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From "Stian Soiland-Reyes (JIRA)" <j...@apache.org>
Subject [jira] [Commented] (TAVERNA-1013) The workflow created by Taverna 3 not run
Date Wed, 12 Oct 2016 10:38:20 GMT

    [ 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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