[ome-users] teething problems

Curtis Rueden ctrueden at wisc.edu
Tue Sep 12 16:48:40 BST 2006 

Hi Steve,

Ah, I should have realized you'd be using the Mac OS X version of Shoola;
sorry for my inaccuracies.

Anyway, I have good news, sort of. I tested Shoola on a Mac OS X machine in
our lab and encountered the same problem. Further investigation revealed
that it is also an issue with VisBio. The problem stems from OME's Java
remote framework library (ome-java.jar) being unable to load the XML-RPC
client class from xmlrpc-1.2-b1.jar. I tried a fresh copy of the
xmlrpc-1.2-b1 binary; I tried everything in a directory structure (no JAR
files); I tried downloading the source and compiling it on the Mac myself;
nothing seems to work. And Java on the Mac can load the class fine directly;
it's only when the OME remote framework library tries to load it that it
fails.

I'm currently investigating further, since this is a major issue for OME
client/server communication on the Mac.

Sorry for the trouble, and I'll email again when I have a solution for you.

-Curtis

On 9/11/06, Stephen Ogg <stephen at cmm.a-star.edu.sg> wrote:
>
> Curtis-
> Thanks for your comments. Here are some more details about my specific
> system installation. I'm using Mac OS X 10.4.7, recently installed ome
> with the graphical installer,  and here is the version of java that I'm
> running:
> steve$ java -version
> java version "1.5.0_06"
> Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-112)
> Java HotSpot(TM) Client VM (build 1.5.0_06-64, mixed mode, sharing)
>
> After running the graphical installer, I found a "Shoola" folder in my
> applications folder. Within this folder there was the "Shoola.app"
> application and a config folder.The "container.xml" file had been
> modiffied so that the OMEDS and OMEIS urls were set to my installation
> location.
>
> I guess that in mac, the library folder is actually within the ".app"
> folder. In this case I found the following file hierarchy within
> Shoola.app
> /Applications/Shoola.app steve$ ls -lsR
> total 0
> 0 drwxr-xr-x   6 steve  admin  204 Sep  7 09:25 Contents
>
> ./Contents:
> total 16
> 8 -rw-r--r--   1 steve  admin  2304 Sep  7 09:25 Info.plist
> 0 drwxr-xr-x   3 steve  admin   102 Sep  7 09:25 MacOS
> 8 -rw-r--r--   1 steve  admin     9 Sep  7 09:25 PkgInfo
> 0 drwxr-xr-x   4 steve  admin   136 Sep  7 09:25 Resources
>
> ./Contents/MacOS:
> total 104
> 104 -rwxr-xr-x   1 steve  admin  51856 Sep  7 09:25 JavaApplicationStub
>
> ./Contents/Resources:
> total 96
> 0 drwxr-xr-x   10 steve  admin    340 Sep  7 09:25 Java
> 96 -rw-r--r--    1 steve  admin  45646 Sep  7 09:25 shoola.icns
>
> ./Contents/Resources/Java:
> total 6616
> 432 -rw-r--r--   1 steve  admin   217713 Sep  7 09:25
> commons-httpclient-2.0-rc2.jar
>   64 -rw-r--r--   1 steve  admin    31605 Sep  7 09:25 commons-logging.jar
> 696 -rw-r--r--   1 steve  admin   352668 Sep  7 09:25 log4j-1.2.8.jar
> 592 -rw-r--r--   1 steve  admin   301568 Sep  7 09:25 ome-java.jar
> 160 -rw-r--r--   1 steve  admin    78077 Sep  7 09:25 piccolo.jar
> 200 -rw-r--r--   1 steve  admin   101004 Sep  7 09:25 piccolox.jar
> 4256 -rw-r--r--   1 steve  admin  2176213 Sep  7 09:25 shoola.jar
> 216 -rw-r--r--   1 steve  admin   108476 Sep  7 09:25 xmlrpc-1.2-b1.jar
>
>
>
>
> Any comments welcome
> Regards
> Steve
>
>
> Dr. Stephen Ogg
> 61 Biopolis Drive (Proteos)
> Singapore 138673
> +65 65869844 office
> +65 65869841lab
> stephen at cmm.a-star.edu.sg
>
>
>
> On 12 Sep 2006, at 12:06 AM, Curtis Rueden wrote:
>
> Hi Steve,
>
> It sounds to me like it can't find the xmlrpc-1.2-b1.jar library. It
> should be in the "lib" subdirectory of the shoola distribution. What is your
> OS, and what version of Java are you running? It is possible that it failed
> to load the library because your version of Java is older than the one used
> to create the JAR file. Maybe one of the Shoola developers can comment
> further.
>
> -Curtis
>
> On 9/11/06, Stephen Ogg < stephen at cmm.a-star.edu.sg> wrote:
> >
> > I have been playing with ome and findspots now for a couple of days now.
> > A great bit thanks to David Schiffmann, Paul Appleton and Ilya Goldberg for
> > a lucid description of how to optimize parameters for and analyze the data
> > from findspots in their pdf file found at
> > http://www.openmicroscopy.org/howto/FindSpots-v2.pdf. It answered all my
> > questions.
> > On another note, I would like to use Shoola, the java client, to connect
> > to my ome. I get the following error when double clicking on Shoola
> > application icon.
> > Abnormal termination due to an uncaught exception.
> > java.lang.NoClassDefFoundError: org/apache/xmlrpc/XmlRpcClient
> > at org.openmicroscopy.ds.DataServer.getDefaultCaller(DataServer.java:90)
> > at org.openmicroscopy.ds.DataServer.getDefaultServices(DataServer.java
> > :113)
> > at org.openmicroscopy.shoola.env.data.OMEDSGateway.<init>(
> > OMEDSGateway.java:182)
> >  at org.openmicroscopy.shoola.env.data.DataServicesFactory.<init>(
> > DataServicesFactory.java:103)
> > at org.openmicroscopy.shoola.env.data.DataServicesFactory.getInstance (
> > DataServicesFactory.java:73)
> > at org.openmicroscopy.shoola.env.init.DataServicesInit.execute(
> > DataServicesInit.java:98)
> > at org.openmicroscopy.shoola.env.init.Initializer.doInit(
> > Initializer.java:224)
> > at org.openmicroscopy.shoola.env.Container.runStartupProcedure(
> > Container.java:110)
> > at org.openmicroscopy.shoola.env.Container.access$000(Container.java:76)
> > at org.openmicroscopy.shoola.env.Container$1.run(Container.java:152)
> > at java.lang.Thread.run(Thread.java:613)
> > Exception in thread "Initializer"
> >
> > Knowing even less about java than permissions, I have no clue what the
> > output above might be referring to.
> > Any help would be appreciated.
> > Regards
> > Steve
> >
> >
> >  Dr. Stephen Ogg
> > 61 Biopolis Drive (Proteos)
> > Singapore 138673
> > +65 65869844 office
> > +65 65869841lab
> > stephen at cmm.a-star.edu.sg
> >
> >
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >
> >
>
>
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