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yenaoh90 / chibe

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Crash on PC level 2 neighborhood query #29

Closed GoogleCodeExporter closed 8 years ago

GoogleCodeExporter commented 8 years ago 
Query > PC (l2) > Neighborhood
Enter "PER1"
We get an exception:

org.biopax.paxtools.util.BioPaxIOException: Unexpected element at start: error
    at org.biopax.paxtools.io.SimpleIOHandler.readNameSpaces(SimpleIOHandler.java:135)
    at org.biopax.paxtools.io.BioPAXIOHandlerAdapter.convertFromOWL(BioPAXIOHandlerAdapter.java:216)
    at cpath.client.PathwayCommonsIOHandler.readBioPAXfromURL(PathwayCommonsIOHandler.java:120)
    at cpath.client.PathwayCommonsIOHandler.getNeighbors(PathwayCommonsIOHandler.java:245)
    at org.gvt.action.QueryNeighborsAction.run(QueryNeighborsAction.java:169)
    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$5.handleEvent(ActionContributionItem.java:400)
    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:207)
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
    at java.lang.reflect.Method.invoke(Method.java:597)
    at com.intellij.rt.execution.application.AppMain.main(AppMain.java:115)

Original issue reported on code.google.com by ugurdogr...@gmail.com on 26 Sep 2012 at 8:41

GoogleCodeExporter commented 8 years ago 
L2 queries accept either Uniprot ID or Entrez Gene ID. HGNC Gene Symbols do not 
work here. So PER1 is treated as if a Uniprot ID here. I changed the code so 
that it does not print this exception, but opens a "no result" dialog. And the 
dialog says: "Nothing found. Make sure that the input is either a UniProt ID or 
an Entrez Gene ID. Gene Symbols do not work here."

Original comment by ozgunba...@gmail.com on 26 Sep 2012 at 7:23