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  1. Apache Taverna
  2. TAVERNA-43

ClosedByInterruptException prevents deleting of workflow runs

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      Description

      Raul Palma had a problem where he had a bunch of workflow runs in Taverna 2.4.1 - which he then selected to remove. He left it for two hours without it finishing, so he clicked the "Shutdown" button in the dialogue.

      After restarting it was not possible to remove these runs. He had to delete the `t2-database` to clear the runs.

      log-file (attached) indicate a java.nio.channels.ClosedByInterruptException
      within Derby, which breaks the progress tree table constructor:

      WARN  2014-07-29 13:13:35,488 (net.sf.taverna.t2.provenance.connector.DerbyProvenanceConnector:95) - Could not create table Port : 
      java.sql.SQLException: Derby thread received an interrupt during a disk I/O operation, please check your application for the source of the interrupt.
      	at org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
      	at org.apache.derby.impl.jdbc.Util.newEmbedSQLException(Unknown Source)
      	at org.apache.derby.impl.jdbc.Util.seeNextException(Unknown Source)
      	at org.apache.derby.impl.jdbc.TransactionResourceImpl.wrapInSQLException(Unknown Source)
      	at org.apache.derby.impl.jdbc.TransactionResourceImpl.handleException(Unknown Source)
      	at org.apache.derby.impl.jdbc.EmbedConnection.handleException(Unknown Source)
      	at org.apache.derby.impl.jdbc.ConnectionChild.handleException(Unknown Source)
      	at org.apache.derby.impl.jdbc.EmbedStatement.executeStatement(Unknown Source)
      	at org.apache.derby.impl.jdbc.EmbedStatement.execute(Unknown Source)
      	at org.apache.derby.impl.jdbc.EmbedStatement.executeUpdate(Unknown Source)
      	at org.apache.commons.dbcp.DelegatingStatement.executeUpdate(DelegatingStatement.java:228)
      	at org.apache.commons.dbcp.DelegatingStatement.executeUpdate(DelegatingStatement.java:228)
      	at net.sf.taverna.t2.provenance.connector.DerbyProvenanceConnector.createDatabase(DerbyProvenanceConnector.java:92)
      	at net.sf.taverna.t2.provenance.connector.DerbyProvenanceConnector.init(DerbyProvenanceConnector.java:182)
      	at net.sf.taverna.t2.provenance.api.ProvenanceAccess.init(ProvenanceAccess.java:204)
      	at net.sf.taverna.t2.provenance.api.ProvenanceAccess.init(ProvenanceAccess.java:190)
      	at net.sf.taverna.t2.provenance.api.ProvenanceAccess.<init>(ProvenanceAccess.java:89)
      	at net.sf.taverna.t2.workbench.views.monitor.progressreport.WorkflowRunProgressTreeTableModel.<init>(WorkflowRunProgressTreeTableModel.java:149)
      	at net.sf.taverna.t2.workbench.run.WorkflowRun.getOrCreateMonitorViewComponent(WorkflowRun.java:419)
      	at net.sf.taverna.t2.workbench.run.ResultsPerspectiveComponent$LoadPreviousWorkflowRunThread.run(ResultsPerspectiveComponent.java:560)
      Caused by: java.sql.SQLException: Derby thread received an interrupt during a disk I/O operation, please check your application for the source of the interrupt.
      	at org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
      	at org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown Source)
      	... 20 more
      

        Attachments

        1. taverna-2.4.0.log.1
          1.00 MB
          Stian Soiland-Reyes

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            • Assignee:
              Unassigned
              Reporter:
              stain Stian Soiland-Reyes
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              • Created:
                Updated: