[ome-users] teething problems

Ilya Goldberg igg at nih.gov
Tue Sep 12 18:15:41 BST 2006 

Hi Curtis
What happens if you delete ome-java.jar from the Extensions folder,  
but add it to the plug-ins folder for ImageJ - does the Bio-Formats  
plug-in still work?
That might be a better setup than relying on system-wide classpath  
rules.
Unless that doesn't work, of course.
-I


On Sep 12, 2006, at 1:06 PM, Curtis Rueden wrote:

> Hi Steve,
>
> I managed to track down what was causing the NoClassDefFoundErrors,  
> at least
> on our machine here. It was caused by ome-java.jar being present in
> (/Library/Java/Extensions or /System/Library/Java/Extensions).  
> Apparently
> Java on the Mac does something really stupid: it looks first for  
> libraries
> in the Extensions folder, and prefers them to the explicitly set  
> class path;
> in addition, if library A has a partial dependency on library B,  
> library B
> is not in the Extensions folder, and an application tries to use  
> the part of
> library A that needs library B to function, things fail, even if  
> library B
> is included in the class path with the application.
>
> To fix the problem, you can delete ome-java.jar from the Extensions  
> folder.
>
> In our case, we had ome-java.jar in the Extensions folder to use  
> with the
> Bio-Formats plugin for ImageJ. Do you by any chance have that set  
> up as
> well? If so, you probably don't want to delete ome-java.jar from  
> Extensions
> (since Bio-Formats will stop working if you do that). Instead, you  
> can copy
> xmlrpc-1.2-b1.jar, commons-httpclient-2.0-rc2.jar and
> commons-logging.jarinto the Extensions folder as well, and everything
> (both Bio-Formats and
> Shoola) should then work. But beware, if a new version of Shoola is
> released, and those JAR files have been updated, you'll need to  
> recopy them
> into Extensions to keep everything flowing smoothly.
>
> If you do not have any of the Shoola-related JAR files in your  
> Extensions
> folders, then I am once again unsure of what is causing your problem.
>
> I hope that clears things up, and sorry for the confusion.
>
> -Curtis
>
> On 9/12/06, Curtis Rueden <ctrueden at wisc.edu> wrote:
>>
>> 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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