reverse natural order of chromosomes in chrom_sizes to workaround bio…

…perl seqfeature::store buglet
GMOD · Aug 30, 2012 · 49da251 · 49da251
1 parent 0e94bec
commit 49da251
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Showing 2 changed files with 11 additions and 11 deletions.
diff --git 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
@@ -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();