[ 
https://issues.apache.org/jira/browse/TAVERNA-1013?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=15568353#comment-15568353
 ] 

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

My second run of test87.wfbundle.zip just hangs - which is the same behaviour 
Mashael was showing me in person.

{code}
stain@biggiebuntu:~/Downloads/TAVERNA-1013$ executeworkflow test87.wfbundle.zip 
-inputvalue id P01174
pid:9033
log4j:WARN No appenders could be found for logger 
(org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more 
info.
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.
{code}

A ctrl-\ shows the stack traces including:

{code}
"SpringOsgiExtenderThread-58" #90 prio=5 os_prio=0 tid=0x00007f89b0047800 
nid=0x23b7 waiting on condition [0x00007f89b41b3000]
   java.lang.Thread.State: TIMED_WAITING (sleeping)
        at java.lang.Thread.sleep(Native Method)
        at 
org.apache.taverna.commandline.CommandLineTool.setupAndExecute(CommandLineTool.java:263)
        at 
org.apache.taverna.commandline.CommandLineTool.run(CommandLineTool.java:109)
        at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
        at 
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
        at 
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
        at java.lang.reflect.Method.invoke(Method.java:498)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeCustomInitMethod(AbstractAutowireCapableBeanFactory.java:1544)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.invokeInitMethods(AbstractAutowireCapableBeanFactory.java:1485)
        at 
org.springframework.beans.factory.support.AbstractAutowireCapableBeanFactory.initializeBean(AbstractAutowireCapableBeanFactory.java:1417)
        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)
        - locked <0x00000000ed398780> (a java.util.concurrent.ConcurrentHashMap)
        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:580)
        - locked <0x00000000ed398d78> (a java.util.concurrent.ConcurrentHashMap)
        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$4.run(AbstractDelegatedExecutionApplicationContext.java:327)
        - locked <0x00000000ed34cda0> (a java.lang.Object)
        at 
org.springframework.osgi.util.internal.PrivilegedUtils.executeWithCustomTCCL(PrivilegedUtils.java:87)
        at 
org.springframework.osgi.context.support.AbstractDelegatedExecutionApplicationContext.completeRefresh(AbstractDelegatedExecutionApplicationContext.java:292)
        at 
org.springframework.osgi.extender.internal.dependencies.startup.DependencyWaiterApplicationContextExecutor$CompleteRefreshTask.run(DependencyWaiterApplicationContextExecutor.java:138)
        at java.lang.Thread.run(Thread.java:745)


"Retry timer" #93 daemon prio=5 os_prio=0 tid=0x00007f89b8215800 nid=0x23c6 in 
Object.wait() [0x00007f8947efd000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        at java.lang.Object.wait(Object.java:502)
        at java.util.TimerThread.mainLoop(Timer.java:526)
        - locked <0x00000000f074e420> (a java.util.TaskQueue)
        at java.util.TimerThread.run(Timer.java:505)

"Dispatch stack state cleanup" #92 daemon prio=5 os_prio=0 
tid=0x00007f89b8277000 nid=0x23c5 in Object.wait() [0x00007f8945fe2000]
   java.lang.Thread.State: WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        at java.lang.Object.wait(Object.java:502)
        at java.util.TimerThread.mainLoop(Timer.java:526)
        - locked <0x00000000f06b9f30> (a java.util.TaskQueue)
        at java.util.TimerThread.run(Timer.java:505)

"derby.rawStoreDaemon" #83 daemon prio=5 os_prio=0 tid=0x00007f89801ae800 
nid=0x23ab in Object.wait() [0x00007f8945de0000]
   java.lang.Thread.State: TIMED_WAITING (on object monitor)
        at java.lang.Object.wait(Native Method)
        at org.apache.derby.impl.services.daemon.BasicDaemon.rest(Unknown 
Source)
        - locked <0x00000000eb5c4b98> (a 
org.apache.derby.impl.services.daemon.BasicDaemon)
        at org.apache.derby.impl.services.daemon.BasicDaemon.run(Unknown Source)
        at java.lang.Thread.run(Thread.java:745)

(.. + various spring/felix/timer threads)
{code}

That [line in 
CommandLineTool|https://github.com/apache/incubator-taverna-commandline/blob/3.1.0-incubating/taverna-commandline-common/src/main/java/org/apache/taverna/commandline/CommandLineTool.java#L263]
 is just waiting for workflowFinished() - 

but.. it seems it's always asking about the same report and not doing another 
call to runService.getWorkflowReport(runId) - is the report mutable or is it 
just always re-checking the first report without getting the report for when 
it's finished?

> 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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