Hello,
I am trying to start a simple workflow on Taverna Server, but the workflow switches from 'Operating' to 'Finished' in a
second or so, with no output produced. The logs are attached.
Any help would be appreciated!
/Yehia
--
Yehia Elkhatib
School of Computing & Communications
Lancaster University, LA1 4WA, UK
y.elkhatib <then add> lancaster.ac.uk
http://www.comp.lancs.ac.uk/~elkhatib
2013-08-19 00:24:53.359 GMT Thread[main,5,main] Cleanup action starting
ERROR XBM0J: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at org.apache.derby.iapi.error.StandardException.newException(Unknown
Source)
at
org.apache.derby.impl.services.monitor.StorageFactoryService$9.run(Unknown
Source)
at java.security.AccessController.doPrivileged(Native Method)
at
org.apache.derby.impl.services.monitor.StorageFactoryService.createServiceRoot(Unknown
Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.createPersistentService(Unknown
Source)
at
org.apache.derby.iapi.services.monitor.Monitor.createPersistentService(Unknown
Source)
at org.apache.derby.impl.jdbc.EmbedConnection.createDatabase(Unknown
Source)
at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection30.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection40.<init>(Unknown Source)
at org.apache.derby.jdbc.Driver40.getNewEmbedConnection(Unknown Source)
at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
at org.apache.derby.jdbc.AutoloadedDriver.connect(Unknown Source)
at
org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at
org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
at
org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at
org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at
net.sf.taverna.t2.workbench.reference.config.DataManagementHelper.openConnection(DataManagementHelper.java:91)
at
net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler.testDatabaseConnection(DatabaseConfigurationHandler.java:103)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupDatabase(CommandLineLauncher.java:319)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(CommandLineLauncher.java:192)
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)
Cleanup action completed
2013-08-19 00:24:53.362 GMT Thread[main,5,main] Cleanup action starting
java.sql.SQLException: Failed to create database 't2-database', see the next
exception for details.
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.EmbedConnection.createDatabase(Unknown
Source)
at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection30.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection40.<init>(Unknown Source)
at org.apache.derby.jdbc.Driver40.getNewEmbedConnection(Unknown Source)
at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
at org.apache.derby.jdbc.AutoloadedDriver.connect(Unknown Source)
at
org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at
org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
at
org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at
org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at
net.sf.taverna.t2.workbench.reference.config.DataManagementHelper.openConnection(DataManagementHelper.java:91)
at
net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler.testDatabaseConnection(DatabaseConfigurationHandler.java:103)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupDatabase(CommandLineLauncher.java:319)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(CommandLineLauncher.java:192)
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: java.sql.SQLException: Failed to create database 't2-database', see
the next exception for details.
at
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown
Source)
... 30 more
Caused by: java.sql.SQLException: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown
Source)
at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.Util.generateCsSQLException(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)
... 27 more
Caused by: ERROR XBM0J: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at org.apache.derby.iapi.error.StandardException.newException(Unknown
Source)
at
org.apache.derby.impl.services.monitor.StorageFactoryService$9.run(Unknown
Source)
at java.security.AccessController.doPrivileged(Native Method)
at
org.apache.derby.impl.services.monitor.StorageFactoryService.createServiceRoot(Unknown
Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.createPersistentService(Unknown
Source)
at
org.apache.derby.iapi.services.monitor.Monitor.createPersistentService(Unknown
Source)
... 27 more
============= begin nested exception, level (1) ===========
java.sql.SQLException: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.Util.generateCsSQLException(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.EmbedConnection.createDatabase(Unknown
Source)
at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection30.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection40.<init>(Unknown Source)
at org.apache.derby.jdbc.Driver40.getNewEmbedConnection(Unknown Source)
at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
at org.apache.derby.jdbc.AutoloadedDriver.connect(Unknown Source)
at
org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at
org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
at
org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at
org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at
net.sf.taverna.t2.workbench.reference.config.DataManagementHelper.openConnection(DataManagementHelper.java:91)
at
net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler.testDatabaseConnection(DatabaseConfigurationHandler.java:103)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupDatabase(CommandLineLauncher.java:319)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(CommandLineLauncher.java:192)
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: java.sql.SQLException: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown
Source)
... 32 more
Caused by: ERROR XBM0J: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at org.apache.derby.iapi.error.StandardException.newException(Unknown
Source)
at
org.apache.derby.impl.services.monitor.StorageFactoryService$9.run(Unknown
Source)
at java.security.AccessController.doPrivileged(Native Method)
at
org.apache.derby.impl.services.monitor.StorageFactoryService.createServiceRoot(Unknown
Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.createPersistentService(Unknown
Source)
at
org.apache.derby.iapi.services.monitor.Monitor.createPersistentService(Unknown
Source)
... 27 more
============= end nested exception, level (1) ===========
============= begin nested exception, level (2) ===========
java.sql.SQLException: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.wrapArgsForTransportAcrossDRDA(Unknown
Source)
at
org.apache.derby.impl.jdbc.SQLExceptionFactory40.getSQLException(Unknown Source)
at org.apache.derby.impl.jdbc.Util.generateCsSQLException(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.EmbedConnection.createDatabase(Unknown
Source)
at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection30.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection40.<init>(Unknown Source)
at org.apache.derby.jdbc.Driver40.getNewEmbedConnection(Unknown Source)
at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
at org.apache.derby.jdbc.AutoloadedDriver.connect(Unknown Source)
at
org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at
org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
at
org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at
org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at
net.sf.taverna.t2.workbench.reference.config.DataManagementHelper.openConnection(DataManagementHelper.java:91)
at
net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler.testDatabaseConnection(DatabaseConfigurationHandler.java:103)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupDatabase(CommandLineLauncher.java:319)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(CommandLineLauncher.java:192)
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: ERROR XBM0J: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at org.apache.derby.iapi.error.StandardException.newException(Unknown
Source)
at
org.apache.derby.impl.services.monitor.StorageFactoryService$9.run(Unknown
Source)
at java.security.AccessController.doPrivileged(Native Method)
at
org.apache.derby.impl.services.monitor.StorageFactoryService.createServiceRoot(Unknown
Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.createPersistentService(Unknown
Source)
at
org.apache.derby.iapi.services.monitor.Monitor.createPersistentService(Unknown
Source)
... 27 more
============= end nested exception, level (2) ===========
============= begin nested exception, level (3) ===========
ERROR XBM0J: Directory
/tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f//tmp/ed6e1e5d-af99-4791-bf93-15cac1b8fc9f/t2-database
already exists.
at org.apache.derby.iapi.error.StandardException.newException(Unknown
Source)
at
org.apache.derby.impl.services.monitor.StorageFactoryService$9.run(Unknown
Source)
at java.security.AccessController.doPrivileged(Native Method)
at
org.apache.derby.impl.services.monitor.StorageFactoryService.createServiceRoot(Unknown
Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
at
org.apache.derby.impl.services.monitor.BaseMonitor.createPersistentService(Unknown
Source)
at
org.apache.derby.iapi.services.monitor.Monitor.createPersistentService(Unknown
Source)
at org.apache.derby.impl.jdbc.EmbedConnection.createDatabase(Unknown
Source)
at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection30.<init>(Unknown Source)
at org.apache.derby.impl.jdbc.EmbedConnection40.<init>(Unknown Source)
at org.apache.derby.jdbc.Driver40.getNewEmbedConnection(Unknown Source)
at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
at org.apache.derby.jdbc.AutoloadedDriver.connect(Unknown Source)
at
org.apache.commons.dbcp.DriverConnectionFactory.createConnection(DriverConnectionFactory.java:38)
at
org.apache.commons.dbcp.PoolableConnectionFactory.makeObject(PoolableConnectionFactory.java:582)
at
org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1556)
at
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
at
org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at
org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at
net.sf.taverna.t2.workbench.reference.config.DataManagementHelper.openConnection(DataManagementHelper.java:91)
at
net.sf.taverna.t2.commandline.data.DatabaseConfigurationHandler.testDatabaseConnection(DatabaseConfigurationHandler.java:103)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupDatabase(CommandLineLauncher.java:319)
at
net.sf.taverna.t2.commandline.CommandLineLauncher.setupAndExecute(CommandLineLauncher.java:192)
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)
============= end nested exception, level (3) ===========
Cleanup action completed
INFO 2013-08-19 01:24:53,600
(net.sf.taverna.t2.security.credentialmanager.CredentialManager:332) -
Credential Manager: Loaded the Keystore.
INFO 2013-08-19 01:24:53,602
(net.sf.taverna.t2.security.credentialmanager.CredentialManager:510) - Trying
to load Java truststore using password:
INFO 2013-08-19 01:24:53,709
(net.sf.taverna.t2.security.credentialmanager.CredentialManager:528) - Failed
to load the Java truststore to copy over certificates using default password:
from /usr/lib/jvm/java-6-openjdk-amd64/jre/lib/security/cacerts
INFO 2013-08-19 01:24:53,709
(net.sf.taverna.t2.security.credentialmanager.CredentialManager:510) - Trying
to load Java truststore using password: changeit
INFO 2013-08-19 01:24:53,930
(net.sf.taverna.t2.security.credentialmanager.CredentialManager:341) -
Credential Manager: Loaded the Truststore.
------------------------------------------------------------------------------
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