[Gmod-schema-cmts] SF.net SVN: gmod:[25257] schema/trunk/chado/bin/gmod_load_cvterms.pl

[<nm...@us...>]

Revision: 25257
          http://gmod.svn.sourceforge.net/gmod/?rev=25257&view=rev
Author:   nm249
Date:     2012-03-09 18:51:04 +0000 (Fri, 09 Mar 2012)
Log Message:
-----------
disabling loading of cross-ontologies relationships. Temporary solution for loading PO which has cross references among anatomy and growth stages terms 

Modified Paths:
--------------
    schema/trunk/chado/bin/gmod_load_cvterms.pl

Modified: schema/trunk/chado/bin/gmod_load_cvterms.pl
===================================================================
--- schema/trunk/chado/bin/gmod_load_cvterms.pl	2012-03-06 18:54:12 UTC (rev 25256)
+++ schema/trunk/chado/bin/gmod_load_cvterms.pl	2012-03-09 18:51:04 UTC (rev 25257)
@@ -690,7 +690,7 @@
 		    next RELATIONSHIP;
 		}
 		############################################
-		push @novel_relationships, $r;
+                push @novel_relationships, $r;
 		my $predicate_term_name = $file_relationships{$r}->predicate_term()->name();
 
 		my $predicate_term;
@@ -729,7 +729,11 @@
 		}
 		if (!$opt_t) {
 		    message("Storing relationship $r. type cv_id=" . $predicate_term->cv_id() ."\n" ,1);
-		    my $new_rel = $schema->resultset('Cv::CvtermRelationship')->create(
+		    if ( $subject_term->cv_id != $object_term->cv_id ) {
+                        message("Wait!  subjcet term has cv namespace " . $subject_term->cv->name . " which is different from the namespace of the object term (" . $object_term->cv->name . "). Cross referencing relationships across namespaces is not supported (yet.. ) SKIPPING this relationship! \n");
+                        next RELATIONSHIP;
+                    }
+                    my $new_rel = $schema->resultset('Cv::CvtermRelationship')->create(
 			{ subject_id => $subject_term->cvterm_id(),
 			  object_id  => $object_term->cvterm_id(),
 			  type_id    => $predicate_term->cvterm_id(),
@@ -744,14 +748,14 @@
 	    die "TEST RUN! rolling back\n";
 	}
     };
-    
+
     try {
 	$schema->txn_do($coderef);
 	message("Committing! \n If you are using cvtermpath you should now run gmod_make_cvtermpath.pl . See the perldoc for more info. \n\n", 1);
     } catch {
 	# Transaction failed
 	die "An error occured! Rolling back! " . $_ . "\n";
-    }
+    };
 }
 
 sub recursive_children {

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