 > I have tried to install OMERO on a mac running Tiger 1.5 I followed  
 > the installation procedure installing Postgresql  etc and everything  
 > seemed to go well, no error messages or warnings,  but when i  
 > eventually try to log in to the WebAdmin client I get the following  
 > login failure message.
 > 
 > "Connection failure: Error creating bean with name 'init' defined in  
 > class path resource [ome/client/spring.xml]: Cannot resolve reference  
 > to bean 'managed-ome.api.ISession' while setting bean property  
 > 'sessionService'; nested exception is  
 > org.springframework.beans.factory.BeanCreationException: Error  
 > creating bean with name 'managed-ome.api.ISession': FactoryBean threw  
 > exception on object creation; nested exception is  
 > ome.client.OutOfService: Cannot initialize service proxy "
 > 
 > Could anybody direct me to what step in the installation I messed up  
 > (or missed out).
 > 
 > Thanks
 > 
 > Pieta


From josh.moore at gmx.de  Mon Mar 16 15:20:02 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Mon, 16 Mar 2009 16:20:02 +0100
Subject: [ome-users] Installation problem
In-Reply-To: <EAAF69E6-A536-465C-B649-E01FAD3AB1D0@dundee.ac.uk>
References: <B9229075-FB92-41F9-BCEE-F53336088051@dundee.ac.uk>
	<18878.25451.719547.135956@echo.mac>
	<EAAF69E6-A536-465C-B649-E01FAD3AB1D0@dundee.ac.uk>
Message-ID: <18878.28194.518226.450839@echo.mac>


Piet? Schofield writes:
 > Hullo Josh
 > 
 > thanks for the response.

Gladly.

 > I found that going to lunch then trying again  
 > made all the difference. I can now log on to the WebAdmin and I have  
 > successfully used the Beta3.2.1 clients to connect to the server.  

Possibly, the server had not finished its initialization, though a
whole lunch break shouldn't typically be required. :)

 > Trying the Beta4 omero.insight client I got an error when trying to  
 > log on of
 >
 > Failed to log onto
 > OMERO
 > Please check the port
 > or try again later

This will definitely *not* work. The Beta 4 system has an entirely
different server architecture, so the client versions must match.

 > But as I am happy at the moment to have the Server and the Beta3  
 > clients working I am not too worried about the Beta4 client

Understood. And glad to hear!

 > Pieta

Cheers,
~Josh.

 > On 16 Mar 2009, at 14:34, josh.moore at gmx.de wrote:
 > 
 > >
 > > Hi Piet?,
 > >
 > > the OutOfService exception means that no connection to the server is
 > > possible whatsoever. Would it be possible to send us the entire server
 > > log (possibly zipped)?
 > >
 > > Thanks,
 > > ~Josh.
 > >
 > > Piet? Schofield writes:
 > >> Hullo
 > >>
 > >> I have tried to install OMERO on a mac running Tiger 1.5 I followed
 > >> the installation procedure installing Postgresql  etc and everything
 > >> seemed to go well, no error messages or warnings,  but when i
 > >> eventually try to log in to the WebAdmin client I get the following
 > >> login failure message.
 > >>
 > >> "Connection failure: Error creating bean with name 'init' defined in
 > >> class path resource [ome/client/spring.xml]: Cannot resolve reference
 > >> to bean 'managed-ome.api.ISession' while setting bean property
 > >> 'sessionService'; nested exception is
 > >> org.springframework.beans.factory.BeanCreationException: Error
 > >> creating bean with name 'managed-ome.api.ISession': FactoryBean threw
 > >> exception on object creation; nested exception is
 > >> ome.client.OutOfService: Cannot initialize service proxy "
 > >>
 > >> Could anybody direct me to what step in the installation I messed up
 > >> (or missed out).
 > >>
 > >> Thanks
 > >>
 > >> Pieta
 > 
 > Piet? Schofield
 > p.schofield at dundee.ac.uk
 > 
 > The University of Dundee is a Scottish Registered Charity, No. SC015096.
 > 
 > 


From ctrueden at wisc.edu  Mon Mar 16 16:26:34 2009
From: ctrueden at wisc.edu (Curtis Rueden)
Date: Mon, 16 Mar 2009 11:26:34 -0500
Subject: [ome-users] comparison list of TIFF tags and OME-TIFF (XML
	moiety) tags available?
In-Reply-To: <fcb6d8b97fd3.49b83985@mpimf-heidelberg.mpg.de>
References: <49D1C9C37908463BB74C021BE851FCD5@corona>
	<857a86450903111157p27679ff0wc8591512cba1b240@mail.gmail.com>
	<fcb6d8b97fd3.49b83985@mpimf-heidelberg.mpg.de>
Message-ID: <857a86450903160926l10cca2e9q55a13369afecbb66@mail.gmail.com>

Hi Guenter,

Sorry, I should have been more precise: My microscope is a home-built light
> sheet microscope (optically a type of wide field microscope) with different
> mechanical, electronic  and optical components, controlled by a PC. Some of
> the components obviously are addressed neither by TIFF tags nor by OME-XML
> scheme tags.
>
> Basically, I want to store as many microscope and recording parameters as
> possible in appropriate TIFF tags, and additional metadata (plus copies of
> the TIFF tags) in a format which is not proprietary but open and expandable
> (OME-TIFF / XML seems quite a good candidate).
>
> First I want to evaluate the metadata tags already addressed by TIFF as
> well as by the OME XML scheme (trying to avoid "private" data tags).
>

Since TIFF is not a microscopy format, I doubt many of the fields you need
will be available. However, most of the microscopy-specific fields you need
should be available in the OME schema. If not, we are enthusiastic about
expanding the specification to accommodate additional needs; just let us
know which specific fields you are considering. For extremely niche metadata
fields, you can use a feature of OME-XML called structured annotations to
represent the information in a semi-structured way.

Other metadata (many still to be defined) may then in addition be stored as
> (preliminary) XML tags (sometimes hopefully making it into a common, open
> scheme, or finding their equivalent in it).
>

Indeed, the goal is for OME-XML to be able to express the majority of
people's use cases for microscopy metadata.

Did I miss something, or is there a better way to proceed?


What my group did (LOCI) with our home-built systems is to add support for
OME-TIFF to our internal acquisition software. To accomplish this, we use
Bio-Formats (http://www.loci.wisc.edu/ome/formats.html) with Ice, to harness
the Bio-Formats metadata API, and embed OME-XML into our TIFFs using
libtiff. There is a brief, somewhat out of date overview at:

  http://www.loci.wisc.edu/ome/wiscscan.html

Did you also create your own acquisition package, or are you using an
off-the-shelf program?

Lastly, we are almost finished with a C++ wrapper that should make
Bio-Formats easier to use from within acquisition software.

>   https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader
>
> Thanks, this is exactly the stuff I was looking for. I will check in more
> detail tomorrow.
>

Let me know if you have any questions.

To caution you, the fields listed on that wiki are a subset of all available
OME-XML fields. They represent only those currently mapped by Bio-Formats
into our flat metadata API. However, it is quite easy for us to map in
additional fields from the XML schema into Bio-Formats. I can elaborate
further on this process if you are interested.

For a full list of all available OME metadata, see:

  https://openmicroscopy.org/Schemas/OME/2008-09/ome.xsd

And for further documentation:
  https://openmicroscopy.org/Schemas/
  http://ome-xml.org/browser/Documentation
  http://ome-xml.org/

There are other diagrams as well but I don't have the URLs handy at the
moment.

I am not a programmer (others are in charge of this), but highly concerned
> about proper metadata storage handling, and retrieval of course. I have been
> struggling, as a microscopy facility manager, with the mess of proprietary
> (or simply non-existing) metadata since years. I hope an open standard (like
> OME-TIFF /  XML) will meet my demands.
>

Join the club. :-)  The OME data model exists for people in positions like
yours, so please let us know if it does not meet your needs!

Regards,
-Curtis

On Wed, Mar 11, 2009 at 4:21 PM, Guenter Giese <
Guenter.Giese at mpimf-heidelberg.mpg.de> wrote:

> Hi Curtis,
>
> thank you for your rapid answer! It addresses my questions almost
> perfectly.
>
> > I am not sure what you mean by "microscopy-related TIFF tags." There are
> many proprietary microscopy-specific variants of TIFF (e.g.: Flex, Olympus
> Fluoview, Molecular Dynamics GEL, Imaris, Improvision, Metamorph, Nikon,
> Image-Pro Sequence, SVS, Zeiss LSM) that contain extra information, but
> these are not OME-TIFFs. However, Bio-Formats parses each format's
> proprietary metadata and converts what it can into OME-XML.
>
>
> Sorry, I should have been more precise: My microscope is a home-built light
> sheet microscope (optically a type of wide field microscope) with different
> mechanical, electronic  and optical components, controlled by a PC. Some of
> the components obviously are addressed neither by TIFF tags nor by OME-XML
> scheme tags.
>
> Basically, I want to store as many microscope and recording parameters as
> possible in appropriate TIFF tags, and additional metadata (plus copies of
> the TIFF tags) in a format which is not proprietary but open and expandable
> (OME-TIFF / XML seems quite a good candidate).
>
> First I want to evaluate the metadata tags already addressed by TIFF as
> well as by the OME XML scheme (trying to avoid "private" data tags).
>
> Other metadata (many still to be defined) may then in addition be stored as
> (preliminary) XML tags (sometimes hopefully making it into a common, open
> scheme, or finding their equivalent in it).
>
>
> Did I miss something, or is there a better way to proceed?
>
>
> > For example, if you mouse over the entry for TIFF, at the bottom of the
> pop-up you will see a link to "Supported metadata fields":
> >   https://skyking.microscopy.wisc.edu/trac/java/wiki/TiffReader
>
> Thanks, this is exactly the stuff I was looking for. I will check in more
> detail tomorrow.
>
>
> I am not a programmer (others are in charge of this), but highly concerned
> about proper metadata storage handling, and retrieval of course. I have been
> struggling, as a microscopy facility manager, with the mess of proprietary
> (or simply non-existing) metadata since years. I hope an open standard (like
> OME-TIFF /  XML) will meet my demands.
>
>
> Best,
>
> Guenter
>
> > ------------------------------------------
>> > Dr. Guenter Giese
>> > Light Microscopy Facility Manager
>> > Dept. of Biomedical Optics
>> > MPI fuer Medizinische Forschung Jahnstr. 29
>> > D-69120 Heidelberg, Germany
>> > Phone (+49) 6221-486-360 (Fax: -325)
>> > e-mail: guenter.giese at mpimf-heidelberg.mpg.de
>>
>> > _______________________________________________
>> > ome-users mailing list
>> > ome-users at lists.openmicroscopy.org.uk
>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<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
>
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From rubenalves at fm.ul.pt  Mon Mar 16 18:02:08 2009
From: rubenalves at fm.ul.pt (=?ISO-8859-1?Q?=BB_Ruben_Alves?=)
Date: Mon, 16 Mar 2009 18:02:08 +0000
Subject: [ome-users] Error deploying OMERO 3.2 beta | jboss-log4j.xml
Message-ID: <49BE9420.9000001@fm.ul.pt>

Hi all,
I've just mooved to the last omero public release. But I can't 
understand why I can't deploy omero without this error:

17:54:59,383 INFO  [Log4jService$URLWatchTimerTask] Configuring from 
URL: resource:jboss-log4j.xml
2009-03-16 17:55:53,697 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 
java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /root/.java/.userPrefs/prefs.xml
2009-03-16 17:55:53,719 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 
java.util.prefs.FileSystemPreferences$7 run
WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml

I will appreciate any kind of help.

My best regards,

//Ruben

-- 
Ruben Alves 

System Analyst 
USI @ Instituto de Medicina Molecular
Edif?cio Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999411 ext 47026
rubenalves at fm.ul.pt



From josh.moore at gmx.de  Mon Mar 16 18:46:26 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Mon, 16 Mar 2009 19:46:26 +0100
Subject: [ome-users]  Error deploying OMERO 3.2 beta | jboss-log4j.xml
In-Reply-To: <49BE9420.9000001@fm.ul.pt>
References: <49BE9420.9000001@fm.ul.pt>
Message-ID: <18878.40578.365264.204256@echo.mac>

? Ruben Alves writes:
 > Hi all,

Hi Ruben,

 > I've just moved to the last omero public release. But I can't 
 > understand why I can't deploy omero without this error:
 > 
 > 17:54:59,383 INFO  [Log4jService$URLWatchTimerTask] Configuring from 
 > URL: resource:jboss-log4j.xml
 > 2009-03-16 17:55:53,697 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 
 > java.util.prefs.FileSystemPreferences$7 run
 > WARNING: Prefs file removed in background /root/.java/.userPrefs/prefs.xml
 > 2009-03-16 17:55:53,719 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 
 > java.util.prefs.FileSystemPreferences$7 run
 > WARNING: Prefs file removed in background /etc/.java/.systemPrefs/prefs.xml
 > 
 > I will appreciate any kind of help.

First, is everything working properly despite the error messages? In
our experience, this is an issue with how Java was installed, but is
not detrimental to the server's functioning. This bug in the Sun
database might be of interest:

http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751177

 > My best regards,
 > 
 > //Ruben

Hope that helps,
~Josh


From rubenalves at fm.ul.pt  Tue Mar 17 10:09:00 2009
From: rubenalves at fm.ul.pt (=?ISO-8859-1?Q?=BB_Ruben_Alves?=)
Date: Tue, 17 Mar 2009 10:09:00 +0000
Subject: [ome-users] Error deploying OMERO 3.2 beta | jboss-log4j.xml
In-Reply-To: <49BE9420.9000001@fm.ul.pt>
References: <49BE9420.9000001@fm.ul.pt>
Message-ID: <49BF76BC.3080406@fm.ul.pt>

Hi Josh, in fact I've already been in that site via Omero's 
troubleshooting page.
My /etc/.java is already world readable and writable, but the error 
continues.
Omero is running as root in a Debian Lenny Linux.
I've installed Java with apt-get and downloaded the official installer. 
In both, I got the same error.
The problem is because of this error, OMERO don't even start.

To deploy omero I use this script:

omero:/var/omero-Beta3.2# cat deploy_server.sh
#!/bin/bash

export http_proxy="http://proxy.lan:8080/"
export JBOSS_HOME=/var/omero-Beta3.2/jboss-4.2.3.GA/
cd /var/omero-Beta3.2/omero
java omero deploy
$JBOSS_HOME/bin/run.sh

Now, I really don't know how to fix this problem.

Regards



? Ruben Alves writes:
 > Hi all,

Hi Ruben,

 > I've just moved to the last omero public release. But I can't > 
understand why I can't deploy omero without this error:
 > > 17:54:59,383 INFO  [Log4jService$URLWatchTimerTask] Configuring 
from > URL: resource:jboss-log4j.xml
 > 2009-03-16 17:55:53,697 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 > 
java.util.prefs.FileSystemPreferences$7 run
 > WARNING: Prefs file removed in background 
/root/.java/.userPrefs/prefs.xml
 > 2009-03-16 17:55:53,719 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 > 
java.util.prefs.FileSystemPreferences$7 run
 > WARNING: Prefs file removed in background 
/etc/.java/.systemPrefs/prefs.xml
 > > I will appreciate any kind of help.

First, is everything working properly despite the error messages? In
our experience, this is an issue with how Java was installed, but is
not detrimental to the server's functioning. This bug in the Sun
database might be of interest:

http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751177

 > My best regards,
 > > //Ruben

Hope that helps,
~Josh

-- 
Ruben Alves 

System Analyst 
USI @ Instituto de Medicina Molecular
Edif?cio Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999411 ext 47026
rubenalves at fm.ul.pt



From josh.moore at gmx.de  Tue Mar 17 11:07:25 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Tue, 17 Mar 2009 12:07:25 +0100
Subject: [ome-users] Error deploying OMERO 3.2 beta | jboss-log4j.xml
In-Reply-To: <49BF76BC.3080406@fm.ul.pt>
References: <49BE9420.9000001@fm.ul.pt>
	<49BF76BC.3080406@fm.ul.pt>
Message-ID: <18879.33901.755188.753750@echo.mac>


Hi Ruben,

Oh boy. Sounds like we're not getting off the hook so easily. :)

First, I should mention that I couldn't reproduce this running as root
under Ubuntu. I get this message after deleting my preference
directories when I access preferences as root:

  root at millaboula:/etc/.java# java -cp /tmp prefs sys get
  17/03/2009 10:42:44 AM java.util.prefs.FileSystemPreferences$3 run
  INFO: Created system preferences directory in java.home.

? Ruben Alves writes:
 > Hi Josh, in fact I've already been in that site via Omero's 
 > troubleshooting page.
 > My /etc/.java is already world readable and writable, but the error 
 > continues.

Is there also a ".systemPrefs" directory under /etc/.java ? And what
about in ~/.java? There should be a .userPrefs directory.

 > Omero is running as root in a Debian Lenny Linux.
 > I've installed Java with apt-get and downloaded the official installer. 
 > In both, I got the same error.
 > The problem is because of this error, OMERO don't even start.
 > 
 > To deploy omero I use this script:
 > 
 > omero:/var/omero-Beta3.2# cat deploy_server.sh
 > #!/bin/bash
 > 
 > export http_proxy="http://proxy.lan:8080/"
 > export JBOSS_HOME=/var/omero-Beta3.2/jboss-4.2.3.GA/
 > cd /var/omero-Beta3.2/omero
 > java omero deploy
 > $JBOSS_HOME/bin/run.sh
 > 
 > Now, I really don't know how to fix this problem.

One thing mentioned on another bug:

  http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4666397

is to set where the properties get created:

  There is another system property 'java.util.prefs.systemRoot' whose
  default is '/etc/.java'.  Set it on the command line to a directory
  that you have control of and make a .systemPrefs directory in it.

I tested:

  java -Djava.util.prefs.userRoot=/tmp -cp /tmp prefs sys set a 1

This is probably preferable to making everything read/write world,
since some applications may put private information in there.
 
 > Regards

Good luck!
~Josh.

P.S. can you pass along the server logs, possibly after adding:

  set -x

to the top of run.sh?

 > ? Ruben Alves writes:
 >  > Hi all,
 > 
 > Hi Ruben,
 > 
 >  > I've just moved to the last omero public release. But I can't > 
 > understand why I can't deploy omero without this error:
 >  > > 17:54:59,383 INFO  [Log4jService$URLWatchTimerTask] Configuring 
 > from > URL: resource:jboss-log4j.xml
 >  > 2009-03-16 17:55:53,697 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 > 
 > java.util.prefs.FileSystemPreferences$7 run
 >  > WARNING: Prefs file removed in background 
 > /root/.java/.userPrefs/prefs.xml
 >  > 2009-03-16 17:55:53,719 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 > 
 > java.util.prefs.FileSystemPreferences$7 run
 >  > WARNING: Prefs file removed in background 
 > /etc/.java/.systemPrefs/prefs.xml
 >  > > I will appreciate any kind of help.
 > 
 > First, is everything working properly despite the error messages? In
 > our experience, this is an issue with how Java was installed, but is
 > not detrimental to the server's functioning. This bug in the Sun
 > database might be of interest:
 > 
 > http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751177
 > 
 >  > My best regards,
 >  > > //Ruben
 > 
 > Hope that helps,
 > ~Josh
 > 
 > -- 
 > Ruben Alves 
 > 
 > System Analyst 
 > USI @ Instituto de Medicina Molecular
 > Edif?cio Egas Moniz 
 > Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
 > tel: 217999411 ext 47026
 > rubenalves at fm.ul.pt


From rubenalves at fm.ul.pt  Tue Mar 17 15:02:01 2009
From: rubenalves at fm.ul.pt (=?ISO-8859-1?Q?=BB_Ruben_Alves?=)
Date: Tue, 17 Mar 2009 15:02:01 +0000
Subject: [ome-users] Error deploying OMERO 3.2 beta | jboss-log4j.xml
In-Reply-To: <49BF76BC.3080406@fm.ul.pt>
References: <49BE9420.9000001@fm.ul.pt> <49BF76BC.3080406@fm.ul.pt>
Message-ID: <49BFBB69.90208@fm.ul.pt>

Josh, it works now.
I've just change delete all preferences (.java), run OMERO as root, and 
the notice still appear, but OMERO starts perfectly.
I used binaries for PostgresSQL and Java (and not apt-get). And now, 
everything is working fine.
Thank you for your help.

//Ruben


Hi Ruben,

Oh boy. Sounds like we're not getting off the hook so easily. :)

First, I should mention that I couldn't reproduce this running as root
under Ubuntu. I get this message after deleting my preference
directories when I access preferences as root:

  root at millaboula <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>:/etc/.java# java -cp /tmp prefs sys get
  17/03/2009 10:42:44 AM java.util.prefs.FileSystemPreferences$3 run
  INFO: Created system preferences directory in java.home.

? Ruben Alves writes:
 > Hi Josh, in fact I've already been in that site via Omero's 
 > troubleshooting page.
 > My /etc/.java is already world readable and writable, but the error 
 > continues.

Is there also a ".systemPrefs" directory under /etc/.java ? And what
about in ~/.java? There should be a .userPrefs directory.

 > Omero is running as root in a Debian Lenny Linux.
 > I've installed Java with apt-get and downloaded the official installer. 
 > In both, I got the same error.
 > The problem is because of this error, OMERO don't even start.
 > 
 > To deploy omero I use this script:
 > 
 > omero:/var/omero-Beta3.2# cat deploy_server.sh
 > #!/bin/bash
 > 
 > export http_proxy="http://proxy.lan:8080/" <http://proxy.lan:8080/%22>
 > export JBOSS_HOME=/var/omero-Beta3.2/jboss-4.2.3.GA/
 > cd /var/omero-Beta3.2/omero
 > java omero deploy
 > $JBOSS_HOME/bin/run.sh
 > 
 > Now, I really don't know how to fix this problem.

One thing mentioned on another bug:

  http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4666397

is to set where the properties get created:

  There is another system property 'java.util.prefs.systemRoot' whose
  default is '/etc/.java'.  Set it on the command line to a directory
  that you have control of and make a .systemPrefs directory in it.

I tested:

  java -Djava.util.prefs.userRoot=/tmp -cp /tmp prefs sys set a 1

This is probably preferable to making everything read/write world,
since some applications may put private information in there.
 
 > Regards

Good luck!
~Josh.

P.S. can you pass along the server logs, possibly after adding:

  set -x

to the top of run.sh?

 > ? Ruben Alves writes:
 >  > Hi all,
 > 
 > Hi Ruben,
 > 
 >  > I've just moved to the last omero public release. But I can't > 
 > understand why I can't deploy omero without this error:
 >  > > 17:54:59,383 INFO  [Log4jService$URLWatchTimerTask] Configuring 
 > from > URL: resource:jboss-log4j.xml
 >  > 2009-03-16 17:55:53,697 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 > 
 > java.util.prefs.FileSystemPreferences$7 run
 >  > WARNING: Prefs file removed in background 
 > /root/.java/.userPrefs/prefs.xml
 >  > 2009-03-16 17:55:53,719 ERROR [STDERR] (main) 16/Mar/2009 17:55:53 > 
 > java.util.prefs.FileSystemPreferences$7 run
 >  > WARNING: Prefs file removed in background 
 > /etc/.java/.systemPrefs/prefs.xml
 >  > > I will appreciate any kind of help.
 > 
 > First, is everything working properly despite the error messages? In
 > our experience, this is an issue with how Java was installed, but is
 > not detrimental to the server's functioning. This bug in the Sun
 > database might be of interest:
 > 
 > http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4751177
 > 
 >  > My best regards,
 >  > > //Ruben
 > 
 > Hope that helps,
 > ~Josh
 > 
 > -- 
 > Ruben Alves 
 > 
 > System Analyst 
 > USI @ Instituto de Medicina Molecular
 > Edif?cio Egas Moniz 
 > Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
 > tel: 217999411 ext 47026
 > rubenalves at fm.ul.pt <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>



-- 
Ruben Alves 

System Analyst 
USI @ Instituto de Medicina Molecular
Edif?cio Egas Moniz 
Av. Prof. Egas Moniz 1649-028 Lisboa Portugal 
tel: 217999411 ext 47026
rubenalves at fm.ul.pt



From josh.moore at gmx.de  Fri Mar 20 15:31:40 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Fri, 20 Mar 2009 16:31:40 +0100
Subject: [ome-users] OMERO importer question
In-Reply-To: <20090320150002.6c2mxvzbwg0oco4g@www.staffmail.ed.ac.uk>
References: <20090320150002.6c2mxvzbwg0oco4g@www.staffmail.ed.ac.uk>
Message-ID: <18883.46812.485093.978675@echo.mac>

James Perry writes:
 > Hi Josh,

Hi James,

 > I had a quick question about the OMERO importer. I have used it on
 > various different machines and OMERO servers. Sometimes the
 > checkbox for uploading the original file is there and sometimes it
 > isn't. Is there some setting either in the client or the server
 > that could cause this checkbox not to be there? I ask mainly
 > because the integration with DiGS that we've developed only works
 > if the original files are uploaded to OMERO so it would be useful
 > to get this working consistently.

I would think that that has more to do with the client version which
you are using rather than the particular instance you're talking to,
but I may very well be wrong.  I'm passing the buck to the list. :)

Take care,
~Josh.


From palmeida at igc.gulbenkian.pt  Wed Mar 25 18:04:11 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Wed, 25 Mar 2009 18:04:11 +0000
Subject: [ome-users] Making Omero work with Ice
Message-ID: <200903251804.12080.palmeida@igc.gulbenkian.pt>

Hi,

I had an OmeroGrid installation that was working, but I had to reinstall the 
OS and now I am getting an error. When I run:

bin/omero admin start 

there is not output, but then I run:

bin/omero admin deploy etc/grid/default.xml

and I get this:

error: IceGrid::DeploymentException:
couldn't load `Blitz-0' on node `master':
can't set permissions on directory 
`/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'

-----------

When I reinstalled the OS I had to install Ice, PostgreSQL, etc, but I didn't 
touch the Omero folder. Do you have any idea about what I may have forgotten 
that would cause this error? I also tried compiling Omero.blitz, but I get 
this error when running 'bin/omero admin start':

icegridnode: failure occurred in daemon:
service caught unhandled Ice exception:
../../include/Ice/BasicStream.h:412: Ice::UnmarshalOutOfBoundsException:
protocol error: out of bounds during unmarshaling
from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
../../include/Ice/BasicStream.h:412: Ice::UnmarshalOutOfBoundsException:
protocol error: out of bounds during unmarshaling


Thanks for any help,
Paulo


From palmeida at igc.gulbenkian.pt  Wed Mar 25 18:28:44 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Wed, 25 Mar 2009 18:28:44 +0000
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <200903251804.12080.palmeida@igc.gulbenkian.pt>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
Message-ID: <200903251828.45155.palmeida@igc.gulbenkian.pt>

Hi again...

Ignore my last e-mail, it really was a simple permissions problem. I didn't 
think it was because I tried running as root, but the directory was mounted 
in NFS so root didn't have access either. It seems to be running fine now.

Best,
Paulo

On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
> Hi,
>
> I had an OmeroGrid installation that was working, but I had to reinstall
> the OS and now I am getting an error. When I run:
>
> bin/omero admin start
>
> there is not output, but then I run:
>
> bin/omero admin deploy etc/grid/default.xml
>
> and I get this:
>
> error: IceGrid::DeploymentException:
> couldn't load `Blitz-0' on node `master':
> can't set permissions on directory
> `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
>
> -----------
>
> When I reinstalled the OS I had to install Ice, PostgreSQL, etc, but I
> didn't touch the Omero folder. Do you have any idea about what I may have
> forgotten that would cause this error? I also tried compiling Omero.blitz,
> but I get this error when running 'bin/omero admin start':
>
> icegridnode: failure occurred in daemon:
> service caught unhandled Ice exception:
> ../../include/Ice/BasicStream.h:412: Ice::UnmarshalOutOfBoundsException:
> protocol error: out of bounds during unmarshaling
> from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
> ../../include/Ice/BasicStream.h:412: Ice::UnmarshalOutOfBoundsException:
> protocol error: out of bounds during unmarshaling
>
>
> Thanks for any help,
> Paulo
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users




From josh.moore at gmx.de  Wed Mar 25 19:23:11 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Wed, 25 Mar 2009 20:23:11 +0100
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <200903251828.45155.palmeida@igc.gulbenkian.pt>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903251828.45155.palmeida@igc.gulbenkian.pt>
Message-ID: <18890.33951.705444.414496@echo.mac>


Paulo Almeida writes:
 > Hi again...
 > 
 > Ignore my last e-mail, it really was a simple permissions problem. I didn't 
 > think it was because I tried running as root, but the directory was mounted 
 > in NFS so root didn't have access either. It seems to be running fine now.

Whew. Good to hear! :) Thanks for letting us know, Paulo.

~J.

 > Best,
 > Paulo
 > 
 > On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
 > > Hi,
 > >
 > > I had an OmeroGrid installation that was working, but I had to reinstall
 > > the OS and now I am getting an error. When I run:
 > >
 > > bin/omero admin start
 > >
 > > there is not output, but then I run:
 > >
 > > bin/omero admin deploy etc/grid/default.xml
 > >
 > > and I get this:
 > >
 > > error: IceGrid::DeploymentException:
 > > couldn't load `Blitz-0' on node `master':
 > > can't set permissions on directory
 > > `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
 > >
 > > -----------
 > >
 > > When I reinstalled the OS I had to install Ice, PostgreSQL, etc, but I
 > > didn't touch the Omero folder. Do you have any idea about what I may have
 > > forgotten that would cause this error? I also tried compiling Omero.blitz,
 > > but I get this error when running 'bin/omero admin start':
 > >
 > > icegridnode: failure occurred in daemon:
 > > service caught unhandled Ice exception:
 > > ../../include/Ice/BasicStream.h:412: Ice::UnmarshalOutOfBoundsException:
 > > protocol error: out of bounds during unmarshaling
 > > from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
 > > ../../include/Ice/BasicStream.h:412: Ice::UnmarshalOutOfBoundsException:
 > > protocol error: out of bounds during unmarshaling


From ajpatterson at lifesci.dundee.ac.uk  Thu Mar 26 14:29:08 2009
From: ajpatterson at lifesci.dundee.ac.uk (Andrew Patterson)
Date: Thu, 26 Mar 2009 14:29:08 +0000
Subject: [ome-users] OMERO
In-Reply-To: <A31CEC9B5BDD9C46992DD2D02F1EA3F85F0DF4D462@EXC-MBX2.cfs.le.ac.uk>
References: <A31CEC9B5BDD9C46992DD2D02F1EA3F85F0DF4D462@EXC-MBX2.cfs.le.ac.uk>
Message-ID: <5E75911D-36C4-4B3A-8374-1473B0786C69@lifesci.dundee.ac.uk>

Hello Kees,

I am copying this discussion onto the OME-USERS mailing list.

I think some of your questions are general enough to be of interest to  
others and we may get some other advice from our users.

On 24 Mar 2009, at 17:58, Straatman, Dr K.R. wrote:
>
> I run the advanced light microscopy facilities in the University of  
> Leicester, UK. We have microscopes in different buildings and will  
> expand further during this year. Therefore, I look for a way to  
> store data and have easy access to the data at multiple locations.  
> We have some funding for a web server and I have been testing OME  
> and OMERO in collaboration with the computer centre. At the moment  
> we have around 55 active users.

> From what I have seen OMERO seems to be easier to use. However, I  
> have some questions/problems and I am not sure where to ask them as  
> most of the OME website seems to focus on OME and not OMERO.

The OMERO section for the site is located at:
http://www.openmicroscopy.org/site/documents/data-management/omero
We are preparing an update to this section at the moment to go along  
with the release of OMERO4.

A lot of the data links here go to our Trac systems. This is updated  
by the developers and has general documentation as well as detailed  
work tickets and version information.
>
> May be you can direct me in the right direction or you might be able  
> to answer some of the questions
> -          I was able to upload images to the database, but I seem  
> not to be able to delete images. Is that correct?

Deletion is present in OMERO 4 which is being packaged for released as  
we speak.

> -          I have the same problem with Tags. I have created some  
> tags and they are partly nested where I  wanted single layers (don?t  
> know how this happened yet). However, I don?t seem to be able to  
> undo this.

We have tagsets in OMERO.insight. We don't have a flattened view of  
them, they remain in their tagset in the tag tab of the datamanager.  
When adding a new tag to an object it shows all tags flattened.  
Searching will search on a tagset or tag regardless.
Tags don't have to belong to a tagset just as datasets don't have to  
belong to projects anymore. Tagsets are just a tag of a tag.

> -          How can I do a search for images with the same Tag?

There is a search option at the top of the window in the new  
OMERO.insight client. This will search within your current datasets  
for tags, ratings, comments, attachments, etc.

You can also change from a top level project->dataset view to a top  
level Tag view. This allows you to look at all the images you tagged  
with a keyword like "metaphase" for example.

> -          Is it possible to move data within the database. For  
> example, a PI has over the years several students working on the  
> same project, each student with his/her own database under the PIs  
> account and wants to put all the data in one collection and not  
> dependent on the students anymore.

Each user has there own account. Several accounts can belong to the  
same group so they can see each other's data. Using the current  
clients you cannot move the data from belonging to one user to  
another. It would be possible to do this in the server using custom  
code against the API or a script running on the DB directly. Using the  
API would be the safer option.

> Or does this has to be solved by choosing the right tags?

Not really, as I think you are only viewing the Tags for one user  
account at a time.

> -          In our situation we would image on a microscope, add the  
> images to the database and move to a different location to analyse  
> the images. This could be ImageJ, Volocity, Imaris, Huygens  
> deconvolution, or any other software package needed. As far as I can  
> see there seem not to be any option  to do this. I tried the ImageJ  
> OME download option but it failed. Would this be possible and how  
> would this work?

The ImageJ OMERO plug-in is being re-written to work with the new  
server at the moment.

> -          Would it be possible to write images directly from the  
> microscope into the database? This would save a lot of time.

We have a product called OMERO.fs that will watch directories on a  
file-system and import the files automatically to the OMERO.server.  
The resulting import is a metadata only import with the pixel data  
remaining in the original file on the file-system. Thus, the original  
file will be reread by OMERO.fs if pixel data for the image is  
requested. The OMERO.fs process can either be on a different machine  
to the OMERO.server process or the same machine.

> -          What if the analysis software does not read OME-tiff  
> files? For example, if we want to analyse data in the future with  
> not yet developed software?

An OME-TIFF file conforms to the TIFF standard so can be read by any  
application that can read a TIFF. If the application does not  
understand OME-TIFF it will not see the metadata in the file and may  
or may not preserve it.

If you are developing you own software you can use our Bio-Formats  
Java library to read/write OME-TIFF.

> Are there somewhere options to upload the data in its original  
> format? Or will other software just read the tiff information?

You can at import time archive the original file on the server. The  
OMERO.insight client will then let you retrieve this original format  
file at a future date. This means the OMERO.server can also function  
as your main image archive. This does use additional disk space so may  
or may not make sense depending on you IT setup.

> -          What is the support in the community for the OMERO format?
> 6-7 years ago we changed images to the ICS/IDS format,
> but never got funding for a server system and now there seems no  
> development on the SIDB anymore. As we have many users I need a  
> system that is as much future proof as possible.

OMERO can read ICS/IDS files.

This is a hard question to answer but I think we are doing well. For  
example, just looking at some stats I see we have over 500 unique  
server instances that have been started up in the last year.

We have good funding in place for the next few years and have no  
intention to stop development any time soon. We have had several  
successful collaborations with academia and also with companies and  
publishers through our commercial partner Glencoe Software. See:
http://glencoesoftware.com/
for details about Glencoe, and:
http://jcb-dataviewer.rupress.org/
for a good example of something which utilises parts of OMERO.server /  
OMERO.web in a commercial application. Some of our other commercial  
partners include PerkinElmer and Deltavision.

Hope this helps,

Andrew

Andrew Patterson
ajpatterson at lifesci.dundee.ac.uk
Software Developer, Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression, University  
of Dundee




From palmeida at igc.gulbenkian.pt  Thu Mar 26 17:28:05 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Thu, 26 Mar 2009 17:28:05 +0000
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <18890.33951.705444.414496@echo.mac>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903251828.45155.palmeida@igc.gulbenkian.pt>
	<18890.33951.705444.414496@echo.mac>
Message-ID: <200903261728.05846.palmeida@igc.gulbenkian.pt>

Hello,

Unfortunately I got stuck again... After running 'bin/omero admin start' 
and 'bin/omero admin deploy', when I run 'bin/omero admin status' I get:

palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin status
node is up
Server not reachable

Running 'bin/omero admin adduser' displays the usage help message for the 
omero command and trying the script in

 http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid

returns an error after 'sf = c.createSession()'

>>> sf = c.createSession()
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py", line 334, 
in createSession
    prx = self.getRouter(self.__ic).createSession(username, password)
  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py", line 104, 
in createSession
    return _M_Glacier2.Router._op_createSession.invoke(self, ((userId, 
password), _ctx))
Glacier2.PermissionDeniedException: 
exception ::Glacier2::PermissionDeniedException
{
    reason = internal server error
}


But I guess that is expected if the server is unreachable and I can't add 
users. Do you have any idea why this would happen? I checked that postgre is 
running and the database omero4 exists and is owned by omero, but it is 
empty:

omero4=> \d
No relations found.

Shouldn't the deploy command create the tables?

Thanks,
Paulo

On Wednesday 25 March 2009 19:23:11 you wrote:
> Paulo Almeida writes:
>  > Hi again...
>  >
>  > Ignore my last e-mail, it really was a simple permissions problem. I
>  > didn't think it was because I tried running as root, but the directory
>  > was mounted in NFS so root didn't have access either. It seems to be
>  > running fine now.
>
> Whew. Good to hear! :) Thanks for letting us know, Paulo.
>
> ~J.
>
>  > Best,
>  > Paulo
>  >
>  > On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
>  > > Hi,
>  > >
>  > > I had an OmeroGrid installation that was working, but I had to
>  > > reinstall the OS and now I am getting an error. When I run:
>  > >
>  > > bin/omero admin start
>  > >
>  > > there is not output, but then I run:
>  > >
>  > > bin/omero admin deploy etc/grid/default.xml
>  > >
>  > > and I get this:
>  > >
>  > > error: IceGrid::DeploymentException:
>  > > couldn't load `Blitz-0' on node `master':
>  > > can't set permissions on directory
>  > > `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
>  > >
>  > > -----------
>  > >
>  > > When I reinstalled the OS I had to install Ice, PostgreSQL, etc, but I
>  > > didn't touch the Omero folder. Do you have any idea about what I may
>  > > have forgotten that would cause this error? I also tried compiling
>  > > Omero.blitz, but I get this error when running 'bin/omero admin
>  > > start':
>  > >
>  > > icegridnode: failure occurred in daemon:
>  > > service caught unhandled Ice exception:
>  > > ../../include/Ice/BasicStream.h:412:
>  > > Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
>  > > during unmarshaling
>  > > from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
>  > > ../../include/Ice/BasicStream.h:412:
>  > > Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
>  > > during unmarshaling




From josh.moore at gmx.de  Thu Mar 26 18:07:44 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Thu, 26 Mar 2009 19:07:44 +0100
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <200903261728.05846.palmeida@igc.gulbenkian.pt>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903251828.45155.palmeida@igc.gulbenkian.pt>
	<18890.33951.705444.414496@echo.mac>
	<200903261728.05846.palmeida@igc.gulbenkian.pt>
Message-ID: <18891.50288.216698.840303@echo.mac>

Paulo Almeida writes:
 > Hello,

Hi Paulo.

 > Unfortunately I got stuck again... After running 'bin/omero admin start' 
 > and 'bin/omero admin deploy', when I run 'bin/omero admin status' I get:
 > 
 > palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin status
 > node is up
 > Server not reachable

Hmmmm.....ok. That could be various things. Could you send us the
var/log/* files?

 > Running 'bin/omero admin adduser' displays the usage help message for the 
 > omero command and trying the script in

adduser got taken out of this release for lack of testing. Can you
point me to where you found it listed in the documentation so I can
quietly delete it? :)

 >  http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
 > 
 > returns an error after 'sf = c.createSession()'
 > 
 > >>> sf = c.createSession()
 > Traceback (most recent call last):
 >   File "<stdin>", line 1, in <module>
 >   File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py", line 334, 
 > in createSession
 >     prx = self.getRouter(self.__ic).createSession(username, password)
 >   File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py", line 104, 
 > in createSession
 >     return _M_Glacier2.Router._op_createSession.invoke(self, ((userId, 
 > password), _ctx))
 > Glacier2.PermissionDeniedException: 
 > exception ::Glacier2::PermissionDeniedException
 > {
 >     reason = internal server error
 > }

This is most likely that your database is not properly configured. But
the logs would tell us.

 > But I guess that is expected if the server is unreachable and I can't add 
 > users. Do you have any idea why this would happen? I checked that postgre is 
 > running and the database omero4 exists and is owned by omero, but it is 
 > empty:
 > 
 > omero4=> \d
 > No relations found.

Aha. Cancel the logs, that would be the problem.

 > Shouldn't the deploy command create the tables?

No. The deploy command -- which is no longer necessary by the way --
deploys the definition of your grid, i.e. etc/grid/default.xml. It
defines which processes will be started and what properties they
receive. It doesn't do anything with the database, since that persists
longer than a single server start. (When I say deploy is no longer
necessary, I mean that a deploy happens automatically every time you
call "bin/omero admin start" so only if you want to change the
configuration of a running grid do you need "deploy".)

Now, we're hard at work on the release documentation and they're *almost*
done, but for now you'll need to look at the RC1 email I sent:

 http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/001184.html

for how to create your database. In summary, your next steps are:

  bin/omero db script

which creates OMERO4__0.sql. If you haven't added the PLPGSQL language
to your database, then you'll need to:

  createlang plpgsql omero4

and finally:

  psql omero4 < OMERO4__0.sql
  bin/omero admin stop
  bin/omero admin start

For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin to
add new users. If the command-line addition is of interest, we'll
certainly have that re-scheduled for an upcoming release.

 > Thanks,
 > Paulo

No problem and cheers,
~Josh

 > On Wednesday 25 March 2009 19:23:11 you wrote:
 > > Paulo Almeida writes:
 > >  > Hi again...
 > >  >
 > >  > Ignore my last e-mail, it really was a simple permissions problem. I
 > >  > didn't think it was because I tried running as root, but the directory
 > >  > was mounted in NFS so root didn't have access either. It seems to be
 > >  > running fine now.
 > >
 > > Whew. Good to hear! :) Thanks for letting us know, Paulo.
 > >
 > > ~J.
 > >
 > >  > Best,
 > >  > Paulo
 > >  >
 > >  > On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
 > >  > > Hi,
 > >  > >
 > >  > > I had an OmeroGrid installation that was working, but I had to
 > >  > > reinstall the OS and now I am getting an error. When I run:
 > >  > >
 > >  > > bin/omero admin start
 > >  > >
 > >  > > there is not output, but then I run:
 > >  > >
 > >  > > bin/omero admin deploy etc/grid/default.xml
 > >  > >
 > >  > > and I get this:
 > >  > >
 > >  > > error: IceGrid::DeploymentException:
 > >  > > couldn't load `Blitz-0' on node `master':
 > >  > > can't set permissions on directory
 > >  > > `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
 > >  > >
 > >  > > -----------
 > >  > >
 > >  > > When I reinstalled the OS I had to install Ice, PostgreSQL, etc, but I
 > >  > > didn't touch the Omero folder. Do you have any idea about what I may
 > >  > > have forgotten that would cause this error? I also tried compiling
 > >  > > Omero.blitz, but I get this error when running 'bin/omero admin
 > >  > > start':
 > >  > >
 > >  > > icegridnode: failure occurred in daemon:
 > >  > > service caught unhandled Ice exception:
 > >  > > ../../include/Ice/BasicStream.h:412:
 > >  > > Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
 > >  > > during unmarshaling
 > >  > > from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
 > >  > > ../../include/Ice/BasicStream.h:412:
 > >  > > Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
 > >  > > during unmarshaling
 > 


From michael.j.mccaughey at Vanderbilt.Edu  Thu Mar 26 18:15:17 2009
From: michael.j.mccaughey at Vanderbilt.Edu (McCaughey, Michael J)
Date: Thu, 26 Mar 2009 13:15:17 -0500
Subject: [ome-users] Blitz build problem
Message-ID: <1EB11BDDD4FDAE4F88B04C3E0615F671F51819@mailbe05.mc.vanderbilt.edu>

I'm trying to a new build of Omero4-rc3 (FC10 x64), and blitz build is complaining about missing files:

Entering /home/mrmike/Documents/omero-4.0-rc3/components/blitz...

retrieve:
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/libs
:: Ivy 2.0.0 - 20090108225011 :: http://ant.apache.org/ivy/ ::
:: loading settings :: file = /home/mrmike/Documents/omero-4.0-rc3/etc/ivysettings.xml

prepare:
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/generated/.done
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/generated/src
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/classes
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/test-classes
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/reports
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/generated/resources
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/classes
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/generated/resources
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/classes
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/generated/resources
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/classes
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/generated/resources
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/classes

generate:
Copying 10 files to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/classes
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/classes

icegen-init:
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/combined/omero/api
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/target/combined/omero/model
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/generated/omero/api
Created dir: /home/mrmike/Documents/omero-4.0-rc3/components/blitz/generated/omero/model

icegen1:
Parsing 7 file(s).
Parsing 7 file(s).
Parsing 7 file(s).
Parsing 7 file(s).
Parsing 7 file(s).

icegen2:
Copying 126 files to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/generated
Copying 126 files to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/generated
Copying 126 files to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/generated
Copying 126 files to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/generated
Copying 126 files to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/generated
Copying 1 file to /home/mrmike/Documents/omero-4.0-rc3/components/blitz/generated
os.chdir('/home/mrmike/Documents/omero-4.0-rc3/components/blitz/resources')
slice(["omero/API.h", "omero/API.cpp"], ["omero/API.ice"])
os.chdir('/home/mrmike/Documents/omero-4.0-rc3/components/blitz')
scons: *** [omero/API.h] No such file or directory

BUILD FAILED
/home/mrmike/Documents/omero-4.0-rc3/build.xml:117: The following error occurred while executing this line:
/home/mrmike/Documents/omero-4.0-rc3/components/antlib/resources/global.xml:77: The following error occurred while executing this line:
/home/mrmike/Documents/omero-4.0-rc3/components/blitz/build.xml:201: The following error occurred while executing this line:
/home/mrmike/Documents/omero-4.0-rc3/components/antlib/resources/global.xml:161: exec returned: 2


I've checked /omero-4.0-rc3/components/blitz/resources/omero and while API.ice is there, API.h and API.cc are not.
Anyone seen this before or can make a suggestion?

I also had an issue with a non-UTF-8 character in a comment in /omero-4.0-rc3/components/src/ome/api/IRenderingSettings.java, but that was easily fixed.
I did the svn co about 1700GMT today, so it should be current.

Thanks,
Mike

Michael J. McCaughey, PhD
Molecular Physiology and Biophysics
U9203 MRBIII
6-6175
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From josh.moore at gmx.de  Thu Mar 26 18:47:18 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Thu, 26 Mar 2009 19:47:18 +0100
Subject: [ome-users]  Blitz build problem
In-Reply-To: <1EB11BDDD4FDAE4F88B04C3E0615F671F51819@mailbe05.mc.vanderbilt.edu>
References: <1EB11BDDD4FDAE4F88B04C3E0615F671F51819@mailbe05.mc.vanderbilt.edu>
Message-ID: <18891.52662.679038.400565@echo.mac>


Hi Mike,

McCaughey, Michael J writes:
 > I'm trying to a new build of Omero4-rc3 (FC10 x64), and blitz build is complaining about missing files:
 > 
 > Entering /home/mrmike/Documents/omero-4.0-rc3/components/blitz...
...
 > os.chdir('/home/mrmike/Documents/omero-4.0-rc3/components/blitz')
 > scons: *** [omero/API.h] No such file or directory


 > Anyone seen this before or can make a suggestion?

Another case of a horrible, horrible error message. The file that
scons can't find while trying to *create* omero/API.h is actually the
executable:

  slice2cpp

You may need to add another rpm to have all the slice2* generators
installed. How did you install Ice?

 > I also had an issue with a non-UTF-8 character in a comment in
 > /omero-4.0-rc3/components/src/ome/api/IRenderingSettings.java, but
 > that was easily fixed.  I did the svn co about 1700GMT today, so it
 > should be current.

Ah, thanks. We'll look into that.

 > Thanks,
 > Mike

Cheers,
~Josh.


From palmeida at igc.gulbenkian.pt  Thu Mar 26 20:00:33 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Thu, 26 Mar 2009 20:00:33 +0000
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <18891.50288.216698.840303@echo.mac>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903261728.05846.palmeida@igc.gulbenkian.pt>
	<18891.50288.216698.840303@echo.mac>
Message-ID: <200903262000.34165.palmeida@igc.gulbenkian.pt>

Hi Josh,

Thank you very much for the instructions. Regarding your questions, I saw the 
adduser option when I ran /bin/omero admin with no argument. That returns 
usage instructions that include 'adduser' as an option. Command line addition 
is not important to us, I was trying that because I thought it was the only 
way.

But now I'm not sure I'm using the right version. I have been using svn and 
just did 'svn up' (at revision 4134), but when I tried:

bin/omero db script

I got:

Unknown command: db script

Running bin/omero without arguments and typing '?' gives me this list of 
commands:

admin
 config
 download
 help
 load
 node
 quit
 script
 server
 setup
 submit
 upload
 version

The version is "OmeroCli client, version 1.0".

I also tried installing omero3.2 and I get the same error when creating the 
session within an omero script:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py", line 334, 
in createSession
    prx = self.getRouter(self.__ic).createSession(username, password)
  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py", line 104, 
in createSession
    return _M_Glacier2.Router._op_createSession.invoke(self, ((userId, 
password), _ctx))
Ice.ConnectionRefusedException: Ice.ConnectionRefusedException:
Connection refused

I am attaching omero-Beta3.2/jboss-4.2.3.GA/server/default/log/server.log in 
case it may help understand that error.

Thanks again,
Paulo


On Thursday 26 March 2009 18:07:44 you wrote:
> Paulo Almeida writes:
>  > Hello,
>
> Hi Paulo.
>
>  > Unfortunately I got stuck again... After running 'bin/omero admin start'
>  > and 'bin/omero admin deploy', when I run 'bin/omero admin status' I get:
>  >
>  > palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin status
>  > node is up
>  > Server not reachable
>
> Hmmmm.....ok. That could be various things. Could you send us the
> var/log/* files?
>
>  > Running 'bin/omero admin adduser' displays the usage help message for
>  > the omero command and trying the script in
>
> adduser got taken out of this release for lack of testing. Can you
> point me to where you found it listed in the documentation so I can
> quietly delete it? :)
>
>  >  http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
>  >
>  > returns an error after 'sf = c.createSession()'
>  >
>  > >>> sf = c.createSession()
>  >
>  > Traceback (most recent call last):
>  >   File "<stdin>", line 1, in <module>
>  >   File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
>  > line 334, in createSession
>  >     prx = self.getRouter(self.__ic).createSession(username, password)
>  >   File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py", line
>  > 104, in createSession
>  >     return _M_Glacier2.Router._op_createSession.invoke(self, ((userId,
>  > password), _ctx))
>  > Glacier2.PermissionDeniedException:
>  > exception ::Glacier2::PermissionDeniedException
>  > {
>  >     reason = internal server error
>  > }
>
> This is most likely that your database is not properly configured. But
> the logs would tell us.
>
>  > But I guess that is expected if the server is unreachable and I can't
>  > add users. Do you have any idea why this would happen? I checked that
>  > postgre is running and the database omero4 exists and is owned by omero,
>  > but it is empty:
>  >
>  > omero4=> \d
>  > No relations found.
>
> Aha. Cancel the logs, that would be the problem.
>
>  > Shouldn't the deploy command create the tables?
>
> No. The deploy command -- which is no longer necessary by the way --
> deploys the definition of your grid, i.e. etc/grid/default.xml. It
> defines which processes will be started and what properties they
> receive. It doesn't do anything with the database, since that persists
> longer than a single server start. (When I say deploy is no longer
> necessary, I mean that a deploy happens automatically every time you
> call "bin/omero admin start" so only if you want to change the
> configuration of a running grid do you need "deploy".)
>
> Now, we're hard at work on the release documentation and they're *almost*
> done, but for now you'll need to look at the RC1 email I sent:
>
> 
> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/001184.ht
>ml
>
> for how to create your database. In summary, your next steps are:
>
>   bin/omero db script
>
> which creates OMERO4__0.sql. If you haven't added the PLPGSQL language
> to your database, then you'll need to:
>
>   createlang plpgsql omero4
>
> and finally:
>
>   psql omero4 < OMERO4__0.sql
>   bin/omero admin stop
>   bin/omero admin start
>
> For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin to
> add new users. If the command-line addition is of interest, we'll
> certainly have that re-scheduled for an upcoming release.
>
>  > Thanks,
>  > Paulo
>
> No problem and cheers,
> ~Josh
>
>  > On Wednesday 25 March 2009 19:23:11 you wrote:
>  > > Paulo Almeida writes:
>  > >  > Hi again...
>  > >  >
>  > >  > Ignore my last e-mail, it really was a simple permissions problem.
>  > >  > I didn't think it was because I tried running as root, but the
>  > >  > directory was mounted in NFS so root didn't have access either. It
>  > >  > seems to be running fine now.
>  > >
>  > > Whew. Good to hear! :) Thanks for letting us know, Paulo.
>  > >
>  > > ~J.
>  > >
>  > >  > Best,
>  > >  > Paulo
>  > >  >
>  > >  > On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
>  > >  > > Hi,
>  > >  > >
>  > >  > > I had an OmeroGrid installation that was working, but I had to
>  > >  > > reinstall the OS and now I am getting an error. When I run:
>  > >  > >
>  > >  > > bin/omero admin start
>  > >  > >
>  > >  > > there is not output, but then I run:
>  > >  > >
>  > >  > > bin/omero admin deploy etc/grid/default.xml
>  > >  > >
>  > >  > > and I get this:
>  > >  > >
>  > >  > > error: IceGrid::DeploymentException:
>  > >  > > couldn't load `Blitz-0' on node `master':
>  > >  > > can't set permissions on directory
>  > >  > > `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
>  > >  > >
>  > >  > > -----------
>  > >  > >
>  > >  > > When I reinstalled the OS I had to install Ice, PostgreSQL, etc,
>  > >  > > but I didn't touch the Omero folder. Do you have any idea about
>  > >  > > what I may have forgotten that would cause this error? I also
>  > >  > > tried compiling Omero.blitz, but I get this error when running
>  > >  > > 'bin/omero admin start':
>  > >  > >
>  > >  > > icegridnode: failure occurred in daemon:
>  > >  > > service caught unhandled Ice exception:
>  > >  > > ../../include/Ice/BasicStream.h:412:
>  > >  > > Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
>  > >  > > during unmarshaling
>  > >  > > from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
>  > >  > > ../../include/Ice/BasicStream.h:412:
>  > >  > > Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
>  > >  > > during unmarshaling


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From michael.j.mccaughey at Vanderbilt.Edu  Thu Mar 26 20:21:59 2009
From: michael.j.mccaughey at Vanderbilt.Edu (McCaughey, Michael J)
Date: Thu, 26 Mar 2009 15:21:59 -0500
Subject: [ome-users] Blitz build problem
References: <1EB11BDDD4FDAE4F88B04C3E0615F671F51819@mailbe05.mc.vanderbilt.edu>
	<18891.52662.679038.400565@echo.mac>
Message-ID: <1EB11BDDD4FDAE4F88B04C3E0615F671F5181A@mailbe05.mc.vanderbilt.edu>

I installed Ice from rpm, and didn't get all the devel packages.  That was the problem.

FYI, the two files that had non UTF-8 chars are:
omero-4.0-rc3/components/src/ome/api/IRenderingSettings.java  Line 75
omero-4.0-rc3/components/blitz/src/ome/api/client.java  Line 797

Possibly generated during the co, but I thought you might want to know in case they are actually present in the source files.

Thanks for the help!

Mike

Michael J. McCaughey, PhD
Molecular Physiology and Biophysics
U9203 MRBIII
6-6175



-----Original Message-----
From: ome-users-bounces at lists.openmicroscopy.org.uk on behalf of josh.moore at gmx.de
Sent: Thu 3/26/2009 1:47 PM
To: McCaughey, Michael J
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: [ome-users]  Blitz build problem
 

Hi Mike,

McCaughey, Michael J writes:
 > I'm trying to a new build of Omero4-rc3 (FC10 x64), and blitz build is complaining about missing files:
 > 
 > Entering /home/mrmike/Documents/omero-4.0-rc3/components/blitz...
...
 > os.chdir('/home/mrmike/Documents/omero-4.0-rc3/components/blitz')
 > scons: *** [omero/API.h] No such file or directory


 > Anyone seen this before or can make a suggestion?

Another case of a horrible, horrible error message. The file that
scons can't find while trying to *create* omero/API.h is actually the
executable:

  slice2cpp

You may need to add another rpm to have all the slice2* generators
installed. How did you install Ice?

 > I also had an issue with a non-UTF-8 character in a comment in
 > /omero-4.0-rc3/components/src/ome/api/IRenderingSettings.java, but
 > that was easily fixed.  I did the svn co about 1700GMT today, so it
 > should be current.

Ah, thanks. We'll look into that.

 > Thanks,
 > Mike

Cheers,
~Josh.
_______________________________________________
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 callan at blackcat.ca  Thu Mar 26 20:42:06 2009
From: callan at blackcat.ca (Chris Allan)
Date: Thu, 26 Mar 2009 20:42:06 +0000
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <200903262000.34165.palmeida@igc.gulbenkian.pt>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903261728.05846.palmeida@igc.gulbenkian.pt>
	<18891.50288.216698.840303@echo.mac>
	<200903262000.34165.palmeida@igc.gulbenkian.pt>
Message-ID: <E3F1AD52-2869-4BA1-A8AB-25B6916C8A59@blackcat.ca>

Hi Paulo,

Something seems very wonky here. r4134 is OMERO Trunk and "db script"  
has been present for a while. Also, the Beta4 series does not use  
JBoss so is that server.log from your production installation?

I'd start from "scratch" on your test OMERO checkout by running:

  * ./build.py clean ; ./build.py
  * cd dist
  * bin/omero db script

and then see where we are.

Ciao.

-Chris

On 26 Mar 2009, at 20:00, Paulo Almeida wrote:

> Hi Josh,
>
> Thank you very much for the instructions. Regarding your questions,  
> I saw the
> adduser option when I ran /bin/omero admin with no argument. That  
> returns
> usage instructions that include 'adduser' as an option. Command line  
> addition
> is not important to us, I was trying that because I thought it was  
> the only
> way.
>
> But now I'm not sure I'm using the right version. I have been using  
> svn and
> just did 'svn up' (at revision 4134), but when I tried:
>
> bin/omero db script
>
> I got:
>
> Unknown command: db script
>
> Running bin/omero without arguments and typing '?' gives me this  
> list of
> commands:
>
> admin
> config
> download
> help
> load
> node
> quit
> script
> server
> setup
> submit
> upload
> version
>
> The version is "OmeroCli client, version 1.0".
>
> I also tried installing omero3.2 and I get the same error when  
> creating the
> session within an omero script:
>
> Traceback (most recent call last):
>  File "<stdin>", line 1, in <module>
>  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",  
> line 334,
> in createSession
>    prx = self.getRouter(self.__ic).createSession(username, password)
>  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",  
> line 104,
> in createSession
>    return _M_Glacier2.Router._op_createSession.invoke(self, ((userId,
> password), _ctx))
> Ice.ConnectionRefusedException: Ice.ConnectionRefusedException:
> Connection refused
>
> I am attaching omero-Beta3.2/jboss-4.2.3.GA/server/default/log/ 
> server.log in
> case it may help understand that error.
>
> Thanks again,
> Paulo
>
>
> On Thursday 26 March 2009 18:07:44 you wrote:
>> Paulo Almeida writes:
>>> Hello,
>>
>> Hi Paulo.
>>
>>> Unfortunately I got stuck again... After running 'bin/omero admin  
>>> start'
>>> and 'bin/omero admin deploy', when I run 'bin/omero admin status'  
>>> I get:
>>>
>>> palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin status
>>> node is up
>>> Server not reachable
>>
>> Hmmmm.....ok. That could be various things. Could you send us the
>> var/log/* files?
>>
>>> Running 'bin/omero admin adduser' displays the usage help message  
>>> for
>>> the omero command and trying the script in
>>
>> adduser got taken out of this release for lack of testing. Can you
>> point me to where you found it listed in the documentation so I can
>> quietly delete it? :)
>>
>>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
>>>
>>> returns an error after 'sf = c.createSession()'
>>>
>>>>>> sf = c.createSession()
>>>
>>> Traceback (most recent call last):
>>>  File "<stdin>", line 1, in <module>
>>>  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
>>> line 334, in createSession
>>>    prx = self.getRouter(self.__ic).createSession(username, password)
>>>  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",  
>>> line
>>> 104, in createSession
>>>    return _M_Glacier2.Router._op_createSession.invoke(self,  
>>> ((userId,
>>> password), _ctx))
>>> Glacier2.PermissionDeniedException:
>>> exception ::Glacier2::PermissionDeniedException
>>> {
>>>    reason = internal server error
>>> }
>>
>> This is most likely that your database is not properly configured.  
>> But
>> the logs would tell us.
>>
>>> But I guess that is expected if the server is unreachable and I  
>>> can't
>>> add users. Do you have any idea why this would happen? I checked  
>>> that
>>> postgre is running and the database omero4 exists and is owned by  
>>> omero,
>>> but it is empty:
>>>
>>> omero4=> \d
>>> No relations found.
>>
>> Aha. Cancel the logs, that would be the problem.
>>
>>> Shouldn't the deploy command create the tables?
>>
>> No. The deploy command -- which is no longer necessary by the way --
>> deploys the definition of your grid, i.e. etc/grid/default.xml. It
>> defines which processes will be started and what properties they
>> receive. It doesn't do anything with the database, since that  
>> persists
>> longer than a single server start. (When I say deploy is no longer
>> necessary, I mean that a deploy happens automatically every time you
>> call "bin/omero admin start" so only if you want to change the
>> configuration of a running grid do you need "deploy".)
>>
>> Now, we're hard at work on the release documentation and they're  
>> *almost*
>> done, but for now you'll need to look at the RC1 email I sent:
>>
>>
>> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/001184.ht
>> ml
>>
>> for how to create your database. In summary, your next steps are:
>>
>>  bin/omero db script
>>
>> which creates OMERO4__0.sql. If you haven't added the PLPGSQL  
>> language
>> to your database, then you'll need to:
>>
>>  createlang plpgsql omero4
>>
>> and finally:
>>
>>  psql omero4 < OMERO4__0.sql
>>  bin/omero admin stop
>>  bin/omero admin start
>>
>> For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin  
>> to
>> add new users. If the command-line addition is of interest, we'll
>> certainly have that re-scheduled for an upcoming release.
>>
>>> Thanks,
>>> Paulo
>>
>> No problem and cheers,
>> ~Josh
>>
>>> On Wednesday 25 March 2009 19:23:11 you wrote:
>>>> Paulo Almeida writes:
>>>>> Hi again...
>>>>>
>>>>> Ignore my last e-mail, it really was a simple permissions problem.
>>>>> I didn't think it was because I tried running as root, but the
>>>>> directory was mounted in NFS so root didn't have access either. It
>>>>> seems to be running fine now.
>>>>
>>>> Whew. Good to hear! :) Thanks for letting us know, Paulo.
>>>>
>>>> ~J.
>>>>
>>>>> Best,
>>>>> Paulo
>>>>>
>>>>> On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
>>>>>> Hi,
>>>>>>
>>>>>> I had an OmeroGrid installation that was working, but I had to
>>>>>> reinstall the OS and now I am getting an error. When I run:
>>>>>>
>>>>>> bin/omero admin start
>>>>>>
>>>>>> there is not output, but then I run:
>>>>>>
>>>>>> bin/omero admin deploy etc/grid/default.xml
>>>>>>
>>>>>> and I get this:
>>>>>>
>>>>>> error: IceGrid::DeploymentException:
>>>>>> couldn't load `Blitz-0' on node `master':
>>>>>> can't set permissions on directory
>>>>>> `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
>>>>>>
>>>>>> -----------
>>>>>>
>>>>>> When I reinstalled the OS I had to install Ice, PostgreSQL, etc,
>>>>>> but I didn't touch the Omero folder. Do you have any idea about
>>>>>> what I may have forgotten that would cause this error? I also
>>>>>> tried compiling Omero.blitz, but I get this error when running
>>>>>> 'bin/omero admin start':
>>>>>>
>>>>>> icegridnode: failure occurred in daemon:
>>>>>> service caught unhandled Ice exception:
>>>>>> ../../include/Ice/BasicStream.h:412:
>>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
>>>>>> during unmarshaling
>>>>>> from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
>>>>>> ../../include/Ice/BasicStream.h:412:
>>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
>>>>>> during unmarshaling
>
>
> <server.log>_______________________________________________
> 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  Fri Mar 27 11:15:09 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Fri, 27 Mar 2009 11:15:09 +0000
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <E3F1AD52-2869-4BA1-A8AB-25B6916C8A59@blackcat.ca>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903262000.34165.palmeida@igc.gulbenkian.pt>
	<E3F1AD52-2869-4BA1-A8AB-25B6916C8A59@blackcat.ca>
Message-ID: <200903271115.10359.palmeida@igc.gulbenkian.pt>

Hi Chris,

Thanks, that was the problem. I forgot I had to rebuild after 'svn up'.

That log was from an omero3.2 server I set up just for tests, but it's not 
important now that I built omero4. Now bin/omero db script worked and I 
created the database with

psql omero4 -U omero -h localhost < OMERO4__0.sql

but when I run 

bin/omero admin start

it still fails. I am attaching the logs, but this bit doesn't seem good:

Caused by: org.postgresql.util.PSQLException: FATAL: password authentication 
failed for user "omero"

Is it getting the database user and password from etc/omero.properties? I 
think that is correctly set, and

psql -U omero -h localhost omero4 

works, with password omero, which is what I put in etc/local.properties and 
etc/omero.properties .

Thank you,
Paulo

On Thursday 26 March 2009 20:42:06 Chris Allan wrote:
> Hi Paulo,
>
> Something seems very wonky here. r4134 is OMERO Trunk and "db script"
> has been present for a while. Also, the Beta4 series does not use
> JBoss so is that server.log from your production installation?
>
> I'd start from "scratch" on your test OMERO checkout by running:
>
>   * ./build.py clean ; ./build.py
>   * cd dist
>   * bin/omero db script
>
> and then see where we are.
>
> Ciao.
>
> -Chris
>
> On 26 Mar 2009, at 20:00, Paulo Almeida wrote:
> > Hi Josh,
> >
> > Thank you very much for the instructions. Regarding your questions,
> > I saw the
> > adduser option when I ran /bin/omero admin with no argument. That
> > returns
> > usage instructions that include 'adduser' as an option. Command line
> > addition
> > is not important to us, I was trying that because I thought it was
> > the only
> > way.
> >
> > But now I'm not sure I'm using the right version. I have been using
> > svn and
> > just did 'svn up' (at revision 4134), but when I tried:
> >
> > bin/omero db script
> >
> > I got:
> >
> > Unknown command: db script
> >
> > Running bin/omero without arguments and typing '?' gives me this
> > list of
> > commands:
> >
> > admin
> > config
> > download
> > help
> > load
> > node
> > quit
> > script
> > server
> > setup
> > submit
> > upload
> > version
> >
> > The version is "OmeroCli client, version 1.0".
> >
> > I also tried installing omero3.2 and I get the same error when
> > creating the
> > session within an omero script:
> >
> > Traceback (most recent call last):
> >  File "<stdin>", line 1, in <module>
> >  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
> > line 334,
> > in createSession
> >    prx = self.getRouter(self.__ic).createSession(username, password)
> >  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
> > line 104,
> > in createSession
> >    return _M_Glacier2.Router._op_createSession.invoke(self, ((userId,
> > password), _ctx))
> > Ice.ConnectionRefusedException: Ice.ConnectionRefusedException:
> > Connection refused
> >
> > I am attaching omero-Beta3.2/jboss-4.2.3.GA/server/default/log/
> > server.log in
> > case it may help understand that error.
> >
> > Thanks again,
> > Paulo
> >
> > On Thursday 26 March 2009 18:07:44 you wrote:
> >> Paulo Almeida writes:
> >>> Hello,
> >>
> >> Hi Paulo.
> >>
> >>> Unfortunately I got stuck again... After running 'bin/omero admin
> >>> start'
> >>> and 'bin/omero admin deploy', when I run 'bin/omero admin status'
> >>> I get:
> >>>
> >>> palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin status
> >>> node is up
> >>> Server not reachable
> >>
> >> Hmmmm.....ok. That could be various things. Could you send us the
> >> var/log/* files?
> >>
> >>> Running 'bin/omero admin adduser' displays the usage help message
> >>> for
> >>> the omero command and trying the script in
> >>
> >> adduser got taken out of this release for lack of testing. Can you
> >> point me to where you found it listed in the documentation so I can
> >> quietly delete it? :)
> >>
> >>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
> >>>
> >>> returns an error after 'sf = c.createSession()'
> >>>
> >>>>>> sf = c.createSession()
> >>>
> >>> Traceback (most recent call last):
> >>>  File "<stdin>", line 1, in <module>
> >>>  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
> >>> line 334, in createSession
> >>>    prx = self.getRouter(self.__ic).createSession(username, password)
> >>>  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
> >>> line
> >>> 104, in createSession
> >>>    return _M_Glacier2.Router._op_createSession.invoke(self,
> >>> ((userId,
> >>> password), _ctx))
> >>> Glacier2.PermissionDeniedException:
> >>> exception ::Glacier2::PermissionDeniedException
> >>> {
> >>>    reason = internal server error
> >>> }
> >>
> >> This is most likely that your database is not properly configured.
> >> But
> >> the logs would tell us.
> >>
> >>> But I guess that is expected if the server is unreachable and I
> >>> can't
> >>> add users. Do you have any idea why this would happen? I checked
> >>> that
> >>> postgre is running and the database omero4 exists and is owned by
> >>> omero,
> >>> but it is empty:
> >>>
> >>> omero4=> \d
> >>> No relations found.
> >>
> >> Aha. Cancel the logs, that would be the problem.
> >>
> >>> Shouldn't the deploy command create the tables?
> >>
> >> No. The deploy command -- which is no longer necessary by the way --
> >> deploys the definition of your grid, i.e. etc/grid/default.xml. It
> >> defines which processes will be started and what properties they
> >> receive. It doesn't do anything with the database, since that
> >> persists
> >> longer than a single server start. (When I say deploy is no longer
> >> necessary, I mean that a deploy happens automatically every time you
> >> call "bin/omero admin start" so only if you want to change the
> >> configuration of a running grid do you need "deploy".)
> >>
> >> Now, we're hard at work on the release documentation and they're
> >> *almost*
> >> done, but for now you'll need to look at the RC1 email I sent:
> >>
> >>
> >> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/001184
> >>.ht ml
> >>
> >> for how to create your database. In summary, your next steps are:
> >>
> >>  bin/omero db script
> >>
> >> which creates OMERO4__0.sql. If you haven't added the PLPGSQL
> >> language
> >> to your database, then you'll need to:
> >>
> >>  createlang plpgsql omero4
> >>
> >> and finally:
> >>
> >>  psql omero4 < OMERO4__0.sql
> >>  bin/omero admin stop
> >>  bin/omero admin start
> >>
> >> For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin
> >> to
> >> add new users. If the command-line addition is of interest, we'll
> >> certainly have that re-scheduled for an upcoming release.
> >>
> >>> Thanks,
> >>> Paulo
> >>
> >> No problem and cheers,
> >> ~Josh
> >>
> >>> On Wednesday 25 March 2009 19:23:11 you wrote:
> >>>> Paulo Almeida writes:
> >>>>> Hi again...
> >>>>>
> >>>>> Ignore my last e-mail, it really was a simple permissions problem.
> >>>>> I didn't think it was because I tried running as root, but the
> >>>>> directory was mounted in NFS so root didn't have access either. It
> >>>>> seems to be running fine now.
> >>>>
> >>>> Whew. Good to hear! :) Thanks for letting us know, Paulo.
> >>>>
> >>>> ~J.
> >>>>
> >>>>> Best,
> >>>>> Paulo
> >>>>>
> >>>>> On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
> >>>>>> Hi,
> >>>>>>
> >>>>>> I had an OmeroGrid installation that was working, but I had to
> >>>>>> reinstall the OS and now I am getting an error. When I run:
> >>>>>>
> >>>>>> bin/omero admin start
> >>>>>>
> >>>>>> there is not output, but then I run:
> >>>>>>
> >>>>>> bin/omero admin deploy etc/grid/default.xml
> >>>>>>
> >>>>>> and I get this:
> >>>>>>
> >>>>>> error: IceGrid::DeploymentException:
> >>>>>> couldn't load `Blitz-0' on node `master':
> >>>>>> can't set permissions on directory
> >>>>>> `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
> >>>>>>
> >>>>>> -----------
> >>>>>>
> >>>>>> When I reinstalled the OS I had to install Ice, PostgreSQL, etc,
> >>>>>> but I didn't touch the Omero folder. Do you have any idea about
> >>>>>> what I may have forgotten that would cause this error? I also
> >>>>>> tried compiling Omero.blitz, but I get this error when running
> >>>>>> 'bin/omero admin start':
> >>>>>>
> >>>>>> icegridnode: failure occurred in daemon:
> >>>>>> service caught unhandled Ice exception:
> >>>>>> ../../include/Ice/BasicStream.h:412:
> >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
> >>>>>> during unmarshaling
> >>>>>> from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
> >>>>>> ../../include/Ice/BasicStream.h:412:
> >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
> >>>>>> during unmarshaling
> >
> > <server.log>_______________________________________________
> > 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 josh.moore at gmx.de  Fri Mar 27 11:54:33 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Fri, 27 Mar 2009 12:54:33 +0100
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <200903271115.10359.palmeida@igc.gulbenkian.pt>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903262000.34165.palmeida@igc.gulbenkian.pt>
	<E3F1AD52-2869-4BA1-A8AB-25B6916C8A59@blackcat.ca>
	<200903271115.10359.palmeida@igc.gulbenkian.pt>
Message-ID: <18892.48761.545559.101846@echo.mac>



Paulo Almeida writes:
 > Hi Chris,
 > 
 > Thanks, that was the problem. I forgot I had to rebuild after 'svn up'.
 > 
 > That log was from an omero3.2 server I set up just for tests, but
 > it's not important now that I built omero4. Now bin/omero db script
 > worked and I created the database with
 > 
 > psql omero4 -U omero -h localhost < OMERO4__0.sql
 > 
 > but when I run 
 > 
 > bin/omero admin start
 > 
 > it still fails. I am attaching the logs, but this bit doesn't seem
 > good:
 > 
 > Caused by: org.postgresql.util.PSQLException: FATAL: password
 > authentication failed for user "omero"
 > 
 > Is it getting the database user and password from
 > etc/omero.properties? I think that is correctly set, and

etc/omero.properties is compiled into the jar and so changes you made
after building will not take effect. Try:

 $ bin/omero config set omero.db.name omero4

 > psql -U omero -h localhost omero4 
 > 
 > works, with password omero, which is what I put in
 > etc/local.properties and etc/omero.properties .
 >
 > Thank you,
 > Paulo

Best wishes,
~Josh.
 
 > On Thursday 26 March 2009 20:42:06 Chris Allan wrote:
 > > Hi Paulo,
 > >
 > > Something seems very wonky here. r4134 is OMERO Trunk and "db script"
 > > has been present for a while. Also, the Beta4 series does not use
 > > JBoss so is that server.log from your production installation?
 > >
 > > I'd start from "scratch" on your test OMERO checkout by running:
 > >
 > >   * ./build.py clean ; ./build.py
 > >   * cd dist
 > >   * bin/omero db script
 > >
 > > and then see where we are.
 > >
 > > Ciao.
 > >
 > > -Chris
 > >
 > > On 26 Mar 2009, at 20:00, Paulo Almeida wrote:
 > > > Hi Josh,
 > > >
 > > > Thank you very much for the instructions. Regarding your
 > > > questions, I saw the adduser option when I ran /bin/omero admin
 > > > with no argument. That returns usage instructions that include
 > > > 'adduser' as an option. Command line addition is not important
 > > > to us, I was trying that because I thought it was the only way.
 > > >
 > > > But now I'm not sure I'm using the right version. I have been
 > > > using svn and just did 'svn up' (at revision 4134), but when I
 > > > tried:
 > > >
 > > > bin/omero db script
 > > >
 > > > I got:
 > > >
 > > > Unknown command: db script
 > > >
 > > > Running bin/omero without arguments and typing '?' gives me this
 > > > list of
 > > > commands:
 > > >
 > > > admin
 > > > config
 > > > download
 > > > help
 > > > load
 > > > node
 > > > quit
 > > > script
 > > > server
 > > > setup
 > > > submit
 > > > upload
 > > > version
 > > >
 > > > The version is "OmeroCli client, version 1.0".
 > > >
 > > > I also tried installing omero3.2 and I get the same error when
 > > > creating the
 > > > session within an omero script:
 > > >
 > > > Traceback (most recent call last):
 > > >  File "<stdin>", line 1, in <module>
 > > >  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
 > > > line 334,
 > > > in createSession
 > > >    prx = self.getRouter(self.__ic).createSession(username, password)
 > > >  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
 > > > line 104,
 > > > in createSession
 > > >    return _M_Glacier2.Router._op_createSession.invoke(self, ((userId,
 > > > password), _ctx))
 > > > Ice.ConnectionRefusedException: Ice.ConnectionRefusedException:
 > > > Connection refused
 > > >
 > > > I am attaching omero-Beta3.2/jboss-4.2.3.GA/server/default/log/
 > > > server.log in
 > > > case it may help understand that error.
 > > >
 > > > Thanks again,
 > > > Paulo
 > > >
 > > > On Thursday 26 March 2009 18:07:44 you wrote:
 > > >> Paulo Almeida writes:
 > > >>> Hello,
 > > >>
 > > >> Hi Paulo.
 > > >>
 > > >>> Unfortunately I got stuck again... After running 'bin/omero admin
 > > >>> start'
 > > >>> and 'bin/omero admin deploy', when I run 'bin/omero admin status'
 > > >>> I get:
 > > >>>
 > > >>> palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin status
 > > >>> node is up
 > > >>> Server not reachable
 > > >>
 > > >> Hmmmm.....ok. That could be various things. Could you send us the
 > > >> var/log/* files?
 > > >>
 > > >>> Running 'bin/omero admin adduser' displays the usage help message
 > > >>> for
 > > >>> the omero command and trying the script in
 > > >>
 > > >> adduser got taken out of this release for lack of testing. Can you
 > > >> point me to where you found it listed in the documentation so I can
 > > >> quietly delete it? :)
 > > >>
 > > >>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
 > > >>>
 > > >>> returns an error after 'sf = c.createSession()'
 > > >>>
 > > >>>>>> sf = c.createSession()
 > > >>>
 > > >>> Traceback (most recent call last):
 > > >>>  File "<stdin>", line 1, in <module>
 > > >>>  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
 > > >>> line 334, in createSession
 > > >>>    prx = self.getRouter(self.__ic).createSession(username, password)
 > > >>>  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
 > > >>> line
 > > >>> 104, in createSession
 > > >>>    return _M_Glacier2.Router._op_createSession.invoke(self,
 > > >>> ((userId,
 > > >>> password), _ctx))
 > > >>> Glacier2.PermissionDeniedException:
 > > >>> exception ::Glacier2::PermissionDeniedException
 > > >>> {
 > > >>>    reason = internal server error
 > > >>> }
 > > >>
 > > >> This is most likely that your database is not properly configured.
 > > >> But
 > > >> the logs would tell us.
 > > >>
 > > >>> But I guess that is expected if the server is unreachable and I
 > > >>> can't
 > > >>> add users. Do you have any idea why this would happen? I checked
 > > >>> that
 > > >>> postgre is running and the database omero4 exists and is owned by
 > > >>> omero,
 > > >>> but it is empty:
 > > >>>
 > > >>> omero4=> \d
 > > >>> No relations found.
 > > >>
 > > >> Aha. Cancel the logs, that would be the problem.
 > > >>
 > > >>> Shouldn't the deploy command create the tables?
 > > >>
 > > >> No. The deploy command -- which is no longer necessary by the way --
 > > >> deploys the definition of your grid, i.e. etc/grid/default.xml. It
 > > >> defines which processes will be started and what properties they
 > > >> receive. It doesn't do anything with the database, since that
 > > >> persists
 > > >> longer than a single server start. (When I say deploy is no longer
 > > >> necessary, I mean that a deploy happens automatically every time you
 > > >> call "bin/omero admin start" so only if you want to change the
 > > >> configuration of a running grid do you need "deploy".)
 > > >>
 > > >> Now, we're hard at work on the release documentation and they're
 > > >> *almost*
 > > >> done, but for now you'll need to look at the RC1 email I sent:
 > > >>
 > > >>
 > > >> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/001184
 > > >>.ht ml
 > > >>
 > > >> for how to create your database. In summary, your next steps are:
 > > >>
 > > >>  bin/omero db script
 > > >>
 > > >> which creates OMERO4__0.sql. If you haven't added the PLPGSQL
 > > >> language
 > > >> to your database, then you'll need to:
 > > >>
 > > >>  createlang plpgsql omero4
 > > >>
 > > >> and finally:
 > > >>
 > > >>  psql omero4 < OMERO4__0.sql
 > > >>  bin/omero admin stop
 > > >>  bin/omero admin start
 > > >>
 > > >> For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin
 > > >> to
 > > >> add new users. If the command-line addition is of interest, we'll
 > > >> certainly have that re-scheduled for an upcoming release.
 > > >>
 > > >>> Thanks,
 > > >>> Paulo
 > > >>
 > > >> No problem and cheers,
 > > >> ~Josh
 > > >>
 > > >>> On Wednesday 25 March 2009 19:23:11 you wrote:
 > > >>>> Paulo Almeida writes:
 > > >>>>> Hi again...
 > > >>>>>
 > > >>>>> Ignore my last e-mail, it really was a simple permissions problem.
 > > >>>>> I didn't think it was because I tried running as root, but the
 > > >>>>> directory was mounted in NFS so root didn't have access either. It
 > > >>>>> seems to be running fine now.
 > > >>>>
 > > >>>> Whew. Good to hear! :) Thanks for letting us know, Paulo.
 > > >>>>
 > > >>>> ~J.
 > > >>>>
 > > >>>>> Best,
 > > >>>>> Paulo
 > > >>>>>
 > > >>>>> On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
 > > >>>>>> Hi,
 > > >>>>>>
 > > >>>>>> I had an OmeroGrid installation that was working, but I had to
 > > >>>>>> reinstall the OS and now I am getting an error. When I run:
 > > >>>>>>
 > > >>>>>> bin/omero admin start
 > > >>>>>>
 > > >>>>>> there is not output, but then I run:
 > > >>>>>>
 > > >>>>>> bin/omero admin deploy etc/grid/default.xml
 > > >>>>>>
 > > >>>>>> and I get this:
 > > >>>>>>
 > > >>>>>> error: IceGrid::DeploymentException:
 > > >>>>>> couldn't load `Blitz-0' on node `master':
 > > >>>>>> can't set permissions on directory
 > > >>>>>> `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
 > > >>>>>>
 > > >>>>>> -----------
 > > >>>>>>
 > > >>>>>> When I reinstalled the OS I had to install Ice, PostgreSQL, etc,
 > > >>>>>> but I didn't touch the Omero folder. Do you have any idea about
 > > >>>>>> what I may have forgotten that would cause this error? I also
 > > >>>>>> tried compiling Omero.blitz, but I get this error when running
 > > >>>>>> 'bin/omero admin start':
 > > >>>>>>
 > > >>>>>> icegridnode: failure occurred in daemon:
 > > >>>>>> service caught unhandled Ice exception:
 > > >>>>>> ../../include/Ice/BasicStream.h:412:
 > > >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
 > > >>>>>> during unmarshaling
 > > >>>>>> from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
 > > >>>>>> ../../include/Ice/BasicStream.h:412:
 > > >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of bounds
 > > >>>>>> during unmarshaling
 > > >
 > > > <server.log>_______________________________________________
 > > > 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  Fri Mar 27 14:13:50 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Fri, 27 Mar 2009 14:13:50 +0000
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <18892.48761.545559.101846@echo.mac>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903271115.10359.palmeida@igc.gulbenkian.pt>
	<18892.48761.545559.101846@echo.mac>
Message-ID: <200903271413.51723.palmeida@igc.gulbenkian.pt>

Hi Josh,

It's working now! The problem was indeed the password in omero.properties 
being set to a different thing when I cleaned and rebuilt. I had changed it 
after building, but I didn't know it was pointless. Now the server starts and 
I can create sessions in python, so I think everything is good.

Thanks a lot Josh and Chris,
Paulo

On Friday 27 March 2009 11:54:33 josh.moore at gmx.de wrote:
> Paulo Almeida writes:
>  > Hi Chris,
>  >
>  > Thanks, that was the problem. I forgot I had to rebuild after 'svn up'.
>  >
>  > That log was from an omero3.2 server I set up just for tests, but
>  > it's not important now that I built omero4. Now bin/omero db script
>  > worked and I created the database with
>  >
>  > psql omero4 -U omero -h localhost < OMERO4__0.sql
>  >
>  > but when I run
>  >
>  > bin/omero admin start
>  >
>  > it still fails. I am attaching the logs, but this bit doesn't seem
>  > good:
>  >
>  > Caused by: org.postgresql.util.PSQLException: FATAL: password
>  > authentication failed for user "omero"
>  >
>  > Is it getting the database user and password from
>  > etc/omero.properties? I think that is correctly set, and
>
> etc/omero.properties is compiled into the jar and so changes you made
> after building will not take effect. Try:
>
>  $ bin/omero config set omero.db.name omero4
>
>  > psql -U omero -h localhost omero4
>  >
>  > works, with password omero, which is what I put in
>  > etc/local.properties and etc/omero.properties .
>  >
>  > Thank you,
>  > Paulo
>
> Best wishes,
> ~Josh.
>
>  > On Thursday 26 March 2009 20:42:06 Chris Allan wrote:
>  > > Hi Paulo,
>  > >
>  > > Something seems very wonky here. r4134 is OMERO Trunk and "db script"
>  > > has been present for a while. Also, the Beta4 series does not use
>  > > JBoss so is that server.log from your production installation?
>  > >
>  > > I'd start from "scratch" on your test OMERO checkout by running:
>  > >
>  > >   * ./build.py clean ; ./build.py
>  > >   * cd dist
>  > >   * bin/omero db script
>  > >
>  > > and then see where we are.
>  > >
>  > > Ciao.
>  > >
>  > > -Chris
>  > >
>  > > On 26 Mar 2009, at 20:00, Paulo Almeida wrote:
>  > > > Hi Josh,
>  > > >
>  > > > Thank you very much for the instructions. Regarding your
>  > > > questions, I saw the adduser option when I ran /bin/omero admin
>  > > > with no argument. That returns usage instructions that include
>  > > > 'adduser' as an option. Command line addition is not important
>  > > > to us, I was trying that because I thought it was the only way.
>  > > >
>  > > > But now I'm not sure I'm using the right version. I have been
>  > > > using svn and just did 'svn up' (at revision 4134), but when I
>  > > > tried:
>  > > >
>  > > > bin/omero db script
>  > > >
>  > > > I got:
>  > > >
>  > > > Unknown command: db script
>  > > >
>  > > > Running bin/omero without arguments and typing '?' gives me this
>  > > > list of
>  > > > commands:
>  > > >
>  > > > admin
>  > > > config
>  > > > download
>  > > > help
>  > > > load
>  > > > node
>  > > > quit
>  > > > script
>  > > > server
>  > > > setup
>  > > > submit
>  > > > upload
>  > > > version
>  > > >
>  > > > The version is "OmeroCli client, version 1.0".
>  > > >
>  > > > I also tried installing omero3.2 and I get the same error when
>  > > > creating the
>  > > > session within an omero script:
>  > > >
>  > > > Traceback (most recent call last):
>  > > >  File "<stdin>", line 1, in <module>
>  > > >  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
>  > > > line 334,
>  > > > in createSession
>  > > >    prx = self.getRouter(self.__ic).createSession(username, password)
>  > > >  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
>  > > > line 104,
>  > > > in createSession
>  > > >    return _M_Glacier2.Router._op_createSession.invoke(self,
>  > > > ((userId, password), _ctx))
>  > > > Ice.ConnectionRefusedException: Ice.ConnectionRefusedException:
>  > > > Connection refused
>  > > >
>  > > > I am attaching omero-Beta3.2/jboss-4.2.3.GA/server/default/log/
>  > > > server.log in
>  > > > case it may help understand that error.
>  > > >
>  > > > Thanks again,
>  > > > Paulo
>  > > >
>  > > > On Thursday 26 March 2009 18:07:44 you wrote:
>  > > >> Paulo Almeida writes:
>  > > >>> Hello,
>  > > >>
>  > > >> Hi Paulo.
>  > > >>
>  > > >>> Unfortunately I got stuck again... After running 'bin/omero admin
>  > > >>> start'
>  > > >>> and 'bin/omero admin deploy', when I run 'bin/omero admin status'
>  > > >>> I get:
>  > > >>>
>  > > >>> palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin
>  > > >>> status node is up
>  > > >>> Server not reachable
>  > > >>
>  > > >> Hmmmm.....ok. That could be various things. Could you send us the
>  > > >> var/log/* files?
>  > > >>
>  > > >>> Running 'bin/omero admin adduser' displays the usage help message
>  > > >>> for
>  > > >>> the omero command and trying the script in
>  > > >>
>  > > >> adduser got taken out of this release for lack of testing. Can you
>  > > >> point me to where you found it listed in the documentation so I can
>  > > >> quietly delete it? :)
>  > > >>
>  > > >>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
>  > > >>>
>  > > >>> returns an error after 'sf = c.createSession()'
>  > > >>>
>  > > >>>>>> sf = c.createSession()
>  > > >>>
>  > > >>> Traceback (most recent call last):
>  > > >>>  File "<stdin>", line 1, in <module>
>  > > >>>  File
>  > > >>> "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py", line
>  > > >>> 334, in createSession
>  > > >>>    prx = self.getRouter(self.__ic).createSession(username,
>  > > >>> password) File
>  > > >>> "/var/lib/python-support/python2.5/Glacier2_Router_ice.py", line
>  > > >>> 104, in createSession
>  > > >>>    return _M_Glacier2.Router._op_createSession.invoke(self,
>  > > >>> ((userId,
>  > > >>> password), _ctx))
>  > > >>> Glacier2.PermissionDeniedException:
>  > > >>> exception ::Glacier2::PermissionDeniedException
>  > > >>> {
>  > > >>>    reason = internal server error
>  > > >>> }
>  > > >>
>  > > >> This is most likely that your database is not properly configured.
>  > > >> But
>  > > >> the logs would tell us.
>  > > >>
>  > > >>> But I guess that is expected if the server is unreachable and I
>  > > >>> can't
>  > > >>> add users. Do you have any idea why this would happen? I checked
>  > > >>> that
>  > > >>> postgre is running and the database omero4 exists and is owned by
>  > > >>> omero,
>  > > >>> but it is empty:
>  > > >>>
>  > > >>> omero4=> \d
>  > > >>> No relations found.
>  > > >>
>  > > >> Aha. Cancel the logs, that would be the problem.
>  > > >>
>  > > >>> Shouldn't the deploy command create the tables?
>  > > >>
>  > > >> No. The deploy command -- which is no longer necessary by the way
>  > > >> -- deploys the definition of your grid, i.e. etc/grid/default.xml.
>  > > >> It defines which processes will be started and what properties they
>  > > >> receive. It doesn't do anything with the database, since that
>  > > >> persists
>  > > >> longer than a single server start. (When I say deploy is no longer
>  > > >> necessary, I mean that a deploy happens automatically every time
>  > > >> you call "bin/omero admin start" so only if you want to change the
>  > > >> configuration of a running grid do you need "deploy".)
>  > > >>
>  > > >> Now, we're hard at work on the release documentation and they're
>  > > >> *almost*
>  > > >> done, but for now you'll need to look at the RC1 email I sent:
>  > > >>
>  > > >>
>  > > >> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/0
>  > > >>01184 .ht ml
>  > > >>
>  > > >> for how to create your database. In summary, your next steps are:
>  > > >>
>  > > >>  bin/omero db script
>  > > >>
>  > > >> which creates OMERO4__0.sql. If you haven't added the PLPGSQL
>  > > >> language
>  > > >> to your database, then you'll need to:
>  > > >>
>  > > >>  createlang plpgsql omero4
>  > > >>
>  > > >> and finally:
>  > > >>
>  > > >>  psql omero4 < OMERO4__0.sql
>  > > >>  bin/omero admin stop
>  > > >>  bin/omero admin start
>  > > >>
>  > > >> For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin
>  > > >> to
>  > > >> add new users. If the command-line addition is of interest, we'll
>  > > >> certainly have that re-scheduled for an upcoming release.
>  > > >>
>  > > >>> Thanks,
>  > > >>> Paulo
>  > > >>
>  > > >> No problem and cheers,
>  > > >> ~Josh
>  > > >>
>  > > >>> On Wednesday 25 March 2009 19:23:11 you wrote:
>  > > >>>> Paulo Almeida writes:
>  > > >>>>> Hi again...
>  > > >>>>>
>  > > >>>>> Ignore my last e-mail, it really was a simple permissions
>  > > >>>>> problem. I didn't think it was because I tried running as root,
>  > > >>>>> but the directory was mounted in NFS so root didn't have access
>  > > >>>>> either. It seems to be running fine now.
>  > > >>>>
>  > > >>>> Whew. Good to hear! :) Thanks for letting us know, Paulo.
>  > > >>>>
>  > > >>>> ~J.
>  > > >>>>
>  > > >>>>> Best,
>  > > >>>>> Paulo
>  > > >>>>>
>  > > >>>>> On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
>  > > >>>>>> Hi,
>  > > >>>>>>
>  > > >>>>>> I had an OmeroGrid installation that was working, but I had to
>  > > >>>>>> reinstall the OS and now I am getting an error. When I run:
>  > > >>>>>>
>  > > >>>>>> bin/omero admin start
>  > > >>>>>>
>  > > >>>>>> there is not output, but then I run:
>  > > >>>>>>
>  > > >>>>>> bin/omero admin deploy etc/grid/default.xml
>  > > >>>>>>
>  > > >>>>>> and I get this:
>  > > >>>>>>
>  > > >>>>>> error: IceGrid::DeploymentException:
>  > > >>>>>> couldn't load `Blitz-0' on node `master':
>  > > >>>>>> can't set permissions on directory
>  > > >>>>>> `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
>  > > >>>>>>
>  > > >>>>>> -----------
>  > > >>>>>>
>  > > >>>>>> When I reinstalled the OS I had to install Ice, PostgreSQL,
>  > > >>>>>> etc, but I didn't touch the Omero folder. Do you have any idea
>  > > >>>>>> about what I may have forgotten that would cause this error? I
>  > > >>>>>> also tried compiling Omero.blitz, but I get this error when
>  > > >>>>>> running 'bin/omero admin start':
>  > > >>>>>>
>  > > >>>>>> icegridnode: failure occurred in daemon:
>  > > >>>>>> service caught unhandled Ice exception:
>  > > >>>>>> ../../include/Ice/BasicStream.h:412:
>  > > >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of
>  > > >>>>>> bounds during unmarshaling
>  > > >>>>>> from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
>  > > >>>>>> ../../include/Ice/BasicStream.h:412:
>  > > >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of
>  > > >>>>>> bounds during unmarshaling
>  > > >
>  > > > <server.log>_______________________________________________
>  > > > ome-users mailing list
>  > > > ome-users at lists.openmicroscopy.org.uk
>  > > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users




From josh.moore at gmx.de  Fri Mar 27 14:27:38 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Fri, 27 Mar 2009 15:27:38 +0100
Subject: [ome-users] Making Omero work with Ice
In-Reply-To: <200903271413.51723.palmeida@igc.gulbenkian.pt>
References: <200903251804.12080.palmeida@igc.gulbenkian.pt>
	<200903271115.10359.palmeida@igc.gulbenkian.pt>
	<18892.48761.545559.101846@echo.mac>
	<200903271413.51723.palmeida@igc.gulbenkian.pt>
Message-ID: <18892.57946.969859.947267@echo.mac>


Congratulations, Paulo. Great to hear! We'll look into making the
read-only status of etc/omero.properties clearer. Perhaps it shouldn't
be in the built directory. Enjoy your server. :)

~Josh.


Paulo Almeida writes:
 > Hi Josh,
 > 
 > It's working now! The problem was indeed the password in
 > omero.properties being set to a different thing when I cleaned and
 > rebuilt. I had changed it after building, but I didn't know it was
 > pointless. Now the server starts and I can create sessions in
 > python, so I think everything is good.
 > 
 > Thanks a lot Josh and Chris,
 > Paulo
 > 
 > On Friday 27 March 2009 11:54:33 josh.moore at gmx.de wrote:
 > > Paulo Almeida writes:
 > >  > Hi Chris,
 > >  >
 > >  > Thanks, that was the problem. I forgot I had to rebuild after
 > >  > 'svn up'.
 > >  >
 > >  > That log was from an omero3.2 server I set up just for tests,
 > >  > but it's not important now that I built omero4. Now bin/omero
 > >  > db script worked and I created the database with
 > >  >
 > >  > psql omero4 -U omero -h localhost < OMERO4__0.sql
 > >  >
 > >  > but when I run
 > >  >
 > >  > bin/omero admin start
 > >  >
 > >  > it still fails. I am attaching the logs, but this bit doesn't
 > >  > seem good:
 > >  >
 > >  > Caused by: org.postgresql.util.PSQLException: FATAL: password
 > >  > authentication failed for user "omero"
 > >  >
 > >  > Is it getting the database user and password from
 > >  > etc/omero.properties? I think that is correctly set, and
 > >
 > > etc/omero.properties is compiled into the jar and so changes you made
 > > after building will not take effect. Try:
 > >
 > >  $ bin/omero config set omero.db.name omero4
 > >
 > >  > psql -U omero -h localhost omero4
 > >  >
 > >  > works, with password omero, which is what I put in
 > >  > etc/local.properties and etc/omero.properties .
 > >  >
 > >  > Thank you,
 > >  > Paulo
 > >
 > > Best wishes,
 > > ~Josh.
 > >
 > >  > On Thursday 26 March 2009 20:42:06 Chris Allan wrote:
 > >  > > Hi Paulo,
 > >  > >
 > >  > > Something seems very wonky here. r4134 is OMERO Trunk and "db script"
 > >  > > has been present for a while. Also, the Beta4 series does not use
 > >  > > JBoss so is that server.log from your production installation?
 > >  > >
 > >  > > I'd start from "scratch" on your test OMERO checkout by running:
 > >  > >
 > >  > >   * ./build.py clean ; ./build.py
 > >  > >   * cd dist
 > >  > >   * bin/omero db script
 > >  > >
 > >  > > and then see where we are.
 > >  > >
 > >  > > Ciao.
 > >  > >
 > >  > > -Chris
 > >  > >
 > >  > > On 26 Mar 2009, at 20:00, Paulo Almeida wrote:
 > >  > > > Hi Josh,
 > >  > > >
 > >  > > > Thank you very much for the instructions. Regarding your
 > >  > > > questions, I saw the adduser option when I ran /bin/omero admin
 > >  > > > with no argument. That returns usage instructions that include
 > >  > > > 'adduser' as an option. Command line addition is not important
 > >  > > > to us, I was trying that because I thought it was the only way.
 > >  > > >
 > >  > > > But now I'm not sure I'm using the right version. I have been
 > >  > > > using svn and just did 'svn up' (at revision 4134), but when I
 > >  > > > tried:
 > >  > > >
 > >  > > > bin/omero db script
 > >  > > >
 > >  > > > I got:
 > >  > > >
 > >  > > > Unknown command: db script
 > >  > > >
 > >  > > > Running bin/omero without arguments and typing '?' gives me this
 > >  > > > list of
 > >  > > > commands:
 > >  > > >
 > >  > > > admin
 > >  > > > config
 > >  > > > download
 > >  > > > help
 > >  > > > load
 > >  > > > node
 > >  > > > quit
 > >  > > > script
 > >  > > > server
 > >  > > > setup
 > >  > > > submit
 > >  > > > upload
 > >  > > > version
 > >  > > >
 > >  > > > The version is "OmeroCli client, version 1.0".
 > >  > > >
 > >  > > > I also tried installing omero3.2 and I get the same error when
 > >  > > > creating the
 > >  > > > session within an omero script:
 > >  > > >
 > >  > > > Traceback (most recent call last):
 > >  > > >  File "<stdin>", line 1, in <module>
 > >  > > >  File "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py",
 > >  > > > line 334,
 > >  > > > in createSession
 > >  > > >    prx = self.getRouter(self.__ic).createSession(username, password)
 > >  > > >  File "/var/lib/python-support/python2.5/Glacier2_Router_ice.py",
 > >  > > > line 104,
 > >  > > > in createSession
 > >  > > >    return _M_Glacier2.Router._op_createSession.invoke(self,
 > >  > > > ((userId, password), _ctx))
 > >  > > > Ice.ConnectionRefusedException: Ice.ConnectionRefusedException:
 > >  > > > Connection refused
 > >  > > >
 > >  > > > I am attaching omero-Beta3.2/jboss-4.2.3.GA/server/default/log/
 > >  > > > server.log in
 > >  > > > case it may help understand that error.
 > >  > > >
 > >  > > > Thanks again,
 > >  > > > Paulo
 > >  > > >
 > >  > > > On Thursday 26 March 2009 18:07:44 you wrote:
 > >  > > >> Paulo Almeida writes:
 > >  > > >>> Hello,
 > >  > > >>
 > >  > > >> Hi Paulo.
 > >  > > >>
 > >  > > >>> Unfortunately I got stuck again... After running 'bin/omero admin
 > >  > > >>> start'
 > >  > > >>> and 'bin/omero admin deploy', when I run 'bin/omero admin status'
 > >  > > >>> I get:
 > >  > > >>>
 > >  > > >>> palmeida at polyhymnia:~/OMERO_test/OMERO/dist$ bin/omero admin
 > >  > > >>> status node is up
 > >  > > >>> Server not reachable
 > >  > > >>
 > >  > > >> Hmmmm.....ok. That could be various things. Could you send us the
 > >  > > >> var/log/* files?
 > >  > > >>
 > >  > > >>> Running 'bin/omero admin adduser' displays the usage help message
 > >  > > >>> for
 > >  > > >>> the omero command and trying the script in
 > >  > > >>
 > >  > > >> adduser got taken out of this release for lack of testing. Can you
 > >  > > >> point me to where you found it listed in the documentation so I can
 > >  > > >> quietly delete it? :)
 > >  > > >>
 > >  > > >>> http://trac.openmicroscopy.org.uk/omero/wiki/OmeroGrid
 > >  > > >>>
 > >  > > >>> returns an error after 'sf = c.createSession()'
 > >  > > >>>
 > >  > > >>>>>> sf = c.createSession()
 > >  > > >>>
 > >  > > >>> Traceback (most recent call last):
 > >  > > >>>  File "<stdin>", line 1, in <module>
 > >  > > >>>  File
 > >  > > >>> "/home/palmeida/OMERO_test/OMERO/dist/lib/omero/__init__.py", line
 > >  > > >>> 334, in createSession
 > >  > > >>>    prx = self.getRouter(self.__ic).createSession(username,
 > >  > > >>> password) File
 > >  > > >>> "/var/lib/python-support/python2.5/Glacier2_Router_ice.py", line
 > >  > > >>> 104, in createSession
 > >  > > >>>    return _M_Glacier2.Router._op_createSession.invoke(self,
 > >  > > >>> ((userId,
 > >  > > >>> password), _ctx))
 > >  > > >>> Glacier2.PermissionDeniedException:
 > >  > > >>> exception ::Glacier2::PermissionDeniedException
 > >  > > >>> {
 > >  > > >>>    reason = internal server error
 > >  > > >>> }
 > >  > > >>
 > >  > > >> This is most likely that your database is not properly configured.
 > >  > > >> But
 > >  > > >> the logs would tell us.
 > >  > > >>
 > >  > > >>> But I guess that is expected if the server is unreachable and I
 > >  > > >>> can't
 > >  > > >>> add users. Do you have any idea why this would happen? I checked
 > >  > > >>> that
 > >  > > >>> postgre is running and the database omero4 exists and is owned by
 > >  > > >>> omero,
 > >  > > >>> but it is empty:
 > >  > > >>>
 > >  > > >>> omero4=> \d
 > >  > > >>> No relations found.
 > >  > > >>
 > >  > > >> Aha. Cancel the logs, that would be the problem.
 > >  > > >>
 > >  > > >>> Shouldn't the deploy command create the tables?
 > >  > > >>
 > >  > > >> No. The deploy command -- which is no longer necessary by the way
 > >  > > >> -- deploys the definition of your grid, i.e. etc/grid/default.xml.
 > >  > > >> It defines which processes will be started and what properties they
 > >  > > >> receive. It doesn't do anything with the database, since that
 > >  > > >> persists
 > >  > > >> longer than a single server start. (When I say deploy is no longer
 > >  > > >> necessary, I mean that a deploy happens automatically every time
 > >  > > >> you call "bin/omero admin start" so only if you want to change the
 > >  > > >> configuration of a running grid do you need "deploy".)
 > >  > > >>
 > >  > > >> Now, we're hard at work on the release documentation and they're
 > >  > > >> *almost*
 > >  > > >> done, but for now you'll need to look at the RC1 email I sent:
 > >  > > >>
 > >  > > >>
 > >  > > >> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2009-March/0
 > >  > > >>01184 .ht ml
 > >  > > >>
 > >  > > >> for how to create your database. In summary, your next steps are:
 > >  > > >>
 > >  > > >>  bin/omero db script
 > >  > > >>
 > >  > > >> which creates OMERO4__0.sql. If you haven't added the PLPGSQL
 > >  > > >> language
 > >  > > >> to your database, then you'll need to:
 > >  > > >>
 > >  > > >>  createlang plpgsql omero4
 > >  > > >>
 > >  > > >> and finally:
 > >  > > >>
 > >  > > >>  psql omero4 < OMERO4__0.sql
 > >  > > >>  bin/omero admin stop
 > >  > > >>  bin/omero admin start
 > >  > > >>
 > >  > > >> For 4.0.0 use the webadmin panel at: http://localhost:8000/webadmin
 > >  > > >> to
 > >  > > >> add new users. If the command-line addition is of interest, we'll
 > >  > > >> certainly have that re-scheduled for an upcoming release.
 > >  > > >>
 > >  > > >>> Thanks,
 > >  > > >>> Paulo
 > >  > > >>
 > >  > > >> No problem and cheers,
 > >  > > >> ~Josh
 > >  > > >>
 > >  > > >>> On Wednesday 25 March 2009 19:23:11 you wrote:
 > >  > > >>>> Paulo Almeida writes:
 > >  > > >>>>> Hi again...
 > >  > > >>>>>
 > >  > > >>>>> Ignore my last e-mail, it really was a simple permissions
 > >  > > >>>>> problem. I didn't think it was because I tried running as root,
 > >  > > >>>>> but the directory was mounted in NFS so root didn't have access
 > >  > > >>>>> either. It seems to be running fine now.
 > >  > > >>>>
 > >  > > >>>> Whew. Good to hear! :) Thanks for letting us know, Paulo.
 > >  > > >>>>
 > >  > > >>>> ~J.
 > >  > > >>>>
 > >  > > >>>>> Best,
 > >  > > >>>>> Paulo
 > >  > > >>>>>
 > >  > > >>>>> On Wednesday 25 March 2009 18:04:11 Paulo Almeida wrote:
 > >  > > >>>>>> Hi,
 > >  > > >>>>>>
 > >  > > >>>>>> I had an OmeroGrid installation that was working, but I had to
 > >  > > >>>>>> reinstall the OS and now I am getting an error. When I run:
 > >  > > >>>>>>
 > >  > > >>>>>> bin/omero admin start
 > >  > > >>>>>>
 > >  > > >>>>>> there is not output, but then I run:
 > >  > > >>>>>>
 > >  > > >>>>>> bin/omero admin deploy etc/grid/default.xml
 > >  > > >>>>>>
 > >  > > >>>>>> and I get this:
 > >  > > >>>>>>
 > >  > > >>>>>> error: IceGrid::DeploymentException:
 > >  > > >>>>>> couldn't load `Blitz-0' on node `master':
 > >  > > >>>>>> can't set permissions on directory
 > >  > > >>>>>> `/mnt/OMERO_test/OMERO/dist/var/master/servers/Blitz-0'
 > >  > > >>>>>>
 > >  > > >>>>>> -----------
 > >  > > >>>>>>
 > >  > > >>>>>> When I reinstalled the OS I had to install Ice, PostgreSQL,
 > >  > > >>>>>> etc, but I didn't touch the Omero folder. Do you have any idea
 > >  > > >>>>>> about what I may have forgotten that would cause this error? I
 > >  > > >>>>>> also tried compiling Omero.blitz, but I get this error when
 > >  > > >>>>>> running 'bin/omero admin start':
 > >  > > >>>>>>
 > >  > > >>>>>> icegridnode: failure occurred in daemon:
 > >  > > >>>>>> service caught unhandled Ice exception:
 > >  > > >>>>>> ../../include/Ice/BasicStream.h:412:
 > >  > > >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of
 > >  > > >>>>>> bounds during unmarshaling
 > >  > > >>>>>> from /mnt/OMERO_test/OMERO_blitz/dist/var/log/master.err:
 > >  > > >>>>>> ../../include/Ice/BasicStream.h:412:
 > >  > > >>>>>> Ice::UnmarshalOutOfBoundsException: protocol error: out of
 > >  > > >>>>>> bounds during unmarshaling
 > >  > > >
 > >  > > > <server.log>_______________________________________________
 > >  > > > ome-users mailing list
 > >  > > > ome-users at lists.openmicroscopy.org.uk
 > >  > > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
 > 


From jason at lifesci.dundee.ac.uk  Fri Mar 27 19:56:34 2009
From: jason at lifesci.dundee.ac.uk (Jason Swedlow)
Date: Fri, 27 Mar 2009 19:56:34 +0000
Subject: [ome-users] OMERO Beta4.0
Message-ID: <3CD5FD98-3C08-427C-B313-882AABAC5241@lifesci.dundee.ac.uk>

Hi All-

The OME Consortium (http://openmicroscopy.org) is proud to announce  
the release of OMERO Beta4.0.  This release is the product of a huge  
effort from our development team, and marks substantial changes in  
OMERO's infrastructure and significant steps in functionality.  Much  
of the functionality we are releasing has been developed in direct  
response to feedback from users, either through these lists, or at our  
annula OME Users Meeting at Institut Pasteur in Paris.

OME and OMERO resources.
In the past we have used our Trac sites as user resources.  Many of  
you will know these sites from accessing our MilestoneDownloads  
pages.  In response to many requests, we've moved our main portals for  
documentation and downloads to the main project site, http://openmicroscopy.org 
.  The pages here will continue to develop and mature over the next  
few weeks.  However, the site is mature enough to serve as a complete  
Beta4 reference.  The starting point for OMERO is:

http://www.openmicroscopy.org/site/documents/data-management/omero4

You'll find docs, definitions, and of course downloads.

As always, any feedback on mistakes, requests, or comments is much  
appreciated.

What's new in Beta4?
Better to ask, what isn't! Briefly:

-- OMERO.server: remove JBOSS, and switch all remoting to ICE.   
Improve session management, supporting creation of many thousands of  
session.  Addition of an import service, for server-side importing. DB  
upgrades to support the metadata completion facilities.  Substantial  
improvement to interaction between indexing engine and rest of  
server.  Please Note: For those of you running OMERO.server on  
Windows, the Blitz server runs according to the instructions on http://www.openmicroscopy.org/site/documents/data-management/omero4/server/install-windows 
.  However, OMERO.web is not supported yet under Windows.  We will fix  
that imminently.

-- OMERO.importer: Migration to Blitz interface, giving much faster  
performance.  More efficient importing, complete metadata support for  
Zeiss LSM510, Leica LIF, Zeiss ZVI, Applied Precision DV, and  
MetaMorph STK.  Add command line importer for batch import.

-- OMERO.insight:  Migration to Blitz interface, giving much faster  
performance.  Updates to metadata display, include complete support  
for OME Data Model.  Much expanded integration of protocol management  
via OMERO.editor, within OMERO.insight.  Support for image delete.  
Refinement of Projection Interface. 

-- OMERO.web:  all new browser-based client for OMERO.  Enables  
sharing of images with colleagues (must have account on server)

-- OMERO.editor: a management tool for experimental protocols, now  
fully integrated with OMERO.insight, so that protocols and  
experimental descriptions can be saved along with images and  
datasets.  Includes a new parameters function, so that protocols in  
traditional documents can be easily imported into OMERO. Supports,  
tables and .xls files.  Also runs as a standalone application.

-- OMERO.fs: a new OMERO client, that monitors a specific directory  
and enables automatic imports.  In its first incarnation, has quite  
limited functionality, supporting automatic import of LSM510 files  
only.  More coming soon!

As always, if you want the gory details, see

http://trac.openmicroscopy.org.uk/omero/milestone/OMERO-Beta4
http://trac.openmicroscopy.org.uk/shoola/milestone/OMERO-Beta4

Docs & Videos:
We've been pretty busy getting Beta4 ready and documented, so we  
haven;t yet updated the videos at http://www.openmicroscopy.org/site/videos 
.  New videos will appear over the next few weeks (they are really  
alot of work!).  Also, many of docs on our Trac sites are being  
deprecated.  In general, use http://openmicroscopy.org as a pointer  
for up-to-date docs.

Permissions:
Please note that in Beta4, all data in an OMERO server is now  
private-- in response to many requests.  Thus, all your images and  
tags are visible only by you.  You can share images with other users  
with the Share mechanism in OMERO.web.  This is in preparation for  
allowing users to change their own permissions in later releases.

Please let us know if you have any problems or comments.  As always,  
using the "Send a Comment" facility logs your suggestions with OME  
developers, and is an important source of information for us.

Thanks again for your support and interest.

Cheers,

Jason


**************************
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 palmeida at igc.gulbenkian.pt  Mon Mar 30 11:53:38 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Mon, 30 Mar 2009 10:53:38 +0000
Subject: [ome-users] Omero4 installation - [Errno 2] No such file or
	directory
Message-ID: <200903301153.39338.palmeida@igc.gulbenkian.pt>

Hi,

I am installing Omero4, following the instructions here:

http://www.openmicroscopy.org/site/documents/data-management/omero4/server/installation

and when I do 'bin/omero admin start' I get this error:

[Errno 2] No such file or directory

There is nothing in the logs, although the var/master , var/log and 
var/registry directories are created (all empty). Maybe I missed something 
but it's hard to tell what with this error message. I am using the same 
server where Omero 3.2 is installed, but I stopped it and I am using a newly 
created database.

The output from 'bin/omero config get' is:

omero.data.dir=/srv/OMERO4/
omero.db.name=omero4

bin/omero admin status also causes:

[Errno 2] No such file or directory

I noticed there's no line like 

psql -U omero -h localhost omero4 < OMERO4__0.sql

in the install instructions, but I tried that after I got the error and the 
results are the same.

Thanks for any help,
- Paulo


From callan at blackcat.ca  Mon Mar 30 13:01:35 2009
From: callan at blackcat.ca (Chris Allan)
Date: Mon, 30 Mar 2009 13:01:35 +0100
Subject: [ome-users] Omero4 installation - [Errno 2] No such file or
	directory
In-Reply-To: <200903301153.39338.palmeida@igc.gulbenkian.pt>
References: <200903301153.39338.palmeida@igc.gulbenkian.pt>
Message-ID: <F6178C8A-A5E2-46F2-9CCD-EAD35DA74307@blackcat.ca>


On 30 Mar 2009, at 11:53, Paulo Almeida wrote:

> Hi,

Hi Paulo.

> I am installing Omero4, following the instructions here:
>
> http://www.openmicroscopy.org/site/documents/data-management/omero4/server/installation
>
> and when I do 'bin/omero admin start' I get this error:
>
> [Errno 2] No such file or directory
>
> There is nothing in the logs, although the var/master , var/log and
> var/registry directories are created (all empty). Maybe I missed  
> something
> but it's hard to tell what with this error message. I am using the  
> same
> server where Omero 3.2 is installed, but I stopped it and I am using  
> a newly
> created database.
>
> The output from 'bin/omero config get' is:
>
> omero.data.dir=/srv/OMERO4/
> omero.db.name=omero4
>
> bin/omero admin status also causes:
>
> [Errno 2] No such file or directory
>
> I noticed there's no line like
>
> psql -U omero -h localhost omero4 < OMERO4__0.sql

Got this one. Thanks.

Not sure why you're getting the "No such file or directory" errors.  
I'll check into what might be causing the problem.

For the moment, can you give us the output of:

which icegridnode
which icebox
which icegridregistry

> in the install instructions, but I tried that after I got the error  
> and the
> results are the same.
>
> Thanks for any help,
> - Paulo

-Chris


From palmeida at igc.gulbenkian.pt  Mon Mar 30 14:21:29 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Mon, 30 Mar 2009 13:21:29 +0000
Subject: [ome-users] Omero4 installation - [Errno 2] No such file or
	directory
In-Reply-To: <F6178C8A-A5E2-46F2-9CCD-EAD35DA74307@blackcat.ca>
References: <200903301153.39338.palmeida@igc.gulbenkian.pt>
	<F6178C8A-A5E2-46F2-9CCD-EAD35DA74307@blackcat.ca>
Message-ID: <200903301421.30501.palmeida@igc.gulbenkian.pt>

Hi Chris,

The problem was I installed the Ice libraries but not the actual binaries 
(your request for output reminded me of that), so it is working now. 

You might want to add Ice to the prerequisites in the install instructions. It 
is listed in the Getting Started page, but not in the instructions, as far as 
I could tell.

Thanks, looking forward to test all the new features in production.
- Paulo

On Monday 30 March 2009 13:01:35 you wrote:
> On 30 Mar 2009, at 11:53, Paulo Almeida wrote:
> > Hi,
>
> Hi Paulo.
>
> > I am installing Omero4, following the instructions here:
> >
> > http://www.openmicroscopy.org/site/documents/data-management/omero4/serve
> >r/installation
> >
> > and when I do 'bin/omero admin start' I get this error:
> >
> > [Errno 2] No such file or directory
> >
> > There is nothing in the logs, although the var/master , var/log and
> > var/registry directories are created (all empty). Maybe I missed
> > something
> > but it's hard to tell what with this error message. I am using the
> > same
> > server where Omero 3.2 is installed, but I stopped it and I am using
> > a newly
> > created database.
> >
> > The output from 'bin/omero config get' is:
> >
> > omero.data.dir=/srv/OMERO4/
> > omero.db.name=omero4
> >
> > bin/omero admin status also causes:
> >
> > [Errno 2] No such file or directory
> >
> > I noticed there's no line like
> >
> > psql -U omero -h localhost omero4 < OMERO4__0.sql
>
> Got this one. Thanks.
>
> Not sure why you're getting the "No such file or directory" errors.
> I'll check into what might be causing the problem.
>
> For the moment, can you give us the output of:
>
> which icegridnode
> which icebox
> which icegridregistry
>
> > in the install instructions, but I tried that after I got the error
> > and the
> > results are the same.
> >
> > Thanks for any help,
> > - Paulo
>
> -Chris




From callan at blackcat.ca  Mon Mar 30 15:27:46 2009
From: callan at blackcat.ca (Chris Allan)
Date: Mon, 30 Mar 2009 15:27:46 +0100
Subject: [ome-users] Omero4 installation - [Errno 2] No such file or
	directory
In-Reply-To: <200903301421.30501.palmeida@igc.gulbenkian.pt>
References: <200903301153.39338.palmeida@igc.gulbenkian.pt>
	<F6178C8A-A5E2-46F2-9CCD-EAD35DA74307@blackcat.ca>
	<200903301421.30501.palmeida@igc.gulbenkian.pt>
Message-ID: <F2398977-14F0-449F-AAD2-9269BAD78AB7@blackcat.ca>


On 30 Mar 2009, at 14:21, Paulo Almeida wrote:

> Hi Chris,

Hi Paulo.

> The problem was I installed the Ice libraries but not the actual  
> binaries
> (your request for output reminded me of that), so it is working now.
>
> You might want to add Ice to the prerequisites in the install  
> instructions. It
> is listed in the Getting Started page, but not in the instructions,  
> as far as
> I could tell.

Done. Thanks for the feedback.

> Thanks, looking forward to test all the new features in production.
> - Paulo

-Chris


From m.woodbridge at imperial.ac.uk  Mon Mar 30 15:37:44 2009
From: m.woodbridge at imperial.ac.uk (Mark Woodbridge)
Date: Mon, 30 Mar 2009 15:37:44 +0100
Subject: [ome-users] Omero4 installation - [Errno 2] No such file
	or	directory
In-Reply-To: <F6178C8A-A5E2-46F2-9CCD-EAD35DA74307@blackcat.ca>
References: <200903301153.39338.palmeida@igc.gulbenkian.pt>
	<F6178C8A-A5E2-46F2-9CCD-EAD35DA74307@blackcat.ca>
Message-ID: <49D0D938.5010806@imperial.ac.uk>

Hi,

I'm seeing the same error on RHEL, though no problems with Ubuntu. I'm 
probably missing some RPMs but not sure which...

[cisbic at omero omero-Beta4.0.0]$ bin/omero config set omero.data.dir 
/misc/data/omero4
[Errno 2] No such file or directory

[cisbic at omero omero-Beta4.0.0]$ ls /misc/data
omero4

[root at omero ~]# which icegridnode
/usr/bin/icegridnode
[root at omero ~]# which icebox
/usr/bin/icebox
[root at omero ~]# which icegridregistry
/usr/bin/icegridregistry

Is there any way to make the error a bit more verbose?

Mark.

Chris Allan wrote:
> On 30 Mar 2009, at 11:53, Paulo Almeida wrote:
> 
>> Hi,
> 
> Hi Paulo.
> 
>> I am installing Omero4, following the instructions here:
>>
>> http://www.openmicroscopy.org/site/documents/data-management/omero4/server/installation
>>
>> and when I do 'bin/omero admin start' I get this error:
>>
>> [Errno 2] No such file or directory
>>
>> There is nothing in the logs, although the var/master , var/log and
>> var/registry directories are created (all empty). Maybe I missed  
>> something
>> but it's hard to tell what with this error message. I am using the  
>> same
>> server where Omero 3.2 is installed, but I stopped it and I am using  
>> a newly
>> created database.
>>
>> The output from 'bin/omero config get' is:
>>
>> omero.data.dir=/srv/OMERO4/
>> omero.db.name=omero4
>>
>> bin/omero admin status also causes:
>>
>> [Errno 2] No such file or directory
>>
>> I noticed there's no line like
>>
>> psql -U omero -h localhost omero4 < OMERO4__0.sql
> 
> Got this one. Thanks.
> 
> Not sure why you're getting the "No such file or directory" errors.  
> I'll check into what might be causing the problem.
> 
> For the moment, can you give us the output of:
> 
> which icegridnode
> which icebox
> which icegridregistry
> 
>> in the install instructions, but I tried that after I got the error  
>> and the
>> results are the same.
>>
>> Thanks for any help,
>> - Paulo
> 
> -Chris
> _______________________________________________
> 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  Mon Mar 30 17:01:48 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Mon, 30 Mar 2009 16:01:48 +0000
Subject: [ome-users] Accessing web interfaces from other computers
Message-ID: <200903301701.48890.palmeida@igc.gulbenkian.pt>

Hi,

I can access the webadmin and webclient interfaces from the server, but not 
from other machines.

nmap says port 8000 is closed, and the output of: 

netstat -an |grep 8000

is:

tcp        0      0 127.0.0.1:8000          0.0.0.0:*               LISTEN

I think that means it is only listening on 127.0.0.1?  If so, how do I make 
omero listen to computers other than localhost? I tried 'bin/omero config 
simple' (and advanced) but that returned:

unhashable type

I also looked around on the etc directory, especially omero.properties, but I 
couldn't figure it out.

Thanks,
Paulo


From jeremiahtattersall at gmail.com  Mon Mar 30 20:26:36 2009
From: jeremiahtattersall at gmail.com (Jeremiah Tattersall)
Date: Mon, 30 Mar 2009 15:26:36 -0400
Subject: [ome-users] MacPython
Message-ID: <42532c4a0903301226j18cf6671s54167320a7f1afc@mail.gmail.com>

Hello,
I am currently trying to upgrade to the new OMERO v4 server and have hit a
snag. I keep receiving an error message that Python has suddenly quite.
The script reads:
Fatal Python error: Interpreter not initialized (version mismatch?)Abort
trap
I am currently running Python v. 2.5. Should I upgrade to v.2.6?

Thank you for your time.

-- 
-Jeremiah Tattersall
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From josh.moore at gmx.de  Mon Mar 30 20:35:10 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Mon, 30 Mar 2009 21:35:10 +0200
Subject: [ome-users] Omero4 installation - [Errno 2] No such file or
	directory
In-Reply-To: <49D0D938.5010806@imperial.ac.uk>
References: <200903301153.39338.palmeida@igc.gulbenkian.pt>
	<F6178C8A-A5E2-46F2-9CCD-EAD35DA74307@blackcat.ca>
	<49D0D938.5010806@imperial.ac.uk>
Message-ID: <18897.7918.309861.153624@josh-moores-computer.local>


Mark Woodbridge writes:
 > Hi,

Hey Mark,

 > I'm seeing the same error on RHEL, though no problems with
 > Ubuntu. I'm probably missing some RPMs but not sure which...
 > 
 > [cisbic at omero omero-Beta4.0.0]$ bin/omero config set omero.data.dir 
 > /misc/data/omero4
 > [Errno 2] No such file or directory

As with the errors re: icegrid*, this error actually means that
bin/omero is not able to call an executable on your PATH. (This is a
regression which I've filed as #1289). The only executable that
bin/omero tries to call is "java". Is it possible that that's not
available?

 > [cisbic at omero omero-Beta4.0.0]$ ls /misc/data
 > omero4
 > 
 > [root at omero ~]# which icegridnode
 > /usr/bin/icegridnode
 > [root at omero ~]# which icebox
 > /usr/bin/icebox
 > [root at omero ~]# which icegridregistry
 > /usr/bin/icegridregistry
 > 
 > Is there any way to make the error a bit more verbose?

Definitely. Try:

DEBUG=1 bin/omero config get

 > Mark.

Best wishes,
~Josh.


From josh.moore at gmx.de  Mon Mar 30 20:57:37 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Mon, 30 Mar 2009 21:57:37 +0200
Subject: [ome-users]  Accessing web interfaces from other computers
In-Reply-To: <200903301701.48890.palmeida@igc.gulbenkian.pt>
References: <200903301701.48890.palmeida@igc.gulbenkian.pt>
Message-ID: <18897.9265.705825.815@josh-moores-computer.local>


Ola Paulo,

Paulo Almeida writes:
 > I can access the webadmin and webclient interfaces from the server,
 > but not from other machines.
 > 
 > nmap says port 8000 is closed, and the output of: 
 > 
 > netstat -an |grep 8000
 > 
 > is:
 > 
 > tcp        0      0 127.0.0.1:8000          0.0.0.0:*               LISTEN
 > 
 > I think that means it is only listening on 127.0.0.1? 

Exactly. The webclient doesn't come with HTTPS out-of-the-box. In
order to protect your installation, we start it only on 127.0.0.1. To
make it listen elsewhere, you'll need to modify etc/grid/templates.xml

    <server-template id="ShellTemplate">
      <parameter name="id"/>
      <parameter name="exe" default="python"/>
      <parameter name="act" default="always"/>
      <server id="${id}" exe="${exe}" activation="${act}">
        <option>lib/python/shellserver.py</option>
        <option>${id}</option>
        <!-- ADD THE NEXT LINE -->
        <option>http://your.address.com</option>
        <adapter name="${id}Adapter" register-process="true" endpoints="tcp"/>
      </server>
    </server-template>

where the value you add is passed to `python manage.py runserver`
who's command-line option is of the form: ipaddr:port

This installation is meant to get you started with the server, but you
may want to look at the OMERO.web instructions directly. See:
https://trac.openmicroscopy.org.uk/omero/wiki/OmeroWeb

 > If so, how do I make omero listen to computers other than
 > localhost? I tried 'bin/omero config simple' (and advanced) but
 > that returned:

  bin/omero config simple?

Where did you see these commands? I'm not quite sure where it could
have come from. See:

  bin/omero config

for instructions on using config, but unfortunately there is no
configuration parameter for setting the interface used by OMERO.web.

 > unhashable type


This is actually *really* odd, maybe you could help us track it
down. What python version are you using? What java version?

  python --version
  java -version


 > I also looked around on the etc directory, especially
 > omero.properties, but I couldn't figure it out.

 > Thanks,
 > Paulo

Hope we can figure that out.
Cheers,
~Josh


From josh.moore at gmx.de  Mon Mar 30 21:01:20 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Mon, 30 Mar 2009 22:01:20 +0200
Subject: [ome-users]  MacPython
In-Reply-To: <42532c4a0903301226j18cf6671s54167320a7f1afc@mail.gmail.com>
References: <42532c4a0903301226j18cf6671s54167320a7f1afc@mail.gmail.com>
Message-ID: <18897.9488.172647.104765@josh-moores-computer.local>


Hi Jeremiah,

this sounds more like a mismatch between your MacPython installation and
your Ice installation. How did you install Ice? (Also: what command
are you getting this exception on?)

Cheers,
~Josh.

Jeremiah Tattersall writes:
 > I am currently trying to upgrade to the new OMERO v4 server and
 > have hit a snag. I keep receiving an error message that Python has
 > suddenly quite.  The script reads: Fatal Python error: Interpreter
 > not initialized (version mismatch?)Abort trap I am currently
 > running Python v. 2.5. Should I upgrade to v.2.6?
 > 
 > Thank you for your time.
 > 
 > -Jeremiah Tattersall


From m.woodbridge at imperial.ac.uk  Mon Mar 30 23:17:06 2009
From: m.woodbridge at imperial.ac.uk (Mark Woodbridge)
Date: Mon, 30 Mar 2009 23:17:06 +0100
Subject: [ome-users] Accessing web interfaces from other computers
In-Reply-To: <18897.9265.705825.815@josh-moores-computer.local>
References: <200903301701.48890.palmeida@igc.gulbenkian.pt>
	<18897.9265.705825.815@josh-moores-computer.local>
Message-ID: <49D144E2.80804@imperial.ac.uk>

I had the same problem as Paulo. Adding:

<option>0.0.0.0:8000</option>

to etc/grid/templates.xml didn't work. But changing 
lib/python/omero/plugins/server.py to include:

django = 
["python","manage.py","runserver","0.0.0.0:8000","--noreload"]+list(args)

did work. I also needed to install python-imaging and python-sqlite2 on 
RHEL to get webadmin/webclient to work, in case anyone else is having 
problems.

My ICE java/RPM problems were sorted after using DEBUG=1 (thanks Josh!).

Mark.

josh.moore at gmx.de wrote:
> Ola Paulo,
> 
> Paulo Almeida writes:
>  > I can access the webadmin and webclient interfaces from the server,
>  > but not from other machines.
>  > 
>  > nmap says port 8000 is closed, and the output of: 
>  > 
>  > netstat -an |grep 8000
>  > 
>  > is:
>  > 
>  > tcp        0      0 127.0.0.1:8000          0.0.0.0:*               LISTEN
>  > 
>  > I think that means it is only listening on 127.0.0.1? 
> 
> Exactly. The webclient doesn't come with HTTPS out-of-the-box. In
> order to protect your installation, we start it only on 127.0.0.1. To
> make it listen elsewhere, you'll need to modify etc/grid/templates.xml
> 
>     <server-template id="ShellTemplate">
>       <parameter name="id"/>
>       <parameter name="exe" default="python"/>
>       <parameter name="act" default="always"/>
>       <server id="${id}" exe="${exe}" activation="${act}">
>         <option>lib/python/shellserver.py</option>
>         <option>${id}</option>
>         <!-- ADD THE NEXT LINE -->
>         <option>http://your.address.com</option>
>         <adapter name="${id}Adapter" register-process="true" endpoints="tcp"/>
>       </server>
>     </server-template>
> 
> where the value you add is passed to `python manage.py runserver`
> who's command-line option is of the form: ipaddr:port
> 
> This installation is meant to get you started with the server, but you
> may want to look at the OMERO.web instructions directly. See:
> https://trac.openmicroscopy.org.uk/omero/wiki/OmeroWeb
> 
>  > If so, how do I make omero listen to computers other than
>  > localhost? I tried 'bin/omero config simple' (and advanced) but
>  > that returned:
> 
>   bin/omero config simple?
> 
> Where did you see these commands? I'm not quite sure where it could
> have come from. See:
> 
>   bin/omero config
> 
> for instructions on using config, but unfortunately there is no
> configuration parameter for setting the interface used by OMERO.web.
> 
>  > unhashable type
> 
> 
> This is actually *really* odd, maybe you could help us track it
> down. What python version are you using? What java version?
> 
>   python --version
>   java -version
> 
> 
>  > I also looked around on the etc directory, especially
>  > omero.properties, but I couldn't figure it out.
> 
>  > Thanks,
>  > Paulo
> 
> Hope we can figure that out.
> Cheers,
> ~Josh
> _______________________________________________
> 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  Mon Mar 30 23:56:23 2009
From: palmeida at igc.gulbenkian.pt (Paulo Almeida)
Date: Mon, 30 Mar 2009 23:56:23 +0100 (WEST)
Subject: [ome-users] Accessing web interfaces from other computers
In-Reply-To: <18897.9265.705825.815@josh-moores-computer.local>
References: <200903301701.48890.palmeida@igc.gulbenkian.pt>
	<18897.9265.705825.815@josh-moores-computer.local>
Message-ID: <56224.192.168.50.3.1238453783.squirrel@igcns.igc.gulbenkian.pt>

Hello Josh and Mark,

> I tried 'bin/omero config simple' but
> that returned:
>
>   bin/omero config simple?
>
> Where did you see these commands? I'm not quite sure where it could
> have come from. See:

Sorry, that was my mistake, I meant 'bin/omero setup simple', which does
cause the 'unhashable type' output. python is 2.5.2 and java is 1.6.0_12 ,
in case that's still relevant.

Regarding remote connections, I tried adding that option in templates.xml
and it didn't work, as Mark said. I tried the IP of the machine, as well
as 0.0.0.0, with and without http:// in front, and it always caused an
exception when starting the server. Something like this:

2009-03-30 23:18:35,214 INFO  [                ome.services.blitz.Entry] (
main) Creating http://172.22.50.131:8000. Please wait...
2009-03-30 23:18:35,506 ERROR [                ome.services.blitz.Entry] (
main) Error on startup.
org.springframework.beans.factory.access.BootstrapException: Unable to
return specified BeanFactory instance: factory key
[http://172.22.50.131:8000], from grou
p with resource name [classpath*:beanRefContext.xml]; nested exception is
org.sp
ringframework.beans.factory.NoSuchBeanDefinitionException: No bean named
'http://172.22.50.131:8000' is defined

--------

The good news is I tried Mark's suggestion and it worked, so thanks for
that. If you need more feedback to understand why it's not working with
templates.xml I can send the whole log, or try to figure out if I'm doing
something wrong with the <option>.

Best,
Paulo


>
>  > I also looked around on the etc directory, especially
>  > omero.properties, but I couldn't figure it out.
>
>  > Thanks,
>  > Paulo
>
> Hope we can figure that out.
> Cheers,
> ~Josh
>




From mvalle at cscs.ch  Tue Mar 31 04:14:57 2009
From: mvalle at cscs.ch (Mario Valle)
Date: Tue, 31 Mar 2009 05:14:57 +0200
Subject: [ome-users] MacPython
In-Reply-To: <42532c4a0903301226j18cf6671s54167320a7f1afc@mail.gmail.com>
References: <42532c4a0903301226j18cf6671s54167320a7f1afc@mail.gmail.com>
Message-ID: <49D18AB1.2070706@cscs.ch>

Jeremiah Tattersall wrote:
> Hello,
>
> I am currently trying to upgrade to the new OMERO v4 server and have 
> hit a snag. I keep receiving an error message that Python has suddenly 
> quite. 
> The script reads: 
> Fatal Python error: Interpreter not initialized (version mismatch?)
> Abort trap
> I am currently running Python v. 2.5. Should I upgrade to v.2.6?
>
> Thank you for your time.
>
> -- 
> -Jeremiah Tattersall
> ------------------------------------------------------------------------
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>   
I had the same problem when upgraded Python, recompiled Omero, but not ICE.
Try to recompile ICEpy and then OMERO.
Hope it helps
                            mario

-- 
Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82



From stephen.ogg at imb.a-star.edu.sg  Tue Mar 31 06:11:50 2009
From: stephen.ogg at imb.a-star.edu.sg (Stephen Ogg)
Date: Tue, 31 Mar 2009 13:11:50 +0800
Subject: [ome-users] icegridnode
Message-ID: <D86C4F10-E147-4264-BD00-C62B023A7ECD@imb.a-star.edu.sg>

Hi All-

I am trying to install omero4 server on a Mac Xserve running OS X
10.5.6. I have also hit a snag

after issuing the bin/omero admin start command, I get the following
error after the "No descriptor given. Using etc/grid/default.xml"

icegridnode: failure occurred in daemon


output of which:

/opt/local/bin/icebox
/opt/local/bin/icegridnode
/opt/local/icegridregistry


Any help appreciated
Cheers

Steve Ogg



From josh.moore at gmx.de  Tue Mar 31 09:12:04 2009
From: josh.moore at gmx.de (josh.moore at gmx.de)
Date: Tue, 31 Mar 2009 10:12:04 +0200
Subject: [ome-users]  icegridnode
In-Reply-To: <D86C4F10-E147-4264-BD00-C62B023A7ECD@imb.a-star.edu.sg>
References: <D86C4F10-E147-4264-BD00-C62B023A7ECD@imb.a-star.edu.sg>
Message-ID: <18897.53332.766019.567721@josh-moores-computer.local>

Stephen Ogg writes:
 > Hi All-

Hi Stephen,

 > I am trying to install omero4 server on a Mac Xserve running OS X
 > 10.5.6. I have also hit a snag
 > 
 > after issuing the bin/omero admin start command, I get the following
 > error after the "No descriptor given. Using etc/grid/default.xml"
 > 
 > icegridnode: failure occurred in daemon

This almost certainly means that the icegridnode process is already
running. You can check in var/log/master.err to see if that's the
case, or use: ps auxww | grep icegridnode

Had you already tried stopping it with "/bin/omero admin stop"? If
not, that's definitely the place to start. If you had, and it didn't
stop, getting your log files zipped up and the output of the "ps"
command would be useful, but one way or the other it's also safe to
shutdown the server via: killall icegridnode.

 > output of which:
 > 
 > /opt/local/bin/icebox
 > /opt/local/bin/icegridnode
 > /opt/local/icegridregistry
 > 
 > Any help appreciated
 > Cheers
 > 
 > Steve Ogg

Hope that helps!
~Josh.


From mvalle at cscs.ch  Tue Mar 31 10:40:13 2009
From: mvalle at cscs.ch (Mario Valle)
Date: Tue, 31 Mar 2009 11:40:13 +0200
Subject: [ome-users] FYI warnings and small things on OSX
Message-ID: <49D1E4FD.10700@cscs.ch>

Congratulation for 4.0! OMERO installed without problems on OSX 10.4

Now we started testing, so here is the first "small problems" report :-)
Below you find some warning from running build.py (we have Python 2.6.1).
Attached a screenshot of insight. You see, the two image icons overlap.
Also in the build instructions (I'm still using the ones from the mail) add that
PYTHONPATH should be defined before running bin/omero to:
PYTHONPATH={blabla}/Ice-3.3.0/py/python:{blabla}/omero-4.0/dist/lib/python

Hope it helps
			mario


/omero-4.0/components/server/src/ome/security/basic/EventHandler.java:94: warning: 
[deprecation] connection() in org.hibernate.Session has been deprecated
         Statement statement = session.connection().createStatement();
                                      ^
/omero-4.0/components/server/src/ome/services/fulltext/FullTextIndexer.java:125: warning: 
[deprecation] connection() in org.hibernate.Session has been deprecated
                 Statement s = session.connection().createStatement();
                                      ^
/omero-4.0/components/server/src/ome/tools/spring/ManualFlushHibernateTemplate.java:21: 
warning: [deprecation] saveOrUpdateAll(java.util.Collection) in 
org.springframework.orm.hibernate3.HibernateOperations has been deprecated
public class ManualFlushHibernateTemplate extends HibernateTemplate {
        ^
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
3 warnings


/omero-4.0/target/scons/scons-local-1.1.0/SCons/Platform/posix.py:38: DeprecationWarning: 
The popen2 module is deprecated.  Use the subprocess module.
   import popen2
/omero-4.0/target/scons/scons-local-1.1.0/SCons/Tool/msvs.py:37: DeprecationWarning: the 
md5 module is deprecated; use hashlib instead
   import md5

/omero-4.0/components/blitz/resources/omero/Internal.ice:1: warning: Converted [CR+LF] to 
[LF]


/omero-4.0/components/blitz/generated/omero/api/_ServiceFactoryTie.java:80: warning: 
[deprecation] close(Ice.Current) in omero.api._ServiceFactoryOperations has been deprecated
     close(Ice.Current __current)
     ^
/omero-4.0/components/blitz/generated/omero/api/_ServiceFactoryTie.java:82: warning: 
[deprecation] close(Ice.Current) in omero.api._ServiceFactoryOperations has been deprecated
         _ice_delegate.close(__current);
                      ^
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
2 warnings

/omero-4.0/components/tools/OmeroImporter/src/ch/randelshofer/quaqua/jaguar/filechooser/QuaquaJaguarFileChooserPanel.java:51: 
warning: [deprecation] show() in java.awt.Dialog has been deprecated
         d.show();
          ^
/omero-4.0/components/tools/OmeroImporter/src/ch/randelshofer/quaqua/panther/QuaquaPantherFileChooserUI.java:1872: 
warning: [deprecation] show() in java.awt.Dialog has been deprecated
             dialog.show();
                   ^
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
2 warnings


-- 
Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82
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From mvalle at cscs.ch  Tue Mar 31 12:46:03 2009
From: mvalle at cscs.ch (Mario Valle)
Date: Tue, 31 Mar 2009 13:46:03 +0200
Subject: [ome-users] Building OmeroCpp
Message-ID: <49D2027B.2050605@cscs.ch>

As usual :-) I'm trying to build OmeroCpp.

I have done:
	 cd omero-4.0; ./build.py build-cpp

It works for a while, then stops with:

tools-init:
Copying 253 files to /omero-4.0/components/tools/OmeroCpp/target

build:
/omero-4.0/target/scons/scons-local-1.1.0/SCons/Platform/posix.py:38: DeprecationWarning: 
The popen2 module is deprecated.  Use the subprocess module.
   import popen2
/omero-4.0/target/scons/scons-local-1.1.0/SCons/Tool/msvs.py:37: DeprecationWarning: the 
md5 module is deprecated; use hashlib instead
   import md5
Ice/Ice.h not found

I tried to:
1) define ICE_HOME to {ice_top_dir}
2) define ICE_HOME to {ice_top_dir}/cpp
3) run bin/omero config set ice.home {ice_top_dir}/cpp
4) create dist/etc/local.properties with the single line
    ice.home={ice_top_dir}/cpp

But the build process tries always to find Ice includes under /usr/share/Ice/include

Any idea? Afterwards I can contribute with the OmeroCpp build instructions...

Ciao!
	mario

-- 
Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82


From callan at blackcat.ca  Tue Mar 31 13:20:18 2009
From: callan at blackcat.ca (Chris Allan)
Date: Tue, 31 Mar 2009 13:20:18 +0100
Subject: [ome-users] MacPython
In-Reply-To: <42532c4a0903301226j18cf6671s54167320a7f1afc@mail.gmail.com>
References: <42532c4a0903301226j18cf6671s54167320a7f1afc@mail.gmail.com>
Message-ID: <1238502018.24908.10.camel@shadowblade.openmicroscopy.org.uk>

Hi Jeremiah,

Mac OS X 10.4 with a Python 2.5 you compiled/installed yourself or Mac
OS X 10.5 with Apple's shipped Python version?

Ciao.

-Chris

On Mon, 2009-03-30 at 15:26 -0400, Jeremiah Tattersall wrote:
> Hello,
> 
> 
> I am currently trying to upgrade to the new OMERO v4 server and have
> hit a snag. I keep receiving an error message that Python has suddenly
> quite. 
> The script reads: 
> Fatal Python error: Interpreter not initialized (version mismatch?)
> Abort trap
> I am currently running Python v. 2.5. Should I upgrade to v.2.6?
> 
> 
> Thank you for your time.
> 
> 
> -- 
> -Jeremiah Tattersall
> 
> _______________________________________________
> 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  Tue Mar 31 14:59:04 2009
From: callan at blackcat.ca (Chris Allan)
Date: Tue, 31 Mar 2009 14:59:04 +0100
Subject: [ome-users] MacPython
In-Reply-To: <42532c4a0903310550t66cdfe94k8eae0e989874473@mail.gmail.com>
References: <42532c4a0903301226j18cf6671s54167320a7f1afc@mail.gmail.com>
	<1238502018.24908.10.camel@shadowblade.openmicroscopy.org.uk>
	<42532c4a0903310550t66cdfe94k8eae0e989874473@mail.gmail.com>
Message-ID: <1238507944.24908.23.camel@shadowblade.openmicroscopy.org.uk>

On Tue, 2009-03-31 at 08:50 -0400, Jeremiah Tattersall wrote:
> Hello Chris,

Hi Jeremiah,

> I am currently running Max OS X 10.5 and installed Python 2.5.4
> myself. I just upgraded to Python 2.6.1.

Okay. If you've done that you have to compile IcePy by hand and include
the detination in your PYTHONPATH before starting OMERO as Mario has
outlined. Is there some particular reason why you upgraded from Python
2.5.1 that is included with Mac OS X 10.5?

> Thank you,
> 
> 
> -Jeremiah

-Chris



From mvalle at cscs.ch  Tue Mar 31 16:37:42 2009
From: mvalle at cscs.ch (Mario Valle)
Date: Tue, 31 Mar 2009 17:37:42 +0200
Subject: [ome-users] Building OmeroCpp
In-Reply-To: <49D2027B.2050605@cscs.ch>
References: <49D2027B.2050605@cscs.ch>
Message-ID: <49D238C6.9040800@cscs.ch>

An update.

The problem seems to manifest in the file
components/antlib/resources/global.xml at line 63:

         <condition property="ice.home" value="${env.ICE_HOME}">
             <isset property="env.ICE_HOME"/>
         </condition>

here the property "ice.home" has always the value: /usr/share/Ice
even if the ICE_HOME environment variable, and as a consequence the property env.ICE_HOME,
is set to: "/Users/mvalle/Ice-3.3.0/cpp".

To continue OmeroCpp build (not yet finished, but seems to work correctly)
I changed the line:
                     <env key="ICE_HOME" value="${ice.home}"/>
to:
                     <env key="ICE_HOME" value="/Users/mvalle/Ice-3.3.0/cpp"/>
in the "scons_py" macro.

Any idea?
		mario



Mario Valle wrote:
> As usual :-) I'm trying to build OmeroCpp.
> 
> I have done:
> 	 cd omero-4.0; ./build.py build-cpp
> 
> It works for a while, then stops with:
> 
> tools-init:
> Copying 253 files to /omero-4.0/components/tools/OmeroCpp/target
> 
> build:
> /omero-4.0/target/scons/scons-local-1.1.0/SCons/Platform/posix.py:38: DeprecationWarning: 
> The popen2 module is deprecated.  Use the subprocess module.
>    import popen2
> /omero-4.0/target/scons/scons-local-1.1.0/SCons/Tool/msvs.py:37: DeprecationWarning: the 
> md5 module is deprecated; use hashlib instead
>    import md5
> Ice/Ice.h not found
> 
> I tried to:
> 1) define ICE_HOME to {ice_top_dir}
> 2) define ICE_HOME to {ice_top_dir}/cpp
> 3) run bin/omero config set ice.home {ice_top_dir}/cpp
> 4) create dist/etc/local.properties with the single line
>     ice.home={ice_top_dir}/cpp
> 
> But the build process tries always to find Ice includes under /usr/share/Ice/include
> 
> Any idea? Afterwards I can contribute with the OmeroCpp build instructions...
> 
> Ciao!
> 	mario
> 

-- 
Ing. Mario Valle
Data Analysis and Visualization Group            | http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91) 610.82.82