[ome-devel] Errors running scripts
Wood, Christopher
CJW at stowers.org
Fri Sep 24 15:32:51 BST 2010
Thanks,
Do you recommend updating Python? My server has 2.4 right now.
Thanks Chris
On 9/24/10 9:30 AM, "Josh Moore" <josh at glencoesoftware.com> wrote:
Hi Christopher,
this is a problem with the script using Python 2.5+ syntax. See ticket https://trac.openmicroscopy.org.uk/omero/ticket/2832 for an explanation.
In your case, remove the line 726 (except:raise) to make the script work.
Cheers,
~Josh.
On Sep 24, 2010, at 4:17 PM, Wood, Christopher wrote:
> Hi,
> I am getting the following errors when running the "Split View Figure" script:
> This happens with any image, and also happens with export movie
>
> See below:
>> From /OMERO/Files/Dir-003/3407
>
> File "./script", line 727
> finally: client.closeSession()
> ^
> SyntaxError: invalid syntax
>
> --------
>> From ProcessorLog:
>
> 2010-09-24 09:01:58,525 INFO [ omero.remote] (Dummy-3 ) Meth: ProcessorI.willAccept
> 2010-09-24 09:01:58,588 INFO [ omero.remote] (Dummy-3 ) Rslt: True
> 2010-09-24 09:01:58,869 INFO [ omero.remote] (Dummy-9 ) Meth: ProcessorI.willAccept
> 2010-09-24 09:01:58,929 INFO [ omero.remote] (Dummy-9 ) Rslt: True
> 2010-09-24 09:01:59,227 INFO [ omero.remote] (Dummy-6 ) Meth: ProcessorI.parseJob
> 2010-09-24 09:01:59,228 INFO [ omero.processor.ProcessorI] (Dummy-6 ) parseJob: Session = 366c45dd-04e7-418e-824b-407acd61de92, JobId = 515
> 2010-09-24 09:01:59,332 INFO [ omero.processor.ProcessI] (Dummy-6 ) Created 366c45dd-04e7-418e-824b-407acd61de92 in /tmp/omero/tmp/omero_apache/3523/processCW_5Ce.dir
> 2010-09-24 09:01:59,344 INFO [ omero.processor.ProcessorI] (Dummy-6 ) Downloaded file: 3206
> 2010-09-24 09:01:59,353 INFO [ omero.processor.ProcessI] (Dummy-6 ) <proc:15199,rc=-,uuid=366c45dd-04e7-418e-824b-407acd61de92> : Activated
> 2010-09-24 09:01:59,420 INFO [ omero.remote] (Dummy-6 ) Meth: ProcessI.wait
> 2010-09-24 09:01:59,421 INFO [ omero.processor.ProcessI] (Dummy-6 ) <proc:15199,rc=1,uuid=366c45dd-04e7-418e-824b-407acd61de92> : Waiting
> 2010-09-24 09:01:59,422 INFO [ omero.processor.ProcessI] (Dummy-6 ) <proc:15199,rc=1,uuid=366c45dd-04e7-418e-824b-407acd61de92> : Deactivating
> 2010-09-24 09:01:59,422 INFO [ omero.remote] (Dummy-6 ) Meth: ProcessI.shutdown
> 2010-09-24 09:01:59,423 INFO [ omero.remote] (Dummy-6 ) Rslt: None
> 2010-09-24 09:01:59,542 INFO [ omero.processor.ProcessI] (Dummy-6 ) <proc:15199,rc=1,uuid=366c45dd-04e7-418e-824b-407acd61de92> : Changed job status from Running to Error
> 2010-09-24 09:01:59,549 INFO [ omero.processor.ProcessI] (Dummy-6 ) <proc:15199,rc=1,uuid=366c45dd-04e7-418e-824b-407acd61de92> : No stdout
> 2010-09-24 09:02:03,027 INFO [ omero.processor.ProcessI] (Dummy-6 ) <proc:15199,rc=1,uuid=366c45dd-04e7-418e-824b-407acd61de92> : Uploaded 103 bytes of /tmp/omero/tmp/omero_apache/3523/processCW_5Ce.dir/err to 3407
> 2010-09-24 09:02:03,033 INFO [ omero.processor.ProcessI] (Dummy-6 ) <proc:15199,rc=1,uuid=366c45dd-04e7-418e-824b-407acd61de92> : Lived 0s. Deactivation took 3s.
>
>
>
> Error message from Omero Insight:
>
> java.lang.Exception: java.lang.NullPointerException
> at org.openmicroscopy.shoola.env.data.views.ScriptBatchCall.doStep(ScriptBatchCall.java:112)
> at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
> at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
> at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:274)
> at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
> at java.lang.Thread.run(Thread.java:637)
>
> at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:158)
> at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:245)
> at org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:217)
> at org.openmicroscopy.shoola.env.ui.ActivityComponent.showException(ActivityComponent.java:464)
> at org.openmicroscopy.shoola.env.ui.ActivityComponent.actionPerformed(ActivityComponent.java:865)
> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
> at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
> at java.awt.Component.processMouseEvent(Component.java:6348)
> at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
> at java.awt.Component.processEvent(Component.java:6113)
> at java.awt.Container.processEvent(Container.java:2085)
> at java.awt.Component.dispatchEventImpl(Component.java:4714)
> at java.awt.Container.dispatchEventImpl(Container.java:2143)
> at java.awt.Component.dispatchEvent(Component.java:4544)
> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)
> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)
> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
> at java.awt.Container.dispatchEventImpl(Container.java:2129)
> at java.awt.Window.dispatchEventImpl(Window.java:2478)
> at java.awt.Component.dispatchEvent(Component.java:4544)
> at java.awt.EventQueue.dispatchEvent(EventQueue.java:635)
> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
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