[
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.
--
This message was sent by Atlassian JIRA
(v6.3.4#6332)
