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#13 InPhOImporter encounters ArrayIndexOutOfBoundsException

closed-later
1
2010-07-07
2010-06-01
No

When importing the resource

http://inpho.cogs.indiana.edu/owl/db-arch_20100601.owl

an ArrayIndexOutOfBoundsException is thrown - the Stacktrace is as follows:

org.h2.jdbc.JdbcSQLException: Allgemeiner Fehler: java.lang.ArrayIndexOutOfBoundsException: 0
General error: java.lang.ArrayIndexOutOfBoundsException: 0 [50000-107]
at org.h2.message.Message.getSQLException(Message.java:103)
at org.h2.message.Message.convert(Message.java:274)
at org.h2.table.TableData.addRow(TableData.java:135)
at org.h2.command.dml.Insert.update(Insert.java:96)
at org.h2.command.CommandContainer.update(CommandContainer.java:71)
at org.h2.command.Command.executeUpdate(Command.java:207)
at org.h2.jdbc.JdbcPreparedStatement.execute(JdbcPreparedStatement.java:173)
at org.semtinel.core.data.hibernate.SchemeInserterImpl.insertConcept(SchemeInserterImpl.java:243)
at org.semtinel.core.importer.inpho.InPhOImporter.mapConceptURIsToConceptIDsForOntology(InPhOImporter.java:175)
at org.semtinel.core.importer.inpho.InPhOImporter.process(InPhOImporter.java:152)
at org.semtinel.core.importer.inpho.InPhOImporterTopComponent$4.run(InPhOImporterTopComponent.java:207)
at java.lang.Thread.run(Thread.java:619)
Caused by: java.lang.ArrayIndexOutOfBoundsException: 0
at org.h2.util.IntArray.add(IntArray.java:43)
at org.h2.index.BtreeNode.add(BtreeNode.java:102)
at org.h2.index.BtreeIndex.add(BtreeIndex.java:223)
at org.h2.table.TableData.addRow(TableData.java:117)
... 9 more
Caused: java.lang.RuntimeException: SQL Error
at org.semtinel.core.data.hibernate.SchemeInserterImpl.insertConcept(SchemeInserterImpl.java:251)
at org.semtinel.core.importer.inpho.InPhOImporter.mapConceptURIsToConceptIDsForOntology(InPhOImporter.java:175)
at org.semtinel.core.importer.inpho.InPhOImporter.process(InPhOImporter.java:152)
at org.semtinel.core.importer.inpho.InPhOImporterTopComponent$4.run(InPhOImporterTopComponent.java:207)
[catch] at java.lang.Thread.run(Thread.java:619)

Discussion

  • Problem did not last after full rebuild of Semtinel from source. Further observation may be necessary.

     
    • priority: 2 --> 1
    • status: open --> pending-later
     
    • status: pending-later --> closed-later
     
  • This Tracker item was closed automatically by the system. It was
    previously set to a Pending status, and the original submitter
    did not respond within 14 days (the time period specified by
    the administrator of this Tracker).