viewing chado features in gbrowse

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viewing chado features in gbrowse

claudia

Hi,

 I am wondering why I get the follow errors (below) when searching features from chado in gbrowse, I seem to have the chado.conf file set up as per the demo file. I have tried multiple feature name searches and still get the same errors, including "internal server error".  I am root user in all cases and so I have permissions to access the Chado database and select on it. It seems I have all the necessary perl modules; and  I have been able to upload gff3 data to the database without problems.

-- is there a specific way to query features in gbrowse, i.e contig0000 or contig0000:1..100000 ??? I have actually tried both of these query styles and non of the contig related information comes up.

-- one other question, is there an easier way to dump the cache and cookies pertaining to the Gbrowse searches?

Thanks in advance,

Claudia


[Mon Apr 04 14:48:48 2011] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gbrowse/chado/
DBD::Pg::st execute failed: ERROR:  column f.searchable_name does not exist
LINE 1: select f.feature_id  FROM  feature f where f.searchable_name...
                                                   ^ at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm line 1468.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: getting the feature_ids failed
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368
STACK: Bio::DB::Das::Chado::_by_alias_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1468
STACK: Bio::DB::Das::Chado::get_feature_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1281
STACK: Bio::Graphics::Browser::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser.pm:2236
STACK: Bio::Graphics::Browser::name2segments /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser.pm:2169
STACK: main::lookup_features_from_db /usr/lib/cgi-bin/gbrowse:2307
STACK: main::get_features /usr/lib/cgi-bin/gbrowse:2200
STACK: /usr/lib/cgi-bin/gbrowse:199
-----------------------------------------------------------

Can't call method "length" on an undefined value at /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser.pm line 2240.
[Mon Apr 04 14:22:06 2011] [error] [client 127.0.0.1] Premature end of script headers: gbrowse, referer: http://localhost/cgi-bin/gbrowse/chado/
DBD::Pg::st execute failed: ERROR:  column afn.searchable_name does not exist
LINE 5:         afn.searchable_name @@ plainto_tsquery('gene')  and ...
                ^ at /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado/Segment.pm line 599.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: query for name in synonym failed
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368
STACK: Bio::DB::Das::Chado::Segment::_search_by_name /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado/Segment.pm:599
STACK: Bio::DB::Das::Chado::Segment::new /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado/Segment.pm:209
STACK: Bio::DB::Das::Chado::segment /usr/local/share/perl/5.10.1/Bio/DB/Das/Chado.pm:1074
STACK: Bio::Graphics::Browser::_feature_get /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser.pm:2240
STACK: Bio::Graphics::Browser::name2segments /usr/local/lib/perl/5.10.1/Bio/Graphics/Browser.pm:2169
STACK: main::lookup_features_from_db /usr/lib/cgi-bin/gbrowse:2307
STACK: main::get_features /usr/lib/cgi-bin/gbrowse:2200
STACK: /usr/lib/cgi-bin/gbrowse:199


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