#401 Retrieve function of the Phenotype field is misbehaving

closed
None
6
2008-06-20
2008-06-16
Jolene
No

When you do a retrieve on any frequently used phenotype term (such embryonic lethal) in the phenotype field, you no longer get any results.

[java] Jun 16, 2008 2:32:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO: Configured final exception handlers
[java] 2008-06-16 14:32:53,908 [AWT-EventQueue-0] DEBUG main.PhenoteStartupTask - Creating table factory for: default
[java] connected: org.postgresql.jdbc3.Jdbc3Connection@18b3665
[java] SwixML 1.5 (#149)
[java] 2008-06-16 14:32:54,938 [AWT-EventQueue-0] DEBUG gui.CharacterTableController - Adding initial blank character
[java] 2008-06-16 14:32:54,953 [AWT-EventQueue-0] INFO datamodel.AnnotationCharacter - Using regular character model (not obo annotation)
[java] 2008-06-16 14:33:33,673 [AWT-EventQueue-0] DEBUG field.TermCompList - tab or ret hit
[java] 2008-06-16 14:33:33,673 [AWT-EventQueue-0] DEBUG field.TermCompList - update model
[java] rows= 0
[java] 2008-06-16 14:33:33,735 [AWT-EventQueue-0] DEBUG field.TermCompList - Setting model: embryonic_lethal
[java] 2008-06-16 14:33:33,735 [AWT-EventQueue-0] DEBUG field.TermCompList - Action performed: comboBoxEdited
[java] 2008-06-16 14:33:33,735 [AWT-EventQueue-0] DEBUG field.TermCompList - Action updating model: java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=comboBoxEdited,when=1213652013672,modifiers=] on javax.swing.JComboBox[,114,29,241x23,invalid,layout=com.sun.java.swing.plaf.windows.WindowsComboBoxUI$3,alignmentX=0.0,alignmentY=0.0,border=com.sun.java.swing.plaf.windows.XPStyle$XPFillBorder@1b22a8c,flags=20971848,maximumSize=,minimumSize=,preferredSize=,isEditable=true,lightWeightPopupEnabled=true,maximumRowCount=8,selectedItemReminder=]
[java] 2008-06-16 14:33:33,735 [AWT-EventQueue-0] DEBUG field.TermCompList - update model
[java] 2008-06-16 14:33:40,084 [AWT-EventQueue-0] DEBUG field.TermCompList - Action performed: comboBoxEdited
[java] 2008-06-16 14:33:40,084 [AWT-EventQueue-0] DEBUG field.TermCompList - Action updating model: java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=comboBoxEdited,when=1213652020084,modifiers=] on javax.swing.JComboBox[,114,29,241x23,layout=com.sun.java.swing.plaf.windows.WindowsComboBoxUI$3,alignmentX=0.0,alignmentY=0.0,border=com.sun.java.swing.plaf.windows.XPStyle$XPFillBorder@1b22a8c,flags=20971848,maximumSize=,minimumSize=,preferredSize=,isEditable=true,lightWeightPopupEnabled=true,maximumRowCount=8,selectedItemReminder=]
[java] 2008-06-16 14:33:40,084 [AWT-EventQueue-0] DEBUG field.TermCompList - update model
[java] 2008-06-16 14:33:40,084 [AWT-EventQueue-0] DEBUG field.TermCompList - Action performed: comboBoxEdited
[java] 2008-06-16 14:33:40,084 [AWT-EventQueue-0] DEBUG field.TermCompList - Action updating model: java.awt.event.ActionEvent[ACTION_PERFORMED,cmd=comboBoxEdited,when=1213652020084,modifiers=] on javax.swing.JComboBox[,114,29,241x23,invalid,layout=com.sun.java.swing.plaf.windows.WindowsComboBoxUI$3,alignmentX=0.0,alignmentY=0.0,border=com.sun.java.swing.plaf.windows.XPStyle$XPFillBorder@1b22a8c,flags=20971848,maximumSize=,minimumSize=,preferredSize=,isEditable=true,lightWeightPopupEnabled=true,maximumRowCount=8,selectedItemReminder=]
[java] 2008-06-16 14:33:40,084 [AWT-EventQueue-0] DEBUG field.TermCompList - update model
[java] Checking if Driver is registered with DriverManager.
[java] Registered the driver ok, so let's make a connection.
[java] Hooray! We connected to the database!
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO: writing preferences
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO:
[java]
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO: java.lang.NullPointerException
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO:
[java]
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO: Continuing ...
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO:
[java]
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO: java.lang.Exception: XMLEncoder: discarding statement XMLEncoder.writeObject(Preferences);
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO:
[java]
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO: Continuing ...
[java] Jun 16, 2008 2:33:52 PM java.util.logging.LogManager$RootLogger log
[java] INFO:
[java]

BUILD SUCCESSFUL
Total time: 1 minute 25 seconds

Discussion

  • Jolene

    Jolene - 2008-06-16
    • priority: 5 --> 9
    • assigned_to: nobody --> mgibson
     
  • Jolene

    Jolene - 2008-06-16

    Logged In: YES
    user_id=2032724
    Originator: YES

    Hey Mark,
    Turns out this something that Juan Carlos can fix. So what happened was that the naming conventions for WBPhenotype have changed. The obo file for WBPhenotypeXXXXXXX has just changed to WBPhenotype:XXXXXXX ( a colon has been added), but none of the objects in postgres have been modified yet.This explains why the retrieve function comes up empty.

     
  • Jolene

    Jolene - 2008-06-16
    • priority: 9 --> 6
     
  • Jolene

    Jolene - 2008-06-20
    • status: open --> closed
     

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