Something has changed in OBO that breaks Phenote and OBO-Edit
Nomi Harris
seen before. It turns out that the exception happens when I have the
latest obo.jar (the one that you get if you make a jar of the latest
obo). If I revert to the obo.jar that is committed as phenote/jars/
obo.jar (which hasn't been updated for a few days), it works.
The funny thing is, the exception I get involves org.bbop and
org.oboedit classes but NOT obo classes!
2010-03-17 13:58:48,013 [AWT-EventQueue-0] DEBUG main.Phenote -
Ontologies initialized, checking command line for read & write
Warning: class ch.randelshofer.quaqua.filechooser.Files couldn't load
library libquaqua.jnilib.
Exception in thread "AWT-EventQueue-0"
java.lang.IncompatibleClassChangeError
at
org.oboedit.gui.TagFilterEditor.layoutGUI(TagFilterEditor.java:289)
at
org.oboedit.gui.TagFilterEditor.<init>(TagFilterEditor.java:245)
at org.oboedit.gui.AdvancedOBOUI
$IOProfileEditor.<init>(AdvancedOBOUI.java:227)
at org.oboedit.gui.AdvancedOBOUI.<init>(AdvancedOBOUI.java:760)
at
org
.oboedit
.gui
.tasks
.DefaultGUIStartupTask
.getDefaultDataAdapters(DefaultGUIStartupTask.java:521)
at
org
.bbop
.framework
.AbstractApplicationStartupTask
.installDefaultDataAdapters(AbstractApplicationStartupTask.java:233)
at
org
.bbop
.framework
.AbstractApplicationStartupTask
.run(AbstractApplicationStartupTask.java:175)
at
org
.bbop
.framework
.AbstractSingleActionTask.install(AbstractSingleActionTask.java:24)
at org.bbop.framework.GUIManager.installTask(GUIManager.java:
158)
at org.bbop.framework.GUIManager.start(GUIManager.java:219)
at phenote.main.PhenotePlus
$PhenoteRunnable.run(PhenotePlus.java:22)
at
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
at
java
.awt
.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:
269)
at
java
.awt
.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:
190)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:
110)
I then tried running oboedit and it throws the same exception!
bash-3.2$ java -Xmx1024M -Dsun.java2d.opengl=True -DlauncherDir=/Users/
nomi/Documents/workspace/fresh/oboedit/. -DlauncherName=./oboedit -
Xdock:icon=/Users/nomi/Documents/workspace/fresh/oboedit/./docs/images/
oboedit_icon_mac.icns -jar /Users/nomi/Documents/workspace/fresh/
oboedit/./runtime/oboedit.jar ""
[INFO] Configured final exception handlers
java.lang.IncompatibleClassChangeError
at
org.oboedit.gui.TagFilterEditor.layoutGUI(TagFilterEditor.java:289)
at
org.oboedit.gui.TagFilterEditor.<init>(TagFilterEditor.java:245)
at org.oboedit.gui.AdvancedOBOUI
$IOProfileEditor.<init>(AdvancedOBOUI.java:227)
at org.oboedit.gui.AdvancedOBOUI.<init>(AdvancedOBOUI.java:760)
at
org
.oboedit
.gui
.tasks
.DefaultGUIStartupTask
.getDefaultDataAdapters(DefaultGUIStartupTask.java:522)
at
org
.bbop
.framework
.AbstractApplicationStartupTask
.installDefaultDataAdapters(AbstractApplicationStartupTask.java:224)
at
org
.bbop
.framework
.AbstractApplicationStartupTask
.run(AbstractApplicationStartupTask.java:166)
at
org
.bbop
.framework
.AbstractSingleActionTask.install(AbstractSingleActionTask.java:24)
at org.bbop.framework.GUIManager.installTask(GUIManager.java:
163)
at org.bbop.framework.GUIManager.start(GUIManager.java:236)
at org.oboedit.launcher.OBOEdit$1.run(OBOEdit.java:204)
at
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:199)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
at
java
.awt
.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:
269)
at
java
.awt
.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:
190)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:
110)
This is in a fresh checkout.
Nomi
Amina Abdulla
One way to test is to remove the bbop, obo and obo-edit jar from
phenote and reference the projects.
I just tried it and it loads fine.
- Amina
On Mar 17, 2010, at 2:04 PM, Nomi Harris wrote:
> Phenote has suddenly started throwing an exception that I've never
> seen before. It turns out that the exception happens when I have
> the latest obo.jar (the one that you get if you make a jar of the
> latest obo). If I revert to the obo.jar that is committed as
> phenote/jars/obo.jar (which hasn't been updated for a few days), it
> .pumpOneEventForHierarchy(EventDispatchThread.java:269)
> at
> java
> .awt
> .EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:
> 190)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:
> 110)
>
>
> I then tried running oboedit and it throws the same exception!
>
> bash-3.2$ java -Xmx1024M -Dsun.java2d.opengl=True -DlauncherDir=/
> Users/nomi/Documents/workspace/fresh/oboedit/. -DlauncherName=./
> oboedit -Xdock:icon=/Users/nomi/Documents/workspace/fresh/oboedit/./
> docs/images/oboedit_icon_mac.icns -jar /Users/nomi/Documents/
> workspace/fresh/oboedit/./runtime/oboedit.jar ""
> .pumpOneEventForHierarchy(EventDispatchThread.java:269)
> at
> java
> .awt
> .EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:
> 190)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:184)
> at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:176)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:
> 110)
>
>
> This is in a fresh checkout.
>
> Nomi
>
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