GPML plugin not working

[piet]

Export a wikipathway as gpml Try to upload it using the most recent version of Cytoscape (2.6.3) and GPML plugin (1.0) GPML is not visible as filetype either...

This gives an error: cytoscape.CytoscapeInit?[WARN]: Plugin loading error: cytoscape.plugin.PluginException?: Unchecked 'java.lang.IncompatibleClassChangeError?'exception while attempting to load plugin org.pathvisio.cytoscape.GpmlPlugin?. This may happen when loading a plugin written for a different version of Cytoscape than this one, or if the plugin is dependent on another plugin that isn't available. Consult the documentation for the plugin or contact the plugin author for more information. Unchecked 'java.lang.IncompatibleClassChangeError?'exception while attempting to load plugin org.pathvisio.cytoscape.GpmlPlugin?. This may happen when loading a plugin written for a different version of Cytoscape than this one, or if the plugin is dependent on another plugin that isn't available. Consult the documentation for the plugin or contact the plugin author for more information. cytoscape.plugin.PluginException?: Unchecked 'java.lang.IncompatibleClassChangeError?'exception while attempting to load plugin org.pathvisio.cytoscape.GpmlPlugin?. This may happen when loading a plugin written for a different version of Cytoscape than this one, or if the plugin is dependent on another plugin that isn't available. Consult the documentation for the plugin or contact the plugin author for more information. at cytoscape.plugin.CytoscapePlugin?.loadPlugin(CytoscapePlugin?.java:170) at cytoscape.plugin.PluginManager?.loadPlugin(PluginManager?.java:947) at cytoscape.plugin.PluginManager?.loadURLPlugins(PluginManager?.java:863) at cytoscape.plugin.PluginManager?.loadPlugins(PluginManager?.java:796) at cytoscape.CytoscapeInit?.init(CytoscapeInit?.java:259) at cytoscape.CyMain?. (CyMain?.java:155) at cytoscape.CyMain?.main(CyMain?.java:119) at sun.reflect.NativeMethodAccessorImpl?.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl?.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl?.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at com.exe4j.runtime.LauncherEngine?.launch(Unknown Source) at com.exe4j.runtime.WinLauncher?.main(Unknown Source)

[thomaskelder]

This looks like a conflict with another plugin. Could you tell me which other plugins you have installed?

[piet]

Replying to thomaskelder:

This looks like a conflict with another plugin. Could you tell me which other plugins you have installed?

Ehm, I've got quite a few plugins installed, might have a problem there indeed, but I did notice that Cytoscape webstart does work with older pathways but doesn't function with newly created ones. Try for example the Apoptosis pathway; this opens in Cytoscape. When creating a simple pathway (two geneproducts and an arrow) however, this is not opened in Cytoscape. Assuming that the Apoptosis gpml was created with a former version of the gpml writer I suspected a versioning issue with the plugin...

[thomaskelder]

Ok, so there are two issues here:

1. You can't import pathways in your local installation of cytoscape
2. The cytoscape webstart on WikiPathways? doesn't work for some pathways

The cytoscape webstart will probably be removed, since it takes too much effort to maintain and the gpml plugin + wikipathways web service interface on a local installation provides a better alternative.

So we need to fix issue 2. Do you happen to have one of these plugins installed?

• cythesaurus
• superpathways-plugin

These are suspects that may include an older, conflicting version of the gpml plugin. I can't reproduce your error with a clean cytoscape 2.6.3 install with only the gpml plugin 1.0, so I suspect it's a conflict. Would it be possible to identify the causing exception or class? Is there any other output in the console or error log?

[piet]

Ai, should've known that; the ever-conflicting-plugins issue; removing the CyThesaurus? plugin did the trick. Didn't expect that one to have GPML code included... Issue solved... Sorry to have bothered you. And thanks for pointing me in the right direction! Cheers, Piet

[thomaskelder]

Ok, great, thanks for helping to identify the cause. We'll update CyThesaurus? with a new version of the code soon to resolve the conflict.