Cannot load BioPax from EcoCyc

GoogleCodeExporter commented 9 years ago

What steps will reproduce the problem?

1. Download BioPax from 
http://biocyc.org/ECOLI/pathway-biopax?type=3&object=BGALACT-PWY

2. Attempt to open in chibe

What is the expected output? What do you see instead?

Loading BioPAX model ...
java.lang.UnsupportedOperationException
        at java.util.AbstractList.remove(AbstractList.java:161)
        at java.util.AbstractList$Itr.remove(AbstractList.java:374)
        at java.util.AbstractCollection.retainAll(AbstractCollection.java:406)
        at org.gvt.action.OpenPathwaysAction.run(OpenPathwaysAction.java:97)
        at org.gvt.action.LoadBioPaxModelAction.run(LoadBioPaxModelAction.java:284)
        at org.eclipse.jface.action.Action.runWithEvent(Action.java:996)
        at org.eclipse.jface.action.ActionContributionItem.handleWidgetSelection(ActionContributionItem.java:538)
        at org.eclipse.jface.action.ActionContributionItem.access$2(ActionContributionItem.java:488)
        at org.eclipse.jface.action.ActionContributionItem$6.handleEvent(ActionContributionItem.java:441)
        at org.eclipse.swt.widgets.EventTable.sendEvent(Unknown Source)
        at org.eclipse.swt.widgets.Widget.sendEvent(Unknown Source)
        at org.eclipse.swt.widgets.Display.runDeferredEvents(Unknown Source)
        at org.eclipse.swt.widgets.Display.readAndDispatch(Unknown Source)
        at org.eclipse.jface.window.Window.runEventLoop(Window.java:809)
        at org.eclipse.jface.window.Window.open(Window.java:787)
        at org.gvt.ChisioMain.main(ChisioMain.java:212)

What version of the product are you using? On what operating system?

chibe version 2.2
OS is ubuntu 14.04

Original issue reported on code.google.com by camr...@gmail.com on 5 May 2015 at 12:57

Attachments:

bgal.owl

GoogleCodeExporter commented 9 years ago

This issue was closed by revision efaf1e4494bb.

Original comment by ozgunba...@gmail.com on 5 May 2015 at 3:01

Changed state: Fixed

GoogleCodeExporter commented 9 years ago

That was due to a bug and now fixed.

Original comment by ozgunba...@gmail.com on 5 May 2015 at 3:01

PathwayCommons / chibe

Cannot load BioPax from EcoCyc #65