[Gmod-schema-cmts] SF.net SVN: gmod:[22138] schema/trunk/chado/load/bin/load_gff3.PLS

[<sco...@us...>]

Revision: 22138
          http://gmod.svn.sourceforge.net/gmod/?rev=22138&view=rev
Author:   scottcain
Date:     2009-10-05 16:53:46 +0000 (Mon, 05 Oct 2009)

Log Message:
-----------
fixing the loader for the case where more than one organism could have the same common name or abbreviation.

Modified Paths:
--------------
    schema/trunk/chado/load/bin/load_gff3.PLS

Modified: schema/trunk/chado/load/bin/load_gff3.PLS
===================================================================
--- schema/trunk/chado/load/bin/load_gff3.PLS	2009-10-05 16:37:25 UTC (rev 22137)
+++ schema/trunk/chado/load/bin/load_gff3.PLS	2009-10-05 16:53:46 UTC (rev 22138)
@@ -922,16 +922,35 @@
     }
     cache_cvterm('region',$so->id); #make sure to get the SO region term
 
-    ($chado_organism) = Bio::Chado::CDBI::Organism->search( common_name => lc($ORGANISM))
-        unless $chado_organism;
-    ($chado_organism) = Bio::Chado::CDBI::Organism->search( abbreviation => ucfirst($ORGANISM))
-        unless($chado_organism);
-    ($chado_organism) = Bio::Chado::CDBI::Organism->search( genus => $ORGANISM  )
-        unless($chado_organism);
+    my @chado_organisms = Bio::Chado::CDBI::Organism->search( common_name => lc($ORGANISM));
+    if (scalar @chado_organisms > 1) {
+        die "More than one organism has the common name $ORGANISM.  Please\n"
+         . "rerun the loader, specifying the the abbreviation or the genus\n"
+         . "and species enclosed in quotes\n\n";
+    }
+    elsif (scalar @chado_organisms == 1) {
+        $chado_organism = $chado_organisms[0];
+    }
+ 
+    @chado_organisms = Bio::Chado::CDBI::Organism->search( abbreviation => ucfirst($ORGANISM)) unless($chado_organism);
+    if (scalar @chado_organisms > 1) {
+        die "More than one organism has the abbreviation $ORGANISM.  Please\n"
+         . "rerun the loader, specifying the the genus and species enclosed in quotes\n\n";
+    }
+    elsif (scalar @chado_organisms == 1) {
+        $chado_organism = $chado_organisms[0];
+    }
+    else {
+        my ($genus, $species) = split /\s+/, $ORGANISM;
+        ($chado_organism) = Bio::Chado::CDBI::Organism->search(
+                                                   genus   => $genus,
+                                                   species => $species  );
+    }
 
-    ($chado_db)       = Bio::Chado::CDBI::Db->search( name              => $SRC_DB ) if $SRC_DB;
-    ($nullpub)        = Bio::Chado::CDBI::Pub->search( miniref          => 'null' );
 
+    ($chado_db) = Bio::Chado::CDBI::Db->search( name    => $SRC_DB ) if $SRC_DB;
+    ($nullpub)  = Bio::Chado::CDBI::Pub->search(miniref => 'null' );
+
     unless ($chado_organism) {
       warn "\n\nCouldn't find or create organism $ORGANISM.\n";
       warn "The current contents of the organism table is:\n\n";


This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.