Thanks for reporting this bug. I have recorded this as http://www.mygrid.org.uk/dev/issues/browse/T2-2025
I have also verified that this log message can be ignored, as provenance is still captured and kept separate for each of the nested workflows with the same identifier. Export both to OPM and Janus, in addition clicking on the individual processes within the nested workflow works fine in the workbench. The error occurs at an early stage when the provenance records the fact that a workflow ID was run - second time we already know that (but fails to check for this already existing in the database), and so the second call failing does not affect anything else. The error is logged both in the workbench and in the command line - but is of course more obvious in the command line. You can ignore this (and similar errors) from the provenance system by adding a magic line to log4j.properties - let me know if you need this. On Wed, Jan 11, 2012 at 14:41, Markus Plangg <[email protected]> wrote: > Hi, > > i tried to run a workflow with two identical nested workflows (imported > from the same file) with the taverna command line tool. When running it > with "-provenance" as: > executeworkflow.sh -provenance -embedded 2_Nested_Workflows.t2flow > or > executeworkflow.sh -provenance -clientserver -startdb > 2_Nested_Workflows.t2flow > i get the following error message: > > Started Derby Server on Port: 1527 > Outputs will be saved to the directory: > /home/markus/Dropbox/Projekte/RAWverna/Workflow/Evaluation/test/Workflow14_output_5 > ERROR 2012-01-11 15:31:25,177 > (net.sf.taverna.t2.provenance.lineageservice.EventProcessor:515) - > Problem processing provenance for dataflow > java.sql.SQLIntegrityConstraintViolationException: The statement was > aborted because it would have caused a duplicate key value in a unique > or primary key constraint or unique index identified by > 'SQL120111150128280' defined on 'WORKFLOWRUN'. > at > org.apache.derby.client.am.SQLExceptionFactory40.getSQLException(Unknown > Source) > at org.apache.derby.client.am.SqlException.getSQLException(Unknown > Source) > at > org.apache.derby.client.am.PreparedStatement.executeUpdate(Unknown Source) > at > org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:105) > at > org.apache.commons.dbcp.DelegatingPreparedStatement.executeUpdate(DelegatingPreparedStatement.java:105) > at > net.sf.taverna.t2.provenance.lineageservice.ProvenanceWriter.addWorkflowRun(ProvenanceWriter.java:274) > at > net.sf.taverna.t2.provenance.lineageservice.EventProcessor.processDataflowStructure(EventProcessor.java:302) > at > net.sf.taverna.t2.provenance.lineageservice.EventProcessor.processDataflowStructure(EventProcessor.java:394) > at > net.sf.taverna.t2.provenance.lineageservice.EventProcessor.processWorkflowStructure(EventProcessor.java:221) > at > net.sf.taverna.t2.provenance.lineageservice.EventProcessor.processWorkflowStructure(EventProcessor.java:184) > at > net.sf.taverna.t2.provenance.lineageservice.Provenance.processEvent(Provenance.java:187) > at > net.sf.taverna.t2.provenance.lineageservice.Provenance.acceptRawProvenanceEvent(Provenance.java:141) > at > net.sf.taverna.t2.provenance.connector.ProvenanceConnector.addProvenanceItem(ProvenanceConnector.java:359) > at > net.sf.taverna.t2.facade.impl.WorkflowInstanceFacadeImpl.fire(WorkflowInstanceFacadeImpl.java:239) > at > net.sf.taverna.t2.commandline.CommandLineLauncher.executeWorkflow(CommandLineLauncher.java:293) > at > net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(CommandLineLauncher.java:256) > at > net.sf.taverna.t2.commandline.CommandLineLauncher.launch(CommandLineLauncher.java:111) > at net.sf.taverna.raven.launcher.Launcher.launchMain(Launcher.java:150) > at net.sf.taverna.raven.launcher.Launcher.main(Launcher.java:66) > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) > at > sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:57) > at > sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) > at java.lang.reflect.Method.invoke(Method.java:616) > at > net.sf.taverna.raven.prelauncher.PreLauncher.runLauncher(PreLauncher.java:115) > at > net.sf.taverna.raven.prelauncher.PreLauncher.launchArgs(PreLauncher.java:69) > at > net.sf.taverna.raven.prelauncher.PreLauncher.main(PreLauncher.java:47) > Caused by: org.apache.derby.client.am.SqlException: The statement was > aborted because it would have caused a duplicate key value in a unique > or primary key constraint or unique index identified by > 'SQL120111150128280' defined on 'WORKFLOWRUN'. > at org.apache.derby.client.am.Statement.completeExecute(Unknown Source) > at > org.apache.derby.client.net.NetStatementReply.parseEXCSQLSTTreply(Unknown > Source) > at org.apache.derby.client.net.NetStatementReply.readExecute(Unknown > Source) > at org.apache.derby.client.net.StatementReply.readExecute(Unknown > Source) > at > org.apache.derby.client.net.NetPreparedStatement.readExecute_(Unknown > Source) > at org.apache.derby.client.am.PreparedStatement.readExecute(Unknown > Source) > at org.apache.derby.client.am.PreparedStatement.flowExecute(Unknown > Source) > at > org.apache.derby.client.am.PreparedStatement.executeUpdateX(Unknown Source) > ... 24 more > > The problem dissappears when i modify one of the embedded workflows. Am > I missing something here or is this a bug when Taverna tries to add both > nested workflows with the same ID to the DB? > > Attached is a simple workflow used for testing. > > Regards, > > Markus > > ------------------------------------------------------------------------------ > Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex > infrastructure or vast IT resources to deliver seamless, secure access to > virtual desktops. With this all-in-one solution, easily deploy virtual > desktops for less than the cost of PCs and save 60% on VDI infrastructure > costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox > _______________________________________________ > taverna-users mailing list > [email protected] > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/about/contact-us/ > -- Stian Soiland-Reyes, myGrid team School of Computer Science The University of Manchester ------------------------------------------------------------------------------ Ridiculously easy VDI. With Citrix VDI-in-a-Box, you don't need a complex infrastructure or vast IT resources to deliver seamless, secure access to virtual desktops. With this all-in-one solution, easily deploy virtual desktops for less than the cost of PCs and save 60% on VDI infrastructure costs. Try it free! http://p.sf.net/sfu/Citrix-VDIinabox _______________________________________________ taverna-users mailing list [email protected] [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/about/contact-us/
