<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><BR><DIV><BR><DIV>Begin forwarded message:</DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>From: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><A href="mailto:debartolomeo@ece.ucsb.edu">debartolomeo@ece.ucsb.edu</A></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>Date: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica">August 22, 2006 5:27:38 PM EDT</FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>To: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><A href="mailto:tm289@cam.ac.uk">tm289@cam.ac.uk</A></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><FONT face="Helvetica" size="3" color="#000000" style="font: 12.0px Helvetica; color: #000000"><B>Subject: </B></FONT><FONT face="Helvetica" size="3" style="font: 12.0px Helvetica"><B>more execution questions</B></FONT></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV> <DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Good day, Tom,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I hope you are well.<SPAN class="Apple-converted-space"> </SPAN>I have a few more questions for you (2).</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Question 1:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I'm having problems executing some analysis chains from the command line.<SPAN class="Apple-converted-space"> </SPAN></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I wrote them myself (they are matlab), so the problem most likely lies</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">with my writing and limited understanding of the Analysis Chain - Module -</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Matlab thing.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I run:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">export OME_DEBUG=1</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ome execute -a "Binarize Chain" -d "AnyDataset"</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">and get:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">...</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ome: Executing!</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ome: Could not find utility library, using the engine instead.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Error message: Can't locate OME/Matlab/Lib/Utility.pm in @INC (@INC</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">contains: /home/omedev/OME-Installed/Inline/lib /etc/perl</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/usr/local/lib/perl/5.8.4 /usr/local/share/perl/5.8.4 /usr/lib/perl5</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/usr/share/perl5 /usr/lib/perl/5.8 /usr/share/perl/5.8</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/usr/local/lib/site_perl .) at (eval 278) line 2.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">BEGIN failed--compilation aborted at (eval 278) line 2.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ome: Matlab src dir is /home/tmacura/OME/src/matlab</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ome: Matlab exec is /home/matlab/bin/matlab</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">ome: <SPAN class="Apple-converted-space"> </SPAN>Errir during execution: Cannot Execute with Feature Granularity</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">without either Feature inputs or outputs at</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/usr/local/share/perl/5.8.4/OME/Analysis/Handlers/MatlabHandler.pm line</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">1177.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">...</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I basically used Histogram Equalization Preprocessing Chain as a chain</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">model .<SPAN class="Apple-converted-space"> </SPAN>I think that more examples would be extremely helpful - or a</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">step-by-step walkthrough of the complete requirements (like the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2005-March/000334.html">http://lists.openmicroscopy.org.uk/pipermail/ome-devel/2005-March/000334.html</A></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">posting).<SPAN class="Apple-converted-space"> </SPAN>The documentation is thorough, but it's difficult to remember</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the particulars of the nomenclature when actually trying to write a chain</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">- for example, links and node specifics are difficult to remember when</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">trying to write a chain from scratch.<SPAN class="Apple-converted-space"> </SPAN>The MATLAB module tutorial on the</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">website is helpful, but very broad.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Question 2:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">when executing a chain from the UI against a dataset, I'm getting weird</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">errors.<SPAN class="Apple-converted-space"> </SPAN>For example, when executing "Histogram Equalization Preprocessing</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Chain" against "Tom_Made_Me_IamA2DImg" I get:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Error serving OME::Web::ExecuteChain: Error executing SQL:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">select<SPAN class="Apple-converted-space"> </SPAN>tasks.task_id as id, tasks.t_last, tasks.session_id,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">tasks.last_step, tasks.n_steps, tasks.name, tasks.t_stop, tasks.message,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">tasks.state, tasks.t_start, tasks.process_id, tasks.session_id,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">tasks.error from tasks where tasks.session_id = ?</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">With Values:</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">1</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Error:DBD::Pg::st execute failed: no connection to the server</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>OME::Factory::findObjects('OME::Factory=HASH(0x9eeb118)', 'OME::Task',</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'session_id', 1) called at</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/usr/local/share/perl/5.8.4/OME/Tasks/NotificationManager.pm line 133</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>OME::Tasks::NotificationManager::ping('OME::Tasks::NotificationManager')</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">called at /usr/local/share/perl/5.8.4/OME/Tasks/NotificationManager.pm</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">line 98</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>OME::Tasks::NotificationManager::new('OME::Tasks::NotificationManager',</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'Executing `Histogram Equalization Preprocessing Chain`', 3) called at</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/usr/local/share/perl/5.8.4/OME/Analysis/Engine.pm line 806</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>OME::Analysis::Engine::executeChain('OME::Analysis::Engine',</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'OME::AnalysisChain=HASH(0xa10b7d8)', 'OME::Dataset=HASH(0xa0ec370)',</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'HASH(0x9ecbd98)', 'undef', 'ReuseResults', 1) called at</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/usr/local/share/perl/5.8.4/OME/Web/ExecuteChain.pm line 83</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>OME::Web::ExecuteChain::getPageBody('OME::Web::ExecuteChain=HASH(0x9fd6ce0)',</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'NO_TEMPLATE') called at /usr/local/share/perl/5.8.4/OME/<A href="http://Web.pm">Web.pm</A> line 557</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>OME::Web::createOMEPage('OME::Web::ExecuteChain=HASH(0x9fd6ce0)',</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'NO_TEMPLATE') called at /usr/local/share/perl/5.8.4/OME/<A href="http://Web.pm">Web.pm</A> line 404</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>OME::Web::serve('OME::Web::ExecuteChain=HASH(0x9fd6ce0)') called at</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">/OME/perl2/serve.pl line 89</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>eval {...} called at /OME/perl2/serve.pl line 77</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>ModPerl::ROOT::ModPerl::Registry::OME_perl2_serve_2epl::handler('Apache::RequestRec=SCALAR(0xa16b8a0)')</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">called at /usr/lib/perl5/Apache2/ModPerl/RegistryCooker.pm line 203</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>eval {...} called at /usr/lib/perl5/Apache2/ModPerl/RegistryCooker.pm</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">line 203</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>ModPerl::RegistryCooker::run('ModPerl::Registry=HASH(0xa393d00)') called</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">at /usr/lib/perl5/Apache2/ModPerl/RegistryCooker.pm line 169</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>ModPerl::RegistryCooker::default_handler('ModPerl::Registry=HASH(0xa393d00)')</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">called at /usr/lib/perl5/Apache2/ModPerl/Registry.pm line 30</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>ModPerl::Registry::handler('ModPerl::Registry',</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">'Apache::RequestRec=SCALAR(0xa16b8a0)') called at -e line 0</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-tab-span" style="white-space:pre"> </SPAN>eval {...} called at -e line 0</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">I have no idea what this means, but I get something similar with all of</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">the chains.</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Thanks,</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Melissa</DIV> </BLOCKQUOTE></DIV><BR></BODY></HTML>