Generic Model Organism System Database

Due to different time zones, I'm not sure Lincoln's comment was before or
after our exchange on the mailing list. It also seemed like a good idea to
put these notes on the bug tracker.

Today (19 Dec 2008) I updated a working Linux installation of GBrowse
1.69+ under apache to the latest stable code using:
$ sudo perl gbrowse_netinstall.pl --gbrowse_dev
--build_param_str="--SELINUX=1"

For sequences where the version number is one, everything seems to work
fine as before. However, as described in my email (17 Dec 2008) the
details page problem remains for sequences with a non-one version number in
the bioentry table.

See also:
https://sourceforge.net/mailarchive/message.php?msg_name=320fb6e00812170600ie1715d8la9ec99678c669816%40mail.gmail.com

e.g. viewing some of E Coli,
http://ppsrv/cgi-bin/gbrowse/biosql/?name=NC_000913:5528..8959
Clicking on a feature takes me to:
http://ppsrv/cgi-bin/gbrowse_details/biosql?feature_id=1213256;ref=NC_000913;start=6529;end=7959
This shows an error 500 message, "Internal Server Error".

$ sudo tail /etc/httpd/logs/error_log
[Fri Dec 19 11:00:46 2008] [error] [client 143.234.97.120] Can't call
method "seq" on an undefined value at /var/www/cgi-bin/gbrowse_details line
72., referer: http://XXX/cgi-bin/gbrowse/biosql/?name=NC_000913:5528..8959
[Fri Dec 19 11:00:46 2008] [error] [client 143.234.97.120] Premature end
of script headers: gbrowse_details, referer:
http://XXX/cgi-bin/gbrowse/biosql/?name=NC_000913:5528..8959

The relevant bit of code (in case my copy doesn't match yours) is:

my @features;
if ($f_id) {
@features =
$CONFIG->_feature_get($db,$name,$class,$start,$end,1,0,$f_id);

# HACK! This is for the BioSQL adaptor, whose sequences aren't
automatically
# attached to feature objects when they are retrieved from the database
if ($db->isa('Bio::DB::Das::BioSQL')) {
for my $f (@features) {
my $ref = $f->seq_id || param('ref');
# Need to fetch out the ENTIRE bioentry (chromosome) in order to attach
it to feature.
# This is horribly inefficient for performance and storage.
my @args = (-name=>$ref);
my ($segment) = $db->segment(@args);
$f->attach_seq($segment->seq); #Line 72, error here
}
}

}

I have reworked how the details page works. Could you try the current
stable branch (or, if you are brave, the HEAD branch) and let me know if
the problem is still there.