[ome-users] Problem with import from imageJ and problem with Java web start

Mon Dec 4 19:19:02 GMT 2006

Hi Keith,

Sorry to hear of your troubles. Please note that both the ImageJ/OME
connectivity and VisBio Web Start support are somewhat in flux right
now, and currently being actively developed to be more robust. We
expect to have a better VisBio JWS link by version 2.6.1, and are
nearly done fixing some known problems with the Java remote interface
to OME.

In the meantime, though, both of these features have significant problems.

> First, I have this error when I try and import images into a new OME
> instance from ImageJ:

I tested the currently released version of the OME Plugin for ImageJ
with the latest version of OME from CVS, on my Ubuntu Dapper system
with DBD::Pg 1.43 installed, and was able to upload an image
successfully. You are running OME 2.6.0rc3, right? And what version of
DBD::Pg are you using? Some of the versions past 1.43 are known to be
incompatible with OME.

> Second,
>
> I have a problem running the Visbio program using the java web start within
> our proxy firewall, the test applications work ok after entering the
> firewall proxy user + password.

Both OME 2.6.0rc3 has an old Web Start configuration for VisBio
hardcoded in. The simplest way to fix this is to change the source
code of OME/src/perl2/OME/Web/VisBio.pm to match the new configuration
(see http://www.loci.wisc.edu/visbio/jws/visbio.jnlp for the current
configuration).

The OME 2.6.0 final release will match the current VisBio
configuration, but still be hardcoded. We are also evaluating how to
make the VisBio link more robust for the next release, OME 2.6.1. We
will probably provide an extra level of indirection in the JNLP
generation (calling a perl script that lives on the LOCI server to do
so), and we may also bundle a version of VisBio with the OME release
as a fallback, or even the default.

> Can I put the visbio package on a local machine and alter the java webstart
> xml to point to this?  Any doc to do this?

Yes, it should be fairly straightforward. Just change the VisBio.pm
file to your liking, and put the necessary JAR files on your own
server. You can copy them from the LOCI server if you wish, or get the
code from the Subversion repository (third-party JARs are in there,
and the LOCI code can be compiled from source using ant). The only
trick if you don't copy them from the LOCI server's jws folder
directly is: the JARs must be signed using the jarsigner tool. Feel
free to email me with any questions about configuring VisBio and OME
for Web Start, and I can point you in the right direction.

-Curtis

On 12/1/06, Keith.Neil at sanofi-aventis.com <Keith.Neil at sanofi-aventis.com> wrote:
>
>
>
>
> First, I have this error when I try and import images into a new OME
> instance from ImageJ:
>
> An exception has occurred:
> org.openmicroscopy.ds.RemoteServerErrorException: error
> executing RPC `dispatch'.
> DBD::Pg::st execute failed: ERROR:  null value in column
> "module_execution_id" violates not-null constraint
>  at /usr/lib/perl5/site_perl/5.8.8/OME/Factory.pm line 858
>  OME::Factory::newObject('OME::Factory=HASH(0xb4cb4d4)',
> 'OME::SemanticType::__DisplayChannel', 'HASH(0xbbdc810)')
> called at /usr/lib/perl5/site_perl/5.8.8/OME/Factory.pm
> line 1022
>  OME::Factory::newAttribute('OME::Factory=HASH(0xb4cb4d4)',
> 'OME::SemanticType=HASH(0xaa05b88)', 'undef', 'undef',
> 'HASH(0xbbdc810)') called at
> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/DTO/GenericAssembler.pm
> line 290
> OME::Remote::DTO::GenericAssembler::__updateDTO('OME::Remote::DTO::GenericAssembler',
> 'OME::SemanticType::__DisplayChannel', 'HASH(0xbbdc810)',
> 'HASH(0xa277ec8)') called at
> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/DTO/GenericAssembler.pm
> line 329
> OME::Remote::DTO::GenericAssembler::updateDTO('OME::Remote::DTO::GenericAssembler',
> '@DisplayChannel', 'HASH(0xbbdc810)') called at
> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facades/GenericFacade.pm
> line 133
> OME::Remote::Facades::GenericFacade::updateObject('OME::Remote::Facades::GenericFacade',
> '@DisplayChannel', 'HASH(0xbbdc810)') called at
> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facade.pm line
> 181
>  eval {...} called at
> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Facade.pm line
> 175
>  OME::Remote::Facade::dispatch('OME::Remote::Facade',
> 'f5333f330b6b334240c9ba28a1e70961', 'updateObject',
> '@DisplayChannel', 'HASH(0xbbdc810)') called at
> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/RPC2.pm line 142
>  eval {...} called at
> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/RPC2.pm line 141
> OME::Remote::RPC2::serve('OME::Remote::RPC2=HASH(0xb96a9d8)',
> '<?xml version="1.0"
> encoding="ISO-8859-1"?><methodCall><metho...') called at
> /usr/lib/perl5/site_perl/5.8.8/OME/Remote/Apache2/XMLRPC.pm
> line 31
> OME::Remote::Apache2::XMLRPC::handler('Apache2::RequestRec=SCALAR(0xbb05100)')
> called at -e line 0
>  eval {...} called at -e line 0
>
>
> Second,
>
> I have a problem running the Visbio program using the java web start within
> our proxy firewall, the test applications work ok after entering the
> firewall proxy user + password.  The Visbio program generates the following
> exception:JNLPException[category: Erreur de téléchargement : Exception:
> java.io.IOException: HTTP response 404 : LaunchDesc: null ]
>  at
> com.sun.javaws.cache.DownloadProtocol.doDownload(Unknown
> Source)
>  at
> com.sun.javaws.cache.DownloadProtocol.getDownloadSize(Unknown
> Source)
>  at com.sun.javaws.LaunchDownload.downloadJarFiles(Unknown
> Source)
>  at
> com.sun.javaws.LaunchDownload.downloadEagerorAll(Unknown
> Source)
>  at com.sun.javaws.Launcher.downloadResources(Unknown
> Source)
>  at com.sun.javaws.Launcher.handleApplicationDesc(Unknown
> Source)
>  at com.sun.javaws.Launcher.handleLaunchFile(Unknown
> Source)
>  at com.sun.javaws.Launcher.run(Unknown Source)
>  at java.lang.Thread.run(Unknown Source)
>
>
> Une erreur est survenue au cours du lancement ou de l'exécution de
> l'application.
>
> Titre : VisBio
> Fournisseur : UW-Madison LOCI
> Catégorie : Erreur de téléchargement
>
> Impossible de charger la ressource :
> http://www.loci.wisc.edu/visbio/jws/bio_formats.jar
>
>
>
> <?xml version="1.0" encoding="utf-8"?>
> <jnlp
>   spec="1.0+"
>   codebase="http://www.loci.wisc.edu/visbio/jws">
>   <information>
>     <title>VisBio</title>
>     <vendor>UW-Madison LOCI</vendor>
>     <homepage
> href="http://www.loci.wisc.edu/visbio/index.html"/>
>     <description>A biological visualization tool designed for easy
>       visualization and analysis of multidimensional image
> data</description>
>     <icon href="visbio-icon.jpg"/>
>     <icon kind="splash" href="visbio-logo.jpg"/>
>     <offline-allowed/>
>   </information>
>   <security>
>     <all-permissions/>
>   </security>
>   <resources>
>     <j2se version="1.4+" max-heap-size="512m"/>
>     <jar href="visbio.jar"/>
>     <jar href="bio_formats.jar"/>
>     <jar href="commons-httpclient-2.0-rc2.jar"/>
>     <jar href="commons-logging.jar"/>
>     <jar href="forms-1.0.4.jar"/>
>     <jar href="ij.jar"/>
>     <jar href="looks-1.2.2.jar"/>
>     <jar href="ome-java.jar"/>
>     <jar href="visad.jar"/>
>     <jar href="xmlrpc-1.2-b1.jar"/>
>   </resources>
>   <application-desc main-class="loci.visbio.VisBio">
>
> <argument>ome-image=key:f5333f330b6b334240c9ba28a1e70961 at xxx.xx.xx.xxxxx:1</argument>
>   </application-desc>
> </jnlp>
>
>
> (I edited out the machine name...)
>
> Can I put the visbio package on a local machine and alter the java webstart
> xml to point to this?  Any doc to do this?
>
>
>
> Thanks very much for your help!
>
>
>
> Keith
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