Hi folks,
I'm trying to run the Taverna Command Line tool (bundled with Taverna Workbench
2.2.0) and generate provenance data during the workflow run. After facing some
max key length problems during table setup in the T2Provenance database
initially, I was setup the T2Provenance database tables manually as mentioned
on this page: http://www.mygrid.org.uk/dev/issues/browse/T2-1605.
However I'm still unable to generate provenance data. The command line I'm
using is -
$ ./executeworkflow.sh -provenance -inputvalue Input Hello -logfile taverna.log
-dbproperties db.properties tmp2.t2flow
ERROR 2011-01-20 12:10:24,368
(net.sf.taverna.t2.provenance.connector.MySQLProvenanceConnector:167) - There
was a problem creating the Provenance database database:
com.mysql.jdbc.exceptions.jdbc4.MySQLSyntaxErrorException: Table 'Datalink'
already exists
at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
at
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
at
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
at com.mysql.jdbc.Util.handleNewInstance(Util.java:406)
at com.mysql.jdbc.Util.getInstance(Util.java:381)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:1031)
at com.mysql.jdbc.SQLError.createSQLException(SQLError.java:957)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3376)
at com.mysql.jdbc.MysqlIO.checkErrorPacket(MysqlIO.java:3308)
at com.mysql.jdbc.MysqlIO.sendCommand(MysqlIO.java:1837)
at com.mysql.jdbc.MysqlIO.sqlQueryDirect(MysqlIO.java:1961)
at com.mysql.jdbc.ConnectionImpl.execSQL(ConnectionImpl.java:2537)
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1564)
at com.mysql.jdbc.StatementImpl.executeUpdate(StatementImpl.java:1485)
at
org.apache.commons.dbcp.DelegatingStatement.executeUpdate(DelegatingStatement.java:228)
at
net.sf.taverna.t2.provenance.connector.MySQLProvenanceConnector.createDatabase(MySQLProvenanceConnector.java:152)
at
net.sf.taverna.t2.provenance.connector.ProvenanceConnector.init(ProvenanceConnector.java:291)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.createInvocationContext(CommandLineLauncher.java:301)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(CommandLineLauncher.java:186)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.launch(CommandLineLauncher.java:104)
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:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
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)
Outputs will be saved to the directory:
/home/workflow/taverna/taverna-workbench-2.2.0/testing/Workflow1_output_1
Error while executing main() of
net.sf.taverna.t2.commandline.CommandLineLauncher
java.lang.NullPointerException
at
net.sf.taverna.t2.provenance.connector.MySQLProvenanceConnector.addProvenanceItem(MySQLProvenanceConnector.java:82)
at
net.sf.taverna.t2.facade.impl.WorkflowInstanceFacadeImpl.fire(WorkflowInstanceFacadeImpl.java:239)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.executeWorkflow(CommandLineLauncher.java:239)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(CommandLineLauncher.java:202)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.launch(CommandLineLauncher.java:104)
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:39)
at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
at java.lang.reflect.Method.invoke(Method.java:597)
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)
Could you please advise what I'm missing? Why is the command line tool trying
to create the tables again? An example of correct usage of command line for
provenance data generation with an external DB would be really helpful in the
documentation.
Many thanks for your help.
Regards,
Ali
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