Wildcard search returning a blank page

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Wildcard search returning a blank page

Chris Childers
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.


Below is the section form the Apache error log from an attempted search:

Thanks,
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/


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Re: Wildcard search returning a blank page

Scott Cain
Hi Chris, 

What adaptor is this with?  Does it matter?

Scott

Sent from my iPhone

On Nov 8, 2013, at 12:50 PM, Chris Childers <[hidden email]> wrote:

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.


Below is the section form the Apache error log from an attempted search:

Thanks,
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/

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Re: Wildcard search returning a blank page

Chris Childers
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?

Thanks,
Chris
 


On Fri, Nov 8, 2013 at 7:55 PM, Scott Cain <[hidden email]> wrote:
Hi Chris, 

What adaptor is this with?  Does it matter?

Scott

Sent from my iPhone

On Nov 8, 2013, at 12:50 PM, Chris Childers <[hidden email]> wrote:

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.


Below is the section form the Apache error log from an attempted search:

Thanks,
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/

------------------------------------------------------------------------------
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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
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--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211


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from the latest Intel processors and coprocessors. See abstracts and register
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Re: Wildcard search returning a blank page

Scott Cain
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:
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?

Thanks,
Chris
 


On Fri, Nov 8, 2013 at 7:55 PM, Scott Cain <[hidden email]> wrote:
Hi Chris, 

What adaptor is this with?  Does it matter?

Scott

Sent from my iPhone

On Nov 8, 2013, at 12:50 PM, Chris Childers <[hidden email]> wrote:

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.


Below is the section form the Apache error log from an attempted search:

Thanks,
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
_______________________________________________
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--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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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
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Re: Wildcard search returning a blank page

Chris Childers
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:
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:
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?

Thanks,
Chris
 


On Fri, Nov 8, 2013 at 7:55 PM, Scott Cain <[hidden email]> wrote:
Hi Chris, 

What adaptor is this with?  Does it matter?

Scott

Sent from my iPhone

On Nov 8, 2013, at 12:50 PM, Chris Childers <[hidden email]> wrote:

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.


Below is the section form the Apache error log from an attempted search:

Thanks,
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
_______________________________________________
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--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
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
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Re: Wildcard search returning a blank page

Chris Childers
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?

Thanks,
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:
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:
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:
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?

Thanks,
Chris
 


On Fri, Nov 8, 2013 at 7:55 PM, Scott Cain <[hidden email]> wrote:
Hi Chris, 

What adaptor is this with?  Does it matter?

Scott

Sent from my iPhone

On Nov 8, 2013, at 12:50 PM, Chris Childers <[hidden email]> wrote:

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.


Below is the section form the Apache error log from an attempted search:

Thanks,
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
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
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OAuth, Users, Roles, SQL, NoSQL, BLOB Storage and External API Access
Free app hosting. Or install the open source package on any LAMP server.
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Re: Wildcard search returning a blank page

Chris Childers
In reply to this post by Chris Childers
I found the solution. 
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.

Thanks!
Chris


On Tue, Nov 12, 2013 at 11:46 AM, Chris Childers <[hidden email]> wrote:
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:
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:
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?

Thanks,
Chris
 


On Fri, Nov 8, 2013 at 7:55 PM, Scott Cain <[hidden email]> wrote:
Hi Chris, 

What adaptor is this with?  Does it matter?

Scott

Sent from my iPhone

On Nov 8, 2013, at 12:50 PM, Chris Childers <[hidden email]> wrote:

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.


Below is the section form the Apache error log from an attempted search:

Thanks,
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
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--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211




--
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
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Re: Wildcard search returning a blank page

Scott Cain
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:
I found the solution. 
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.

Thanks!
Chris



On Tue, Nov 12, 2013 at 11:46 AM, Chris Childers <[hidden email]> wrote:
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:
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:
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?

Thanks,
Chris
 


On Fri, Nov 8, 2013 at 7:55 PM, Scott Cain <[hidden email]> wrote:
Hi Chris, 

What adaptor is this with?  Does it matter?

Scott

Sent from my iPhone

On Nov 8, 2013, at 12:50 PM, Chris Childers <[hidden email]> wrote:

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.


Below is the section form the Apache error log from an attempted search:

Thanks,
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



--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211




--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211




--
Chris Childers
Division of Animal Science
College of Agriculture, Food and Natural Resources
S134B ASRC, 920 East Campus Drive
Columbia, MO  65211




--
------------------------------------------------------------------------
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]
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