[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Jul 25 16:14:34 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv21136/MOBY

Modified Files:
	Central.pm service_instance.pm simple_output.pm 
Log Message:
more of the same.  Pass hashes instead of hashrefs, and avoid passing database ids

moby-live/Perl/MOBY Central.pm,1.181,1.182 service_instance.pm,1.25,1.26 simple_output.pm,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.181
retrieving revision 1.182
diff -u -r1.181 -r1.182
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/07/25 19:53:35	1.181
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/07/25 20:14:34	1.182
@@ -3343,7 +3343,7 @@
 		$output .= "\t</Input>\n";
 		$output .= "\t<Output>\n";
 
-		$result = $adaptor->query_simple_output(service_instance_lsid => $lsid}, collection_output_id => undef);
+		$result = $adaptor->query_simple_output(service_instance_lsid => $lsid, collection_output_id => undef);
 		
 		foreach my $row (@$result)
 		{

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2005/07/25 19:53:35	1.25
+++ /home/repository/moby/moby-live/Perl/MOBY/service_instance.pm	2005/07/25 20:14:34	1.26
@@ -262,9 +262,13 @@
 	}
 	$CONFIG ||= MOBY::Config->new;
 	my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
-	
+
+#********FIX  this should really be delete_input and delete_output
+# the routines below know too much about the database (e.g. that
+# the delete_simple_input routines are broken into two parts - by LSID and
+# by collecion ID...  BAD BAD BAD
 	$adaptor->delete_service_instance({service_instance_lsid => $self->lsid});
-	$adaptor->delete_simple_input({service_instance_lsid => $self->lsid});	
+	$adaptor->delete_simple_input(service_instance_lsid => $self->lsid);
 	$adaptor->delete_simple_output({service_instance_lsid => $self->lsid});
 	
 	my $result = $adaptor->query_collection_input({service_instance_lsid => $self->lsid});

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2005/07/25 19:53:35	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY/simple_output.pm	2005/07/25 20:14:34	1.7
@@ -100,12 +100,12 @@
 	$CONFIG ||= MOBY::Config->new;    # exported by Config.pm
 	my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
 	my $id = $adaptor->insert_simple_output(
-							{object_type_uri      => $self->object_type_uri},
-							{namespace_type_uris  => $self->namespace_type_uris},
-							{article_name         => $self->article_name},
-							{service_instance_lsid  => $self->service_instance_id},
-							{collection_output_id => $self->collection_output_id}
-	);
+		object_type_uri      => $self->object_type_uri,
+		namespace_type_uris  => $self->namespace_type_uris,
+		article_name         => $self->article_name,
+		service_instance_lsid  => $self->service_instance_id,
+		collection_output_id => $self->collection_output_id
+		);
 	return $id;
 }