[ome-users] teething problems

Curtis Rueden ctrueden at wisc.edu
Tue Sep 12 19:49:27 BST 2006 

I thought there was a problem with support libraries in the plugins folder
directly, but some testing just now seems to prove otherwise. (I had on my
todo list to figure out how to allow support libraries to be in the plugins
folder, but it may turn out to be trivial.) I'll do a few more tests on
different machines, and if all looks good, change the installation
instructions for Bio-Formats accordingly.

-Curtis

On 9/12/06, Ilya Goldberg <igg at nih.gov> wrote:
>
> 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
> >> > >
> >> > >
> >> > >
> >> >
> >> >
> >>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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