[ 
https://issues.apache.org/jira/browse/TAVERNA-1013?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15568274#comment-15568274
 ] 

Stian Soiland-Reyes commented on TAVERNA-1013:
----------------------------------------------

Thanks, Mashael. 

I get that the workbench workflows (rest1.*) run with this uniprot identifier 
[P01174|http://www.uniprot.org/uniprot/P01174]:

{code}
stain@biggiebuntu:~/Downloads/TAVERNA-1013$ executeworkflow rest1.t2flow 
-inputvalue id P01174 
pid:8237
Outputs will be saved to the directory: 
/home/stain/Downloads/TAVERNA-1013/Workflow1_output
ERROR 2016-10-12 10:54:11,462 (org.apache.jena.riot:84) - [line: 1, col: 1 ] 
Content is not allowed in prolog.
Workflow completed.
{code}

{code}
stain@biggiebuntu:~/Downloads/TAVERNA-1013$ executeworkflow rest1.wfbundle.zip 
-inputvalue id P01174
pid:8453
log4j:WARN No appenders could be found for logger 
(org.springframework.beans.factory.support.DefaultListableBeanFactory).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more 
info.
Outputs will be saved to the directory: 
/home/stain/Downloads/TAVERNA-1013/Workflow1_output_1
ERROR 2016-10-12 10:55:13,695 (org.apache.jena.riot:84) - [line: 1, col: 1 ] 
Content is not allowed in prolog.
Workflow completed.
{code}

There is some unnecessary warnings in there (see TAVERNA-886 and TAVERNA-884), 
but we get "Workflow completed" so the workflow ran - I find the HTML page from 
Uniprot in both cases.  (If you wanted the [programmatic output from 
Uniprot|http://www.uniprot.org/help/programmatic_access] you would need to 
modify the REST template or add an Accept header of the desired format).

However if I try to run the test87.wfbundle.zip - which I guess is what your 
Taverna Language source code has generated, it fails to run:

{code}
stain@biggiebuntu:~/Downloads/TAVERNA-1013$ executeworkflow test87.wfbundle.zip 
-inputvalue id P01174
pid:8600
ERROR 2016-10-12 10:55:05,328 
(org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52) 
- Application context refresh failed 
(OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.engine.taverna-database-configuration-impl,
 config=osgibundle:/META-INF/spring/*.xml))
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 
'org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean#1': 
Invocation of init method failed; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'databaseManager' defined in URL 
[bundle://70.0:0/META-INF/spring/database-context.xml]: Instantiation of bean 
failed; nested exception is 
org.springframework.beans.BeanInstantiationException: Could not instantiate 
bean class 
[org.apache.taverna.configuration.database.impl.DatabaseManagerImpl]: 
Constructor threw exception; nested exception is 
org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
        at 
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
        at 
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:563)
        at 
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
        at 
org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.access$1600(AbstractDelegatedExecutionApplicationContext.java:62)
        at 
org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext$4.run(AbstractDelegatedExecutionApplicationContext.java:327)
        at 
org.springframework.osgi.util.internal.PrivilegedUtils.executeWithCustomTCCL(PrivilegedUtils.java:87)
        at 
org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:292)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:138)
        at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error 
creating bean with name 'databaseManager' defined in URL 
[bundle://70.0:0/META-INF/spring/database-context.xml]: Instantiation of bean 
failed; nested exception is 
org.springframework.beans.BeanInstantiationException: Could not instantiate 
bean class 
[org.apache.taverna.configuration.database.impl.DatabaseManagerImpl]: 
Constructor threw exception; nested exception is 
org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.)
        at 
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1003)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:907)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
        at 
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
        at 
org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean.afterPropertiesSet(OsgiServiceFactoryBean.java:200)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1477)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
        ... 14 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not 
instantiate bean class 
[org.apache.taverna.configuration.database.impl.DatabaseManagerImpl]: 
Constructor threw exception; nested exception is 
org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.)
        at 
org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:141)
        at 
org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:108)
        at 
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
        ... 25 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.)
        at 
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
        at 
org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
        at 
org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
        at 
org.apache.taverna.configuration.database.impl.DatabaseManagerImpl.getConnection(DatabaseManagerImpl.java:64)
        at 
org.apache.taverna.configuration.database.impl.DatabaseManagerImpl.<init>(DatabaseManagerImpl.java:59)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at 
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
        at 
org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126)
        ... 27 more
Caused by: java.sql.SQLException: Failed to start database 't2-database' with 
class loader org.apache.servicemix.bundles.derby [54], see the next exception 
for details.
        at 
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
        at 
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
        at org.apache.derby.impl.jdbc.Util.seeNextException(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection.bootDatabase(Unknown 
Source)
        at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver$1.run(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.jdbc.InternalDriver.getNewEmbedConnection(Unknown 
Source)
        at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
        at org.apache.derby.jdbc.EmbeddedDriver.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)
        ... 36 more
Caused by: ERROR XJ040: Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.
        at org.apache.derby.iapi.error.StandardException.newException(Unknown 
Source)
        at 
org.apache.derby.impl.jdbc.SQLExceptionFactory.wrapArgsForTransportAcrossDRDA(Unknown
 Source)
        ... 52 more
Caused by: ERROR XSDB6: Another instance of Derby may have already booted the 
database /home/stain/.apache-taverna-command-line-tool-product/t2-database.
        at org.apache.derby.iapi.error.StandardException.newException(Unknown 
Source)
        at org.apache.derby.iapi.error.StandardException.newException(Unknown 
Source)
        at 
org.apache.derby.impl.store.raw.data.BaseDataFileFactory.privGetJBMSLockOnDB(Unknown
 Source)
        at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.run(Unknown 
Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at 
org.apache.derby.impl.store.raw.data.BaseDataFileFactory.getJBMSLockOnDB(Unknown
 Source)
        at 
org.apache.derby.impl.store.raw.data.BaseDataFileFactory.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at 
org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at 
org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.store.raw.RawStore$6.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.store.raw.RawStore.bootServiceModule(Unknown 
Source)
        at org.apache.derby.impl.store.raw.RawStore.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at 
org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at 
org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.store.access.RAMAccessManager$5.run(Unknown 
Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at 
org.apache.derby.impl.store.access.RAMAccessManager.bootServiceModule(Unknown 
Source)
        at org.apache.derby.impl.store.access.RAMAccessManager.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at 
org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at 
org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.db.BasicDatabase$5.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.db.BasicDatabase.bootServiceModule(Unknown 
Source)
        at org.apache.derby.impl.db.BasicDatabase.bootStore(Unknown Source)
        at org.apache.derby.impl.db.BasicDatabase.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startProviderService(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.findProviderAndStartService(Unknown
 Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startPersistentService(Unknown
 Source)
        at 
org.apache.derby.iapi.services.monitor.Monitor.startPersistentService(Unknown 
Source)
        at org.apache.derby.impl.jdbc.EmbedConnection$4.run(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection$4.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at 
org.apache.derby.impl.jdbc.EmbedConnection.startPersistentService(Unknown 
Source)
        ... 49 more
ERROR 2016-10-12 10:55:05,463 
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor:443)
 - Unable to create application context for 
[org.apache.taverna.engine.taverna-database-configuration-impl], unsatisfied 
dependencies: none
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 
'org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean#1': 
Invocation of init method failed; nested exception is 
org.springframework.beans.factory.BeanCreationException: Error creating bean 
with name 'databaseManager' defined in URL 
[bundle://70.0:0/META-INF/spring/database-context.xml]: Instantiation of bean 
failed; nested exception is 
org.springframework.beans.BeanInstantiationException: Could not instantiate 
bean class 
[org.apache.taverna.configuration.database.impl.DatabaseManagerImpl]: 
Constructor threw exception; nested exception is 
org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1420)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:519)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
        at 
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
        at 
org.springframework.beans.factory.support.DefaultListableBeanFactory.preInstantiateSingletons(DefaultListableBeanFactory.java:563)
        at 
org.springframework.context.support.AbstractApplicationContext.finishBeanFactoryInitialization(AbstractApplicationContext.java:895)
        at 
org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.access$1600(AbstractDelegatedExecutionApplicationContext.java:62)
        at 
org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext$4.run(AbstractDelegatedExecutionApplicationContext.java:327)
        at 
org.springframework.osgi.util.internal.PrivilegedUtils.executeWithCustomTCCL(PrivilegedUtils.java:87)
        at 
org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:292)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:138)
        at java.lang.Thread.run(Thread.java:745)
Caused by: org.springframework.beans.factory.BeanCreationException: Error 
creating bean with name 'databaseManager' defined in URL 
[bundle://70.0:0/META-INF/spring/database-context.xml]: Instantiation of bean 
failed; nested exception is 
org.springframework.beans.BeanInstantiationException: Could not instantiate 
bean class 
[org.apache.taverna.configuration.database.impl.DatabaseManagerImpl]: 
Constructor threw exception; nested exception is 
org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.)
        at 
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:288)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.autowireConstructor(AbstractAutowireCapableBeanFactory.java:1003)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBeanInstance(AbstractAutowireCapableBeanFactory.java:907)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.doCreateBean(AbstractAutowireCapableBeanFactory.java:485)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.createBean(AbstractAutowireCapableBeanFactory.java:456)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory$1.getObject(AbstractBeanFactory.java:291)
        at 
org.springframework.beans.factory.support.DefaultSingletonBeanRegistry.getSingleton(DefaultSingletonBeanRegistry.java:222)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory.doGetBean(AbstractBeanFactory.java:288)
        at 
org.springframework.beans.factory.support.AbstractBeanFactory.getBean(AbstractBeanFactory.java:190)
        at 
org.springframework.osgi.service.exporter.support.OsgiServiceFactoryBean.afterPropertiesSet(OsgiServiceFactoryBean.java:200)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1477)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
        ... 14 more
Caused by: org.springframework.beans.BeanInstantiationException: Could not 
instantiate bean class 
[org.apache.taverna.configuration.database.impl.DatabaseManagerImpl]: 
Constructor threw exception; nested exception is 
org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.)
        at 
org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:141)
        at 
org.springframework.beans.factory.support.SimpleInstantiationStrategy.instantiate(SimpleInstantiationStrategy.java:108)
        at 
org.springframework.beans.factory.support.ConstructorResolver.autowireConstructor(ConstructorResolver.java:280)
        ... 25 more
Caused by: org.apache.commons.dbcp.SQLNestedException: Cannot create 
PoolableConnectionFactory (Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.)
        at 
org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1549)
        at 
org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
        at 
org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
        at 
org.apache.taverna.configuration.database.impl.DatabaseManagerImpl.getConnection(DatabaseManagerImpl.java:64)
        at 
org.apache.taverna.configuration.database.impl.DatabaseManagerImpl.<init>(DatabaseManagerImpl.java:59)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at 
sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
        at 
sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
        at 
org.springframework.beans.BeanUtils.instantiateClass(BeanUtils.java:126)
        ... 27 more
Caused by: java.sql.SQLException: Failed to start database 't2-database' with 
class loader org.apache.servicemix.bundles.derby [54], see the next exception 
for details.
        at 
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
        at 
org.apache.derby.impl.jdbc.SQLExceptionFactory.getSQLException(Unknown Source)
        at org.apache.derby.impl.jdbc.Util.seeNextException(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection.bootDatabase(Unknown 
Source)
        at org.apache.derby.impl.jdbc.EmbedConnection.<init>(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver$1.run(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver$1.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.jdbc.InternalDriver.getNewEmbedConnection(Unknown 
Source)
        at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
        at org.apache.derby.jdbc.InternalDriver.connect(Unknown Source)
        at org.apache.derby.jdbc.EmbeddedDriver.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)
        ... 36 more
Caused by: ERROR XJ040: Failed to start database 't2-database' with class 
loader org.apache.servicemix.bundles.derby [54], see the next exception for 
details.
        at org.apache.derby.iapi.error.StandardException.newException(Unknown 
Source)
        at 
org.apache.derby.impl.jdbc.SQLExceptionFactory.wrapArgsForTransportAcrossDRDA(Unknown
 Source)
        ... 52 more
Caused by: ERROR XSDB6: Another instance of Derby may have already booted the 
database /home/stain/.apache-taverna-command-line-tool-product/t2-database.
        at org.apache.derby.iapi.error.StandardException.newException(Unknown 
Source)
        at org.apache.derby.iapi.error.StandardException.newException(Unknown 
Source)
        at 
org.apache.derby.impl.store.raw.data.BaseDataFileFactory.privGetJBMSLockOnDB(Unknown
 Source)
        at org.apache.derby.impl.store.raw.data.BaseDataFileFactory.run(Unknown 
Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at 
org.apache.derby.impl.store.raw.data.BaseDataFileFactory.getJBMSLockOnDB(Unknown
 Source)
        at 
org.apache.derby.impl.store.raw.data.BaseDataFileFactory.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at 
org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at 
org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.store.raw.RawStore$6.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.store.raw.RawStore.bootServiceModule(Unknown 
Source)
        at org.apache.derby.impl.store.raw.RawStore.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at 
org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at 
org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.store.access.RAMAccessManager$5.run(Unknown 
Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at 
org.apache.derby.impl.store.access.RAMAccessManager.bootServiceModule(Unknown 
Source)
        at org.apache.derby.impl.store.access.RAMAccessManager.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startModule(Unknown Source)
        at 
org.apache.derby.impl.services.monitor.FileMonitor.startModule(Unknown Source)
        at 
org.apache.derby.iapi.services.monitor.Monitor.bootServiceModule(Unknown Source)
        at org.apache.derby.impl.db.BasicDatabase$5.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at org.apache.derby.impl.db.BasicDatabase.bootServiceModule(Unknown 
Source)
        at org.apache.derby.impl.db.BasicDatabase.bootStore(Unknown Source)
        at org.apache.derby.impl.db.BasicDatabase.boot(Unknown Source)
        at org.apache.derby.impl.services.monitor.BaseMonitor.boot(Unknown 
Source)
        at org.apache.derby.impl.services.monitor.TopService.bootModule(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.bootService(Unknown Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startProviderService(Unknown 
Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.findProviderAndStartService(Unknown
 Source)
        at 
org.apache.derby.impl.services.monitor.BaseMonitor.startPersistentService(Unknown
 Source)
        at 
org.apache.derby.iapi.services.monitor.Monitor.startPersistentService(Unknown 
Source)
        at org.apache.derby.impl.jdbc.EmbedConnection$4.run(Unknown Source)
        at org.apache.derby.impl.jdbc.EmbedConnection$4.run(Unknown Source)
        at java.security.AccessController.doPrivileged(Native Method)
        at 
org.apache.derby.impl.jdbc.EmbedConnection.startPersistentService(Unknown 
Source)
        ... 49 more
ERROR 2016-10-12 10:59:58,976 
(org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52) 
- Application context refresh failed 
(OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.engine.taverna-run-impl,
 config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context 
initialization for 'org.apache.taverna.engine.taverna-run-impl' has timed out 
waiting for 
(objectClass=org.apache.taverna.platform.execution.api.ExecutionEnvironmentService)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:490)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:55)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:110)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
ERROR 2016-10-12 10:59:58,978 
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor:443)
 - Unable to create application context for 
[org.apache.taverna.engine.taverna-run-impl], unsatisfied dependencies: 
Dependency on 
[(objectClass=org.apache.taverna.platform.execution.api.ExecutionEnvironmentService)]
 (from bean [&executionEnvironmentService])
org.springframework.context.ApplicationContextException: Application context 
initialization for 'org.apache.taverna.engine.taverna-run-impl' has timed out 
waiting for 
(objectClass=org.apache.taverna.platform.execution.api.ExecutionEnvironmentService)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:490)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:55)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:110)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
ERROR 2016-10-12 10:59:58,981 
(org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52) 
- Application context refresh failed 
(OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.engine.taverna-execution-local,
 config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context 
initialization for 'org.apache.taverna.engine.taverna-execution-local' has 
timed out waiting for 
(objectClass=org.apache.taverna.reference.ReferenceService)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:490)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:55)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:110)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
ERROR 2016-10-12 10:59:58,985 
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor:443)
 - Unable to create application context for 
[org.apache.taverna.engine.taverna-execution-local], unsatisfied dependencies: 
Dependency on [(objectClass=org.apache.taverna.reference.ReferenceService)] 
(from bean [&referenceService])
org.springframework.context.ApplicationContextException: Application context 
initialization for 'org.apache.taverna.engine.taverna-execution-local' has 
timed out waiting for 
(objectClass=org.apache.taverna.reference.ReferenceService)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:490)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:55)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:110)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
ERROR 2016-10-12 10:59:58,994 
(org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52) 
- Application context refresh failed 
(OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.engine.taverna-execution-impl,
 config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context 
initialization for 'org.apache.taverna.engine.taverna-execution-impl' has timed 
out waiting for 
(objectClass=org.apache.taverna.platform.execution.api.ExecutionService)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:490)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:55)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:110)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
ERROR 2016-10-12 10:59:58,996 
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor:443)
 - Unable to create application context for 
[org.apache.taverna.engine.taverna-execution-impl], unsatisfied dependencies: 
Dependency on 
[(objectClass=org.apache.taverna.platform.execution.api.ExecutionService)] 
(from bean [&executionServices])
org.springframework.context.ApplicationContextException: Application context 
initialization for 'org.apache.taverna.engine.taverna-execution-impl' has timed 
out waiting for 
(objectClass=org.apache.taverna.platform.execution.api.ExecutionService)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:490)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:55)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:110)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
ERROR 2016-10-12 10:59:59,095 
(org.springframework.osgi.extender.internal.activator.ContextLoaderListener:52) 
- Application context refresh failed 
(OsgiBundleXmlApplicationContext(bundle=org.apache.taverna.engine.taverna-reference-impl,
 config=osgibundle:/META-INF/spring/*.xml))
org.springframework.context.ApplicationContextException: Application context 
initialization for 'org.apache.taverna.engine.taverna-reference-impl' has timed 
out waiting for 
(objectClass=org.apache.taverna.configuration.database.DatabaseManager)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:490)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:55)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:110)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
ERROR 2016-10-12 10:59:59,097 
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor:443)
 - Unable to create application context for 
[org.apache.taverna.engine.taverna-reference-impl], unsatisfied dependencies: 
Dependency on 
[(objectClass=org.apache.taverna.configuration.database.DatabaseManager)] (from 
bean [&databaseManager])
org.springframework.context.ApplicationContextException: Application context 
initialization for 'org.apache.taverna.engine.taverna-reference-impl' has timed 
out waiting for 
(objectClass=org.apache.taverna.configuration.database.DatabaseManager)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.timeout(DependencyWaiterApplicationContextExecutor.java:490)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor.access$000(DependencyWaiterApplicationContextExecutor.java:55)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$WatchDogTask.run(DependencyWaiterApplicationContextExecutor.java:110)
        at java.util.TimerThread.mainLoop(Timer.java:555)
        at java.util.TimerThread.run(Timer.java:505)
{code}

> The workflow created by Taverna 3 not run
> -----------------------------------------
>
>                 Key: TAVERNA-1013
>                 URL: https://issues.apache.org/jira/browse/TAVERNA-1013
>             Project: Apache Taverna
>          Issue Type: Bug
>          Components: Taverna Command-line Tool
>    Affects Versions: command-line 3.1.0
>         Environment: windows 
>            Reporter: Mashael
>             Fix For: command-line 3.2.0
>
>         Attachments: rest1.t2flow, rest1.wfbundle.zip, source_code.txt, 
> test87.wfbundle.zip
>
>
> I have created the same workflow in Taverna 2 which use REST, and can be run, 
> and I was trying to make the same workflow in Taverna 3 but could not be run.



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