[ome-users] teething problems

[Stephen Ogg]

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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