Hi Steve,<br><br>Ah, I should have realized you'd be using the Mac OS X version of Shoola; sorry for my inaccuracies.<br><br>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.
<br><br>I'm currently investigating further, since this is a major issue for OME client/server communication on the Mac.<br><br>Sorry for the trouble, and I'll email again when I have a solution for you.<br><br>-Curtis<br>
<br><div><span class="gmail_quote">On 9/11/06, <b class="gmail_sendername">Stephen Ogg</b> <<a href="mailto:stephen@cmm.a-star.edu.sg">stephen@cmm.a-star.edu.sg</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div style=""><div>Curtis-</div><div>Thanks for your comments. Here are some more details about my specific system installation. <div>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:
</div><div>steve$ java -version</div><div>java version "1.5.0_06"</div><div>Java(TM) 2 Runtime Environment, Standard Edition (build 1.5.0_06-112)</div><div>Java HotSpot(TM) Client VM (build 1.5.0_06-64, mixed mode, sharing)
</div><div><br></div><div>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. </div><div><br></div><div>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</div><div>/Applications/Shoola.app steve$ ls -lsR</div><div>total 0</div><div>0 drwxr-xr-x 6 steve admin 204 Sep 7 09:25 Contents</div><div><br></div><div>./Contents:</div><div>total 16</div><div>8 -rw-r--r-- 1 steve admin 2304 Sep 7 09:25
Info.plist</div><div>0 drwxr-xr-x 3 steve admin 102 Sep 7 09:25 MacOS</div><div>8 -rw-r--r-- 1 steve admin 9 Sep 7 09:25 PkgInfo</div><div>0 drwxr-xr-x 4 steve admin 136 Sep 7 09:25 Resources</div><div>
<br></div><div>./Contents/MacOS:</div><div>total 104</div><div>104 -rwxr-xr-x 1 steve admin 51856 Sep 7 09:25 JavaApplicationStub</div><div><br></div><div>./Contents/Resources:</div><div>total 96</div><div> 0 drwxr-xr-x 10 steve admin 340 Sep 7 09:25 Java
</div><div>96 -rw-r--r-- 1 steve admin 45646 Sep 7 09:25 shoola.icns</div><div><br></div><div>./Contents/Resources/Java:</div><div>total 6616</div><div> 432 -rw-r--r-- 1 steve admin 217713 Sep 7 09:25 commons-httpclient-2.0-rc2.jar
</div><div> 64 -rw-r--r-- 1 steve admin 31605 Sep 7 09:25 commons-logging.jar</div><div> 696 -rw-r--r-- 1 steve admin 352668 Sep 7 09:25 log4j-1.2.8.jar</div><div> 592 -rw-r--r-- 1 steve admin 301568 Sep 7 09:25
ome-java.jar</div><div> 160 -rw-r--r-- 1 steve admin 78077 Sep 7 09:25 piccolo.jar</div><div> 200 -rw-r--r-- 1 steve admin 101004 Sep 7 09:25 piccolox.jar</div><div>4256 -rw-r--r-- 1 steve admin 2176213 Sep 7 09:25
shoola.jar</div><div> 216 -rw-r--r-- 1 steve admin 108476 Sep 7 09:25 xmlrpc-1.2-b1.jar</div><div><br></div><div><br></div><div><br></div><div><br></div><div>Any comments welcome</div><div>Regards</div><div>Steve</div>
<div><br></div><div></div><div><span class="q"><br><div> <span style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
<span style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
<div>Dr. Stephen Ogg</div><div>61 Biopolis Drive (Proteos)</div><div>Singapore 138673</div><div>+65 65869844 office</div><div>+65 65869841lab</div><div><a href="mailto:stephen@cmm.a-star.edu.sg" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
stephen@cmm.a-star.edu.sg</a></div><div><br></div><br></span></span> </div><br></span></div><div><span class="e" id="q_10da021f25879140_2"><div><div>On 12 Sep 2006, at 12:06 AM, Curtis Rueden wrote:</div><br><blockquote type="cite">
Hi Steve,<br><br>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.
<br><br>-Curtis<br><br><div><span class="gmail_quote">On 9/11/06, <b class="gmail_sendername">Stephen Ogg</b> <<a href="mailto:stephen@cmm.a-star.edu.sg" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
stephen@cmm.a-star.edu.sg</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"> <div><div>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
<a href="http://www.openmicroscopy.org/howto/FindSpots-v2.pdf" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">http://www.openmicroscopy.org/howto/FindSpots-v2.pdf</a>. It answered all my questions.
<div><br></div><div>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.<div><br><div>Abnormal termination due to an uncaught exception.
</div><div>java.lang.NoClassDefFoundError: org/apache/xmlrpc/XmlRpcClient</div><div><span style="white-space: pre;"> </span>at org.openmicroscopy.ds.DataServer.getDefaultCaller(DataServer.java:90)</div><div><span style="white-space: pre;">
</span>at org.openmicroscopy.ds.DataServer.getDefaultServices(DataServer.java:113)</div><div><span style="white-space: pre;"> </span>at org.openmicroscopy.shoola.env.data.OMEDSGateway.<init>(OMEDSGateway.java:182)
</div> <div><span style="white-space: pre;"> </span>at org.openmicroscopy.shoola.env.data.DataServicesFactory.<init>(DataServicesFactory.java:103)</div><div><span style="white-space: pre;"> </span>at org.openmicroscopy.shoola.env.data.DataServicesFactory.getInstance
(DataServicesFactory.java:73)</div><div><span style="white-space: pre;"> </span>at org.openmicroscopy.shoola.env.init.DataServicesInit.execute(DataServicesInit.java:98)</div><div><span style="white-space: pre;"> </span>at
org.openmicroscopy.shoola.env.init.Initializer.doInit(Initializer.java:224)</div><div><span style="white-space: pre;"> </span>at org.openmicroscopy.shoola.env.Container.runStartupProcedure(Container.java:110)</div><div><span style="white-space: pre;">
</span>at org.openmicroscopy.shoola.env.Container.access$000(Container.java:76)</div><div><span style="white-space: pre;"> </span>at org.openmicroscopy.shoola.env.Container$1.run(Container.java:152)</div><div><span style="white-space: pre;">
</span>at java.lang.Thread.run(Thread.java:613)</div><div>Exception in thread "Initializer"</div><div><br></div><div>Knowing even less about java than permissions, I have no clue what the output above might be referring to.
</div><div>Any help would be appreciated.</div><div>Regards</div><div>Steve</div><div><br></div><div><br><div> <span style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
<span style="border-collapse: separate; border-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px;">
<div>Dr. Stephen Ogg</div><div>61 Biopolis Drive (Proteos)</div><div>Singapore 138673</div><div>+65 65869844 office</div><div>+65 65869841lab</div><div><a href="mailto:stephen@cmm.a-star.edu.sg" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
stephen@cmm.a-star.edu.sg</a></div><div><br></div><br></span></span> </div><br></div></div></div></div> </div><br>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank" onclick="return top.js.OpenExtLink(window,event,this)">
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