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Unrecoverable java exception when deleting grid view column
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Patrick

Joined: 11 Mar 2009
Posts: 8

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Link to postPosted: Wed Mar 11, 2009 10:24 pmPost subject: Unrecoverable java exception when deleting grid view column Reply with quote

I'm seeing a java exception thrown when I attempt to delete a column in the grid view tab of Instant JChem.  I'm seeing this with both Instant JChem 2.4 and 2.4.2.  I'm only seeing this when running Instant JChem on Ubuntu, however, as it doesn't seem to recreate on Windows.  This is really annoying for me as I'm developing on Ubuntu and am forced to restart Instant JChem after almost everytime I try and delete a column:(





Steps to reproduce bug:

1. Start up instantjchem on Ubuntu


2. Open up the the "Pubchem grid view" panel for the Pubchem demo so that you are viewing the list of molecules in the database.

3. Click the "New Standard Field" and create a new column (I used the Standard Integer Field type but I don't think it matters).

4. Select the newly created column, right-click on it, and choose the "Delete Fields" menu option also choosing to delete the related column

5.  Most times when I do this I this (> 75% of the time) I get the following java exception.  When I try and close the java exception it pops right back up again forcing me to have to kill instantjchem.  I only see this wirth Ubuntu and not Windows.





java.lang.ArrayIndexOutOfBoundsException: -1
    at java.util.Vector.elementData(Vector.java:707)
    at java.util.Vector.elementAt(Vector.java:450)
    at javax.swing.table.DefaultTableColumnModel.getColumn(DefaultTableColumnModel.java:294)
    at javax.swing.plaf.basic.BasicTableHeaderUI.getHeaderRenderer(BasicTableHeaderUI.java:671)
    at javax.swing.plaf.basic.BasicTableHeaderUI.paintCell(BasicTableHeaderUI.java:687)
    at javax.swing.plaf.basic.BasicTableHeaderUI.paint(BasicTableHeaderUI.java:663)
    at javax.swing.plaf.ComponentUI.update(ComponentUI.java:161)
    at javax.swing.JComponent.paintComponent(JComponent.java:774)
    at javax.swing.JComponent.paint(JComponent.java:1038)
    at javax.swing.JComponent.paintToOffscreen(JComponent.java:5147)
    at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:302)
    at javax.swing.RepaintManager.paint(RepaintManager.java:1145)
    at javax.swing.JComponent._paintImmediately(JComponent.java:5095)
    at javax.swing.JComponent.paintImmediately(JComponent.java:4905)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:740)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:696)
    at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:676)
    at javax.swing.RepaintManager.access$700(RepaintManager.java:57)
[catch] at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1550)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:226)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:602)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)
Tim
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Link to postPosted: Wed Mar 11, 2009 10:30 pmPost subject: Reply with quote

Can you tell us which version of java you are using and other details of your Ubuntu installation.
Use Help -> About Instant JChem and copy and paste the contents to this forum topic.

Thanks
Tim
Patrick

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Link to postPosted: Wed Mar 11, 2009 10:47 pmPost subject: Reply with quote

Here's the info from Instant JChem.  Let me know if you have any more questions.





Instant JChem Version: 2.4.2 (build: 090213)
JChem Version: 5.1.5
JChem Table Version: 50103
Marvin Version: 5.1.5 (build date: 2009-02-13)
Java: 1.6.0_0; OpenJDK Server VM 1.6.0_0-b12
System: Linux version 2.6.27-11-generic running on i386; UTF-8; en_US (instantjchem)
NetBeans build: 200711261600
Userdir: /home/patmac/.instantjchem/ijc_2_4
Java Web Start: No
Plugins:
    chemaxon.ijc.updatecenter [2.4.1 090213]
    chemaxon.jchem/1 [5.1.5 090213]
    com.im.commons/1 [2.4 081118]
    com.im.df.api/1 [2.4.2 090213]
    com.im.df.core.derby/1 [2.4.2 090213]
    com.im.df.core.oracle/1 [2.4.2 090213]
    com.im.df.db.mysql/1 [2.4.2 090213]
    com.im.df.localdb/1 [2.4 081118]
    com.im.df.server.local/1 [2.4 081118]
    com.im.df/1 [2.4.2 090213]
    com.im.ijc.autoupdate/1 [2.4 081118]
    com.im.ijc.branding/1 [2.4.2 090213]
    com.im.ijc.chem.overlap/1 [2.4 081118]
    com.im.ijc.core/1 [2.4.2 090213]
    com.im.ijc.examples.addfield [2.4 081118]
    com.im.ijc.examples.ijcrenderers [2.4 081118]
    com.im.ijc.examples.mathcomputationactions [2.4 081118]
    com.im.ijc.extraloaders [2.4 081118]
    com.im.ijc.formview/1 [2.4.2 090213]
    com.im.ijc.gridview/1 [2.4.1 090213]
    com.im.ijc.io [2.4.2 090213]
    com.im.ijc.jrprinting/1 [2.4.1 090213]
    com.im.ijc.project/1 [2.4.2 090213]
    com.im.ijc.querytextpanel [2.4 081118]
    com.im.ijc.renderers/1 [2.4.2 090213]
    com.im.ijc.security/1 [2.4 081118]
    com.im.ijc.server.api/1 [2.4 081118]
    com.im.ijc.server.impl/1 [2.4 081118]
    com.im.ijc.sfs [2.4.2 090213]
    com.im.ijc.standardizer/1 [2.4 081118]
    com.im.ijc.structurefiles/1 [2.4 081118]
    com.im.ijc.update.pack [2.4.2 090213]
    com.im.ijc.versionprovider [2.4.2 090213]
    com.im.ijc.welcome/1 [2.4.2 090213]
    com.im.ijc.widgets/1 [2.4.2 090213]
    com.jacob.com [1.0 081118]
    com.lowagie.iia/1 [2.0.8 081118]
    com.michaelbaranov.microba/1 [0.4.4 081118]
    com.mysql.jdbc/1 [5.0.8 081118]
    net.sf.cglib/1 [2.1.3 081118]
    net.sf.jasperreports/1 [3.0.1 081118]
    oracle.jdbc/1 [11.1.0.6.0 081118]
    org.acegisecurity/1 [1.0.5 081118]
    org.apache.batik/1 [1.1 081118]
    org.apache.commons.beanutils/1 [1.7.0 081118]
    org.apache.commons.collections/1 [3.2 081118]
    org.apache.commons.dbcp/1 [1.2.2 081118]
    org.apache.commons.digester/1 [1.8 081118]
    org.apache.commons.pool/1 [1.3 081118]
    org.apache.derby/1 [10.4.2 081118]
    org.apache.poi [3.0.1 081118]
    org.apache.xml.resolver [1.2.1 1.2 200711261600]
    org.dom4j/1 [1.6.1 090213]
    org.eclipse.jdt.core.compiler/1 [3.1.1 081118]
    org.freehep/1 [2.1.1 081118]
    org.jdesktop.layout/1 [1.4.1 1.0.3 200711261600]
    org.netbeans.api.progress/1 [1.10.1.1 1 200711261600]
    org.netbeans.api.visual [2.9.1 200711261600]
    org.netbeans.api.xml/1 [1.14.1 200711261600]
    org.netbeans.bootstrap/1 [2.7.1 200711261600]
    org.netbeans.core.execution/1 [1.10.1.1 200711261600]
    org.netbeans.core.ide/1 [1.10.1 200711261600]
    org.netbeans.core.output2/1 [1.8.2.1 1 200711261600]
    org.netbeans.core.startup/1 [1.10.1.1 200711261600]
    org.netbeans.core.ui/1 [1.10.1 200711261600]
    org.netbeans.core.windows/2 [2.8.1.1 200711261600]
    org.netbeans.core/2 [3.6.1.0.1.1 081105]
    org.netbeans.libs.commons_logging/1 [1.4.1 1.0.4 200711261600]
    org.netbeans.libs.xerces/1 [1.10.1 2.8.0 200711261600]
    org.netbeans.modules.applemenu/1 [1.7.1 200711261600]
    org.netbeans.modules.autoupdate.services [1.3.1.0.1 080214]
    org.netbeans.modules.autoupdate.ui [1.2.1 200711261600]
    org.netbeans.modules.classfile/1 [1.19.1 200711261600]
    org.netbeans.modules.db.core [1.5.1 200711261600]
    org.netbeans.modules.db.sql.editor [1.5.1.5 200711261600]
    org.netbeans.modules.db.sql.visualeditor/1 [2.1.1.5 200711261600]
    org.netbeans.modules.db/1 [1.24.1.5 5 200711261600]
    org.netbeans.modules.dbapi [1.5.1.5 200711261600]
    org.netbeans.modules.defaults/1 [1.3.1 200711261600]
    org.netbeans.modules.editor.bookmarks/1 [1.4.1 200711261600]
    org.netbeans.modules.editor.bracesmatching/0 [1.3.1 200711261600]
    org.netbeans.modules.editor.codetemplates/1 [1.5.1.1.5 1 200711261600]
    org.netbeans.modules.editor.completion/1 [1.9.1 200711261600]
    org.netbeans.modules.editor.errorstripe.api/1 [2.3.1.1 1 200711261600]
    org.netbeans.modules.editor.errorstripe/2 [2.3.1.1.1 1 200711261600]
    org.netbeans.modules.editor.fold/1 [1.6.1 200711261600]
    org.netbeans.modules.editor.guards/1 [1.0.1 200711261600]
    org.netbeans.modules.editor.highlights/0 [1.2.1.1 1 200711261600]
    org.netbeans.modules.editor.indent/2 [1.6.1.4 200711261600]
    org.netbeans.modules.editor.lib/1 [1.20.1.4.2 4 200711261600]
    org.netbeans.modules.editor.lib2/1 [1.5.1.2 2 200711261600]
    org.netbeans.modules.editor.mimelookup.impl/1 [1.1.1 200711261600]
    org.netbeans.modules.editor.mimelookup/1 [1.8.1 200711261600]
    org.netbeans.modules.editor.plain.lib/1 [1.4.1 200711261600]
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    org.netbeans.modules.editor.settings.storage/1 [1.10.1 200711261600]
    org.netbeans.modules.editor.settings/1 [1.12.1 200711261600]
    org.netbeans.modules.editor.structure/1 [1.15.1.1 1 200711261600]
    org.netbeans.modules.editor.util/1 [1.21.1 200711261600]
    org.netbeans.modules.editor/3 [1.35.1.4.2 200711261600]
    org.netbeans.modules.extbrowser/1 [1.11.1 200711261600]
    org.netbeans.modules.favorites/1 [1.12.1 200711261600]
    org.netbeans.modules.gototest/1 [1.0.1 200711261600]
    org.netbeans.modules.javahelp/1 [2.9.1 200711261600]
    org.netbeans.modules.jumpto/1 [1.3.1 200711261600]
    org.netbeans.modules.lexer.editorbridge/1 [1.4.1 200711261600]
    org.netbeans.modules.lexer.nbbridge/1 [1.2.1.1 200711261600]
    org.netbeans.modules.lexer/2 [1.25.1.1 1 200711261600]
    org.netbeans.modules.masterfs/1 [1.11.1 200711261600]
    org.netbeans.modules.options.api/1 [1.5.1 200711261600]
    org.netbeans.modules.options.editor/1 [1.4.1 200711261600]
    org.netbeans.modules.options.keymap [1.1.1 200711261600]
    org.netbeans.modules.progress.ui [1.0.1.0.0.1 080409]
    org.netbeans.modules.project.ant/1 [1.17.1 200711261600]
    org.netbeans.modules.project.libraries/1 [1.15.1 200711261600]
    org.netbeans.modules.projectapi/1 [1.13.1 200711261600]
    org.netbeans.modules.projectui [1.12.1.1.6 1 200711261600]
    org.netbeans.modules.projectuiapi/1 [1.24.1.6 6 200711261600]
    org.netbeans.modules.properties.syntax/1 [1.18.1 200711261600]
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    org.netbeans.modules.queries/1 [1.10.1 200711261600]
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    org.netbeans.modules.xml.retriever/1 [1.1.1 200711261600]
    org.netbeans.modules.xml.schema.completion [1.0.1 200711261600]
    org.netbeans.modules.xml.schema.model/1 [1.2.1 1 200711261600]
    org.netbeans.modules.xml.text/2 [1.13.1.4.4 4 200711261600]
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    org.netbeans.spi.editor.hints/0 [1.2.1.5 5 200711261600]
    org.netbeans.spi.navigator/1 [1.5.1 200711261600]
    org.netbeans.swing.dirchooser [1.0.1 200711261600]
    org.netbeans.swing.plaf [1.6.1 200711261600]
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    org.openide.actions [6.6.1.1 200711261600]
    org.openide.awt [6.11.1.1 200711261600]
    org.openide.compat [6.5.1 200711261600]
    org.openide.dialogs [7.5.1 200711261600]
    org.openide.execution [1.10.1 200711261600]
    org.openide.explorer [6.12.1 1 200711261600]
    org.openide.filesystems [7.3.1 200711261600]
    org.openide.io [1.11.1 200711261600]
    org.openide.loaders [6.7.1 200711261600]
    org.openide.modules [7.3.1 200711261600]
    org.openide.nodes [7.2.1.1 200711261600]
    org.openide.options [6.7.1 200711261600]
    org.openide.text [6.16.1 200711261600]
    org.openide.util [7.10.1.1 1 200711261600]
    org.openide.windows [6.18.1 200711261600]
    org.openidex.util/3 [3.13.1 200711261600]
    org.springframework/1 [2.5 081118]
Tim
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Joined: 05 Oct 2004
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Link to postPosted: Wed Mar 11, 2009 11:13 pmPost subject: Reply with quote

I think the java version could be the problem (that's why I asked for that info), and the error is very reminsiscent of some bugs we saw with earlier versions of Java 1.6.
You are using: "1.6.0_0; OpenJDK Server VM 1.6.0_0-b12".
Non-Sun JDKs are typically problematical, and we have not tested the OpenJDK distributions.
Can you try runing against a standard Sun JRE that you can download from here:
http://java.sun.com/javase/downloads/?intcmp=1281

To change the Java version edit the following file:
<ijc_install_dir>/etc/instantjchem.conf
and edit the jdkhome property (and uncomment it if necessary).

Let us know if this helps.

Thanks

Tim
Patrick

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Link to postPosted: Thu Mar 12, 2009 12:14 amPost subject: Reply with quote

I'm afarid switching out the JDK didn't work.  I'm still getting the same exception (but with different line numbers of course) which I've included below.  Also here is the updated relevent information from Instant JChem.


Instant JChem Version: 2.4.2 (build: 090213)
JChem Version: 5.1.5
JChem Table Version: 50103
Marvin Version: 5.1.5 (build date: 2009-02-13)
Java: 1.6.0_12; Java HotSpot(TM) Server VM 11.2-b01
System: Linux version 2.6.27-11-generic running on i386; UTF-8; en_US (instantjchem)
NetBeans build: 200711261600
Userdir: /home/patmac/.instantjchem/ijc_2_4
Java Web Start: No


java.lang.ArrayIndexOutOfBoundsException: -1
    at java.util.Vector.elementAt(Vector.java:430)
    at javax.swing.table.DefaultTableColumnModel.getColumn(DefaultTableColumnModel.java:277)
    at javax.swing.plaf.basic.BasicTableHeaderUI.getHeaderRenderer(BasicTableHeaderUI.java:654)
    at javax.swing.plaf.basic.BasicTableHeaderUI.paintCell(BasicTableHeaderUI.java:670)
    at javax.swing.plaf.basic.BasicTableHeaderUI.paint(BasicTableHeaderUI.java:646)
    at javax.swing.plaf.ComponentUI.update(ComponentUI.java:143)
    at javax.swing.JComponent.paintComponent(JComponent.java:763)
    at javax.swing.JComponent.paint(JComponent.java:1027)
    at javax.swing.JComponent.paintToOffscreen(JComponent.java:5122)
    at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:277)
    at javax.swing.RepaintManager.paint(RepaintManager.java:1217)
    at javax.swing.JComponent._paintImmediately(JComponent.java:5070)
    at javax.swing.JComponent.paintImmediately(JComponent.java:4880)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:803)
    at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:714)
    at javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:694)
[catch] at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:128)
    at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Tim
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Link to postPosted: Thu Mar 12, 2009 8:35 amPost subject: Reply with quote

OK, thanks.
We will investigate and try to work out what the problem is.

Tim
Petr
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Link to postPosted: Thu Mar 12, 2009 11:11 amPost subject: Reply with quote

We are able to reproduce this bug on jdk 1.6. Quick workaround is to use jdk 1.5. (http://java.sun.com/javase/downloads/index_jdk5.jsp). The bug will be fixed in IJC 2.4.4. It's to late to integrate it to IJC 2.4.3.

Petr
Tim
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Link to postPosted: Thu Mar 12, 2009 3:44 pmPost subject: Reply with quote

One more comment.
The bug only applies if you are deleting the last column in the grid view table.
So another workaround it just to move the column to an earlier position and then delete it.

Tim
Tim
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Link to postPosted: Thu Mar 19, 2009 3:53 pmPost subject: Reply with quote

This problem should now be fixed in the recent 2.4.3.1 update.

Thanks
Tim
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