[ome-users] Fwd: more execution questions

[Tom Macura]

Begin forwarded message:

> From: debartolomeo at ece.ucsb.edu
> Date: August 22, 2006 5:27:38 PM EDT
> To: tm289 at cam.ac.uk
> Subject: more execution questions
>
> Good day, Tom,
>
> I hope you are well.  I have a few more questions for you (2).
>
> Question 1:
> I'm having problems executing some analysis chains from the command  
> line.
> I wrote them myself (they are matlab), so the problem most likely lies
> with my writing and limited understanding of the Analysis Chain -  
> Module -
> Matlab thing.
>
> I run:
>
> export OME_DEBUG=1
> ome execute -a "Binarize Chain" -d "AnyDataset"
>
> and get:
> ...
> ome: Executing!
> ome: Could not find utility library, using the engine instead.
>      Error message: Can't locate OME/Matlab/Lib/Utility.pm in @INC  
> (@INC
> contains: /home/omedev/OME-Installed/Inline/lib /etc/perl
> /usr/local/lib/perl/5.8.4 /usr/local/share/perl/5.8.4 /usr/lib/perl5
> /usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8
> /usr/local/lib/site_perl .) at (eval 278) line 2.
> BEGIN failed--compilation aborted at (eval 278) line 2.
>
> ome: Matlab src dir is /home/tmacura/OME/src/matlab
> ome: Matlab exec is /home/matlab/bin/matlab
> ome:       Errir during execution: Cannot Execute with Feature  
> Granularity
> without either Feature inputs or outputs at
> /usr/local/share/perl/5.8.4/OME/Analysis/Handlers/MatlabHandler.pm  
> line
> 1177.
>
> ...
>
>
> I basically used Histogram Equalization Preprocessing Chain as a chain
> model .  I think that more examples would be extremely helpful - or a
> step-by-step walkthrough of the complete requirements (like the
> http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2005-March/ 
> 000334.html
> posting).  The documentation is thorough, but it's difficult to  
> remember
> the particulars of the nomenclature when actually trying to write a  
> chain
> - for example, links and node specifics are difficult to remember when
> trying to write a chain from scratch.  The MATLAB module tutorial  
> on the
> website is helpful, but very broad.
>
>
> Question 2:
> when executing a chain from the UI against a dataset, I'm getting  
> weird
> errors.  For example, when executing "Histogram Equalization  
> Preprocessing
> Chain" against "Tom_Made_Me_IamA2DImg" I get:
>
> Error serving OME::Web::ExecuteChain: Error executing SQL:
> select  tasks.task_id as id, tasks.t_last, tasks.session_id,
> tasks.last_step, tasks.n_steps, tasks.name, tasks.t_stop,  
> tasks.message,
> tasks.state, tasks.t_start, tasks.process_id, tasks.session_id,
> tasks.error from tasks where tasks.session_id = ?
> With Values:
> 1
> Error:DBD::Pg::st execute failed: no connection to the server
> 	OME::Factory::findObjects('OME::Factory=HASH(0x9eeb118)',  
> 'OME::Task',
> 'session_id', 1) called at
> /usr/local/share/perl/5.8.4/OME/Tasks/NotificationManager.pm line 133
> 	OME::Tasks::NotificationManager::ping 
> ('OME::Tasks::NotificationManager')
> called at /usr/local/share/perl/5.8.4/OME/Tasks/NotificationManager.pm
> line 98
> 	OME::Tasks::NotificationManager::new 
> ('OME::Tasks::NotificationManager',
> 'Executing `Histogram Equalization Preprocessing Chain`', 3) called at
> /usr/local/share/perl/5.8.4/OME/Analysis/Engine.pm line 806
> 	OME::Analysis::Engine::executeChain('OME::Analysis::Engine',
> 'OME::AnalysisChain=HASH(0xa10b7d8)', 'OME::Dataset=HASH(0xa0ec370)',
> 'HASH(0x9ecbd98)', 'undef', 'ReuseResults', 1) called at
> /usr/local/share/perl/5.8.4/OME/Web/ExecuteChain.pm line 83
> 	OME::Web::ExecuteChain::getPageBody('OME::Web::ExecuteChain=HASH 
> (0x9fd6ce0)',
> 'NO_TEMPLATE') called at /usr/local/share/perl/5.8.4/OME/Web.pm  
> line 557
> 	OME::Web::createOMEPage('OME::Web::ExecuteChain=HASH(0x9fd6ce0)',
> 'NO_TEMPLATE') called at /usr/local/share/perl/5.8.4/OME/Web.pm  
> line 404
> 	OME::Web::serve('OME::Web::ExecuteChain=HASH(0x9fd6ce0)') called at
> /OME/perl2/serve.pl line 89
> 	eval {...} called at /OME/perl2/serve.pl line 77
> 	ModPerl::ROOT::ModPerl::Registry::OME_perl2_serve_2epl::handler 
> ('Apache::RequestRec=SCALAR(0xa16b8a0)')
> called at /usr/lib/perl5/Apache2/ModPerl/RegistryCooker.pm line 203
> 	eval {...} called at /usr/lib/perl5/Apache2/ModPerl/RegistryCooker.pm
> line 203
> 	ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0xa393d00)')  
> called
> at /usr/lib/perl5/Apache2/ModPerl/RegistryCooker.pm line 169
> 	ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH 
> (0xa393d00)')
> called at /usr/lib/perl5/Apache2/ModPerl/Registry.pm line 30
> 	ModPerl::Registry::handler('ModPerl::Registry',
> 'Apache::RequestRec=SCALAR(0xa16b8a0)') called at -e line 0
> 	eval {...} called at -e line 0
>
>
> I have no idea what this means, but I get something similar with  
> all of
> the chains.
>
> Thanks,
>
> Melissa

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