Wildcard search returning a blank page
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Wildcard search returning a blank page
 
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Hi all, Since upgrading to GBrowse2, I've had an issue in which searching results in a blank page. This only seems to happen when using wildcard searches that result in more than one response. a failed search shows the expected "not found" error message.Chris [Fri Nov 08 11:34:48 2013] [error] [client xxx.xxx.xxx.xx] [17352] RUN(): POST: http://server.org/cgi-bin/gb2/gbrowse/test/ force_submit=0;plugin_find=0;name=GB4214%2A;Search=Search at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 240., referer: http://server.org/cgi-bin/gb2/gbrowse/test/ [Fri Nov 08 11:34:48 2013] [error] [client xxx.xxx.xxx.xx] [17352] session id = 476b5d9a79afdcf91b7c8ba7ff254eb0 at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 244., referer: http://server.org/cgi-bin/gb2/gbrowse/test/ [Fri Nov 08 11:34:48 2013] [error] [client xxx.xxx.xxx.xx] [17352] add_user_tracks() at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 273., referer: http://server.org/cgi-bin/gb2/gbrowse/test/ [Fri Nov 08 11:34:48 2013] [error] [client xxx.xxx.xxx.xx] [17352] testing for asynchronous event() at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 276., referer: http://server.org/cgi-bin/gb2/gbrowse/test/ [Fri Nov 08 11:34:48 2013] [error] [client xxx.xxx.xxx.xx] [17352] init() at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 287., referer: http://server.org/cgi-bin/gb2/gbrowse/test/ [Fri Nov 08 11:34:48 2013] [error] [client xxx.xxx.xxx.xx] [17352] update_state() at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 290., referer: http://SERVER.org/cgi-bin/gb2/gbrowse/test/ [Fri Nov 08 11:34:48 2013] [error] [client xxx.xxx.xxx.xx] [17352] render() at /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi/Bio/Graphics/Browser2/Render.pm line 297., referer: http://server.org/cgi-bin/gb2/gbrowse/test/ ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Wildcard search returning a blank page
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Hi Chris, What adaptor is this with? Does it matter? Scott Sent from my iPhone
------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Wildcard search returning a blank page
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Hi Scott, All of our databases are using Bio::DB::SeqFeature::Store adaptors, with some of them pointing to the same seqFeature databases we used with GBrowse1.xx. Some have been created and loaded using the new loader, and they all share this behavior. I wouldn't expect the adaptor to be the issue, since browsing and exact searching seems to work. Have you run into this issue before?Chris On Fri, Nov 8, 2013 at 7:55 PM, Scott Cain <[hidden email]> wrote:
-- Chris Childers
Division of Animal Science College of Agriculture, Food and Natural Resources S134B ASRC, 920 East Campus Drive Columbia, MO 65211 ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Wildcard search returning a blank page
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Hi Chris, I have a vague recollection of this happening with the Chado adaptor but I can't find anything in the Change log that indicated that I fixed something. I can't get it to happen with the Chado adpator or the SeqFeature::Store adaptor using either MySQL (at MODEncode) or memory (local install) adaptors. Is everything up to date on your system?
Scott On Mon, Nov 11, 2013 at 10:56 AM, Chris Childers <[hidden email]> wrote:
------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Wildcard search returning a blank page
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A short update: BioPerl and GBrowse are both at the current version, I checked bp_seqfeature_load.pl for a version, but couldn't find any version info in it. I've also tried "./Build demo" to check out the in memory demo database and see the same behavior; searching for "YAL00*" or "YAL00" results in a blank page. It looks like the issue is not adapter specific. Chris On Mon, Nov 11, 2013 at 10:25 AM, Scott Cain <[hidden email]> wrote:
-- Chris Childers
Division of Animal Science College of Agriculture, Food and Natural Resources S134B ASRC, 920 East Campus Drive Columbia, MO 65211 ------------------------------------------------------------------------------ November Webinars for C, C++, Fortran Developers Accelerate application performance with scalable programming models. Explore techniques for threading, error checking, porting, and tuning. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60136231&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Wildcard search returning a blank page
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I tested an installation on a vanilla server, and it installed and works fine. I pulled the latest version of CPAN (2.55), confirmed the prereqs were installed, and it stalls or freezes on Build test. I checked that there are gff in the testdata/data directories. I've seen other accounts of people with this error and it passing, so don't think this was the issue. I do have Storable 2.45 installed on this machine. Could that be causing the problem?Chris ... ... ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: No suitable files found in /data/childers/gb2/GBrowse-2.55-6Ik6_t/t/testdata/data/volvox4 STACK: Error::throw STACK: Bio::Root::Root::throw /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:486 STACK: Bio::DB::IndexedBase::index_dir /usr/lib/perl5/site_perl/5.8.8/Bio/DB/IndexedBase.pm:444 STACK: Bio::DB::IndexedBase::new /usr/lib/perl5/site_perl/5.8.8/Bio/DB/IndexedBase.pm:361 STACK: Bio::DB::SeqFeature::Store::memory::commit /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/memory.pm:172 STACK: Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/GFF3Loader.pm:352 STACK: Bio::DB::SeqFeature::Store::Loader::load_fh /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:354 STACK: Bio::DB::SeqFeature::Store::Loader::load /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/Loader.pm:243 STACK: Bio::DB::SeqFeature::Store::memory::post_init /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store/memory.pm:164 STACK: Bio::DB::SeqFeature::Store::new /usr/lib/perl5/site_perl/5.8.8/Bio/DB/SeqFeature/Store.pm:395 STACK: Bio::Graphics::Browser2::DataBase::open_database /data/childers/gb2/GBrowse-2.55-6Ik6_t/t/../lib/Bio/Graphics/Browser2/DataBase.pm:44 STACK: Bio::Graphics::Browser2::DataSource::open_database /data/childers/gb2/GBrowse-2.55-6Ik6_t/t/../lib/Bio/Graphics/Browser2/DataSource.pm:997 STACK: Bio::Graphics::Browser2::Render::Slave::load_databases /data/childers/gb2/GBrowse-2.55-6Ik6_t/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:352 STACK: Bio::Graphics::Browser2::Render::Slave::process_request /data/childers/gb2/GBrowse-2.55-6Ik6_t/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:292 STACK: Bio::Graphics::Browser2::Render::Slave::process_connection /data/childers/gb2/GBrowse-2.55-6Ik6_t/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:240 STACK: Bio::Graphics::Browser2::Render::Slave::request_loop /data/childers/gb2/GBrowse-2.55-6Ik6_t/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:229 STACK: Bio::Graphics::Browser2::Render::Slave::run /data/childers/gb2/GBrowse-2.55-6Ik6_t/t/../lib/Bio/Graphics/Browser2/Render/Slave.pm:160 STACK: t/03.render.t:75 ----------------------------------------------------------- t/03.render.t ............. 110/150 On Tue, Nov 12, 2013 at 11:46 AM, Chris Childers <[hidden email]> wrote:
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Re: Wildcard search returning a blank page
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In reply to this post by Chris Childers
I found the solution. Thanks!Based on this old thread, I checked for duplicate Bio:Graphics::Glyph modules and there were legacy modules hiding out in my Perl libraries path. I removed them and it is working now. Chris On Tue, Nov 12, 2013 at 11:46 AM, Chris Childers <[hidden email]> wrote:
-- Chris Childers
Division of Animal Science College of Agriculture, Food and Natural Resources S134B ASRC, 920 East Campus Drive Columbia, MO 65211 ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
Re: Wildcard search returning a blank page
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Chris, I am so glad to hear that--I was baffled :-) ("./Build --uninst 1" is your friend! :-) Scott
On Fri, Nov 15, 2013 at 12:20 PM, Chris Childers <[hidden email]> wrote:
------------------------------------------------------------------------ Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ------------------------------------------------------------------------------ DreamFactory - Open Source REST & JSON Services for HTML5 & Native Apps OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access Free app hosting. Or install the open source package on any LAMP server. Sign up and see examples for AngularJS, jQuery, Sencha Touch and Native! http://pubads.g.doubleclick.net/gampad/clk?id=63469471&iu=/4140/ostg.clktrk _______________________________________________ Gmod-gbrowse mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse |
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