diff --git a/bin/gbrowse_import_ucsc_db.pl b/bin/gbrowse_import_ucsc_db.pl index 4e0a79b45..0fbef7ee7 100755 --- a/bin/gbrowse_import_ucsc_db.pl +++ b/bin/gbrowse_import_ucsc_db.pl @@ -147,7 +147,7 @@ END print STDERR "Fetching chromosome sizes...\n"; - my $query = $dbh->prepare('select chrom,size from chromInfo') + my $query = $dbh->prepare('select chrom,size from chromInfo order by size') or die $dbh->errstr; $query->execute; my @chroms; diff --git a/lib/Bio/Graphics/Browser2/Action.pm b/lib/Bio/Graphics/Browser2/Action.pm index 987978c24..0c141289d 100644 --- a/lib/Bio/Graphics/Browser2/Action.pm +++ b/lib/Bio/Graphics/Browser2/Action.pm @@ -806,16 +806,15 @@ sub ACTION_upload_file { error_msg=>'empty file'} )); - my $upload_id = $q->param('upload_id'); - - my $render = $self->render; - my $state = $self->state; - my $session = $render->session; + my $upload_id = $q->param('upload_id'); + my $render = $self->render; + my $state = $self->state; + my $session = $render->session; my $usertracks = $render->user_tracks; my $name = $fh ? basename($fh) - : $url ? $url - : $q->param('name'); + : $url ? $url + : $q->param('name'); $name ||= 'Uploaded file'; my $content_type = "text/plain"; #? fh? $q->uploadInfo($fh)->{'Content-Type'} : 'text/plain'; - seems to be a problem with UploadInfo(). @@ -834,11 +833,12 @@ sub ACTION_upload_file { ($result,$msg,$tracks,$pid) = (1,'shared track added to your session',$t,$$); } else { - ($result, $msg, $tracks, $pid) = $url ? $usertracks->mirror_url($track_name, $url, 1,$self->render) - :$data ? $usertracks->upload_data($track_name, $data, $content_type, 1) - : $usertracks->upload_file($track_name, $fh, $content_type, $overwrite); + ($result, $msg, $tracks, $pid) = $url ? $usertracks->mirror_url($track_name, $url, 1 , $self->render) + :$data ? $usertracks->upload_data($track_name, $data, $content_type, 1 ) + : $usertracks->upload_file($track_name, $fh, $content_type, $overwrite ); } + $session->lock(); delete $self->state->{uploads}{$upload_id}; $session->flush();