Adding custom pipeline fails

[Len]

Hi,

I have some problems with running pipelines from XNAT. 

First, I tried the manual for installing pipelines (see https://wiki.xnat.org/display/XNAT16/Installing+Pipelines+in+XNAT),

and it doesn’t seem to work in User Interface. I get the screen for selecting the pipeline, but if I click on ‘submit’ I get the the following error:
An error has occurred.
Please contact your IT staff or the application logs for more information.

And in turbine.log:

2014-07-04 11:34:51,631 [http-bio-8443-exec-1] ERROR org.apache.turbine.services.velocity.TurbineVelocityService - Class org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter threw Exception java.lang.NullPointerException        at org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter(TurbineUtils.java:870)        at org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter(TurbineUtils.java:814)        at sun.reflect.GeneratedMethodAccessor181.invoke(Unknown Source)        at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)        at java.lang.reflect.Method.invoke(Method.java:606)        at org.apache.velocity.runtime.parser.node.ASTMethod.execute(ASTMethod.java:260)        at org.apache.velocity.runtime.parser.node.ASTReference.execute(ASTReference.java:207)        at org.apache.velocity.runtime.parser.node.ASTReference.value(ASTReference.java:357)        at org.apache.velocity.runtime.parser.node.ASTSetDirective.render(ASTSetDirective.java:135)        at org.apache.velocity.runtime.parser.node.ASTBlock.render(ASTBlock.java:94)        at org.apache.velocity.runtime.parser.node.ASTIfStatement.render(ASTIfStatement.java:109)        at org.apache.velocity.runtime.parser.node.SimpleNode.render(SimpleNode.java:271)        at org.apache.velocity.Template.merge(Template.java:296)        at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:492)        at org.apache.velocity.app.Velocity.mergeTemplate(Velocity.java:461)        at org.apache.turbine.services.velocity.TurbineVelocityService.executeRequest(TurbineVelocityService.java:415)        at org.apache.turbine.services.velocity.TurbineVelocityService.handleRequest(TurbineVelocityService.java:281)        at org.apache.turbine.services.velocity.TurbineVelocity.handleRequest(TurbineVelocity.java:71)        at org.apache.turbine.modules.screens.VelocityScreen.buildTemplate(VelocityScreen.java:119)        at org.apache.turbine.modules.screens.TemplateScreen.doBuild(TemplateScreen.java:101)        at org.apache.turbine.modules.Screen.build(Screen.java:57)        at org.apache.turbine.modules.ScreenLoader.eval(ScreenLoader.java:104)        at org.apache.turbine.modules.layouts.VelocityOnlyLayout.doBuild(VelocityOnlyLayout.java:92)        at org.apache.turbine.modules.Layout.build(Layout.java:53)        at org.apache.turbine.modules.LayoutLoader.exec(LayoutLoader.java:98)        at org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:146)        at org.apache.turbine.modules.Page.build(Page.java:53)        at org.apache.turbine.modules.PageLoader.exec(PageLoader.java:98)        at org.apache.turbine.Turbine.doGet(Turbine.java:751)        at javax.servlet.http.HttpServlet.service(HttpServlet.java:620)        at javax.servlet.http.HttpServlet.service(HttpServlet.java:727)        at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:303)        at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:208)        at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:163)…
and 
2014-07-04 12:06:35,302 [http-bio-8443-exec-3] ERROR org.apache.turbine.Turbine - Turbine.handleException: java.lang.ClassNotFoundException:         Requested Screen not found: Default        Turbine looked in the following modules.packages path:        [org.apache.turbine.app.xnat.modules, org.nrg.xnat.turbine.modules, org.nrg.xdat.turbine.modules, org.apache.turbine.app.xnat.modules, org.apache.turbine.modules]         at org.apache.turbine.modules.ScreenLoader.getInstance(ScreenLoader.java:190)        at org.apache.turbine.modules.pages.DefaultPage.doBuild(DefaultPage.java:139)
     ….                            

The second problem I have is that I can run the pipeline automatically, but only if I keep the default parameters. 

If I change any of the parameters after the pipeline was added to the project (using the ‘edit’ button), the pipeline fails to run automatically and is not queued, this, without any clear logging.

Any help would really be appreciated, I have been stuck on both issues for quite some time.

Kind regards,

Len Feremans

[Mohana Ramaratnam]

Hi Len

Can you remove the pipeline from the site, make the parameter change, add the pipeline to the site and then to the project and re-try to launch it.

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[Len]

Hi Mohana,

I tried that, but that doesn't resolve the issue. The pipeline is only run (and then only automatic) if no parameters are changed, except the 'run on autoarchive' option.

I attached my pipeline xml descriptors and a screen showing the add pipeline configuration. Note that i use '|' as a separator, because ',' give some, for us, undesired side-effects.

I have struggled with this bug for some time, and looked at other related problems in the forum, but have not found a solution. 

So thank you very much for trying to help me out!

greetings,

Len

Op vrijdag 4 juli 2014 16:26:52 UTC+2 schreef Mohana:

[Mohana Ramaratnam]

Hi Len,

Can you tell me which are the parameters you try to change and what are the values you try to set it to. 

Mohana

[Len]

Hi Mohana,

One scenario that doesn't work is changing protocolVerificationList to T1, snrSelectedModalities also to T1, and motionDetectionModalities to empty.

greetings,

Len

Op woensdag 9 juli 2014 16:57:54 UTC+2 schreef Mohana:

[Mohana Ramaratnam]

Hi Len,

For a pipeline, if a variable is not required for a particular project (as in motionDetectionModalities being set to empty), the way out would be to set the value to a space character and not null. I will look into make code changes to support what you want. 

Regards

Mohana

[Len]

Hi Mohana,

Unfortunately this also does not solve the issue. 

As far as I can estimate, changing any parameters to any value, causes the pipeline from being executed automatically.

How can resolve this issue further? I believe the problem is somewhere in the configuration of our server.

If it helps, I can provide you with credentials to our test server, and you can test for yourself. 

greetings,
Len Feremans

 

Op maandag 14 juli 2014 11:18:12 UTC+2 schreef Mohana:

[Mohana Ramaratnam]

Please let me know tge credentials offline.

[dagmar....@googlemail.com]

Hi Len and Mohana,

I have exactly the same problem trying to launch any pipeline using the User Interface. Clicking on the Submit-Button of the default_pipeline_launche, I end up with the same error message and the turbine.log looks also similar.

Did you solve the problem meanwhile? Would be very interested in the solution.

Best regards

Dagmar

[dagmar....@googlemail.com]

Hmm,
for some reason seems that I put some rubbish in the customwebpage-field - found out looking into the database-table pipe-pipelinedetails.
Now everything works :-)
Is there any possibility changing the customwebpage after adding the pipeline, or is the default way delete and the add again?

best wishes Dagmar

[Robin Koch]

Am Sonntag, 23. November 2014 19:30:30 UTC+1 schrieb dagmar....@googlemail.com:

for some reason seems that I put some rubbish in the customwebpage-field - found out looking into the database-table pipe-pipelinedetails.
Now everything works :-)

Hallo Dagmar,

could you please be a little more specific what you meant by "customwebpage-field" and where to find it?

I'm (very) new to XNAT et al but we've got a very similar error here.

Maybe it's a similar problem with a similar solution, too. :-)

Thank you,

Robin

[Robin Koch]

Never mind! I found it.

Now your question about "delete and add again" makes sense to me, too. :-)

Robin

[suyash Bhogawar]

Hello Dagmar, 

Even I am getting the same error when I select pipeline. Attached is the screen shot. 

Can yuo please direct me how to solve problem like this. 

i am very new to this pipeline engine in XNAT. 

your help is much appreciated. 

Very Gratefull, 

Suyash