SF.net SVN: gmod:[25285] schema/trunk/chado/load/bin/bulk_load_gff3.PLS

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SF.net SVN: gmod:[25285] schema/trunk/chado/load/bin/bulk_load_gff3.PLS

scottcain
Revision: 25285
          http://gmod.svn.sourceforge.net/gmod/?rev=25285&view=rev
Author:   scottcain
Date:     2013-03-04 22:09:03 +0000 (Mon, 04 Mar 2013)
Log Message:
-----------
add a patch from Alexie for the organism from data functionality; not tested yet!

Modified Paths:
--------------
    schema/trunk/chado/load/bin/bulk_load_gff3.PLS

Modified: schema/trunk/chado/load/bin/bulk_load_gff3.PLS
===================================================================
--- schema/trunk/chado/load/bin/bulk_load_gff3.PLS 2013-02-28 19:43:35 UTC (rev 25284)
+++ schema/trunk/chado/load/bin/bulk_load_gff3.PLS 2013-03-04 22:09:03 UTC (rev 25285)
@@ -826,7 +826,11 @@
               ? ($feature->annotation->get_Annotations('organism'))[0]
               : '';
     if($gff_organism && $gff_organism ne $chado->organism()) {
-      $ORGANISM = "$gff_organism";# is it pesky bperl object?
+      #next 4 lines patch by Alexie P.
+      $ORGANISM = "$gff_organism";# is it pesky bperl object? # sadly yes
+      if (ref($gff_organism)){
+         $ORGANISM = $gff_organism->value();
+      }
       warn "Organism $ORGANISM from data\n" unless($seen_organism{$ORGANISM}++);
       $chado->organism($ORGANISM);
       $chado->organism_id($ORGANISM) #? dont die if many orgs? auto-add *

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