[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Wed Jul 27 10:19:42 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv28768/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
ontological relationships not being properly deleted since objects no longer existed

moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.45,1.46
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.45
retrieving revision 1.46
diff -u -r1.45 -r1.46
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/27 14:07:57	1.45
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/27 14:19:42	1.46
@@ -521,17 +521,14 @@
 	my $dbh = $self->dbh;
 	my $term = $args{type};
 	return 0 unless $term;
-	my $statement = "delete from object where ";
-	my $condition;
-	if ($term =~ /^urn\:lsid/){
-	    $condition = " object_lsid = ?";
-	} else {
-	    $condition = " object_type = ?";
-	}
-	$statement = $statement.$condition;
-	$dbh->do( $statement,undef, ($term) );
+	my $result = $self->query_object(type => $term);
+	my $row = shift(@$result);
+	my $id = $row->{object_id};
+	my $lsid = $row->{object_lsid};
+	my $statement = "delete from object where object_lsid = ?";
+	$dbh->do( $statement,undef, ($lsid) );
 	
-	$self->_delete_object_term2term(type => $term);
+	$self->_delete_object_term2term(id => $id);
 	if ($dbh->err){
 		return (1, $dbh->errstr);
 	}
@@ -593,15 +590,11 @@
 # SHOULD NOT BE DOCUMENTED IN THE API
 sub _delete_object_term2term{
 	my ($self, %args) = @_;
-	my $type = $args{type};
-	return 0 unless $type;
-	my $result = $self->query_object(type => $type);
-	my $row = shift @$result;
-	my $id = $row->object_id;
-	
+	my $o1id = $args{id};
+	return 0 unless defined($o1id);
 	my $dbh = $self->dbh;	
 	my $statement = "delete from object_term2term where object1_id=?";
-	$dbh->do( $statement,undef, ($id));
+	$dbh->do( $statement,undef, ($o1id));
 	
 	if ($dbh->err){
 		return (1, $dbh->errstr);
@@ -848,13 +841,18 @@
 	return $dbh->{mysql_insertid};
 }
 
-# pass in service type as LSID (service_lsid)
+# pass in 'type' as LSID term or lsid
 sub delete_service{
 	my ($self, %args) = @_;	
+	my $type = $args{type};
+	my $result = $self->query_service(type => $type);
+	my $row = shift(@$result);
+	my $id = $row->{service_id};
+	my $lsid = $row->{service_lsid};
 	my $dbh = $self->dbh;
 	my $statement = "delete from service where service_lsid = ?";
-	$dbh->do( $statement, undef, ($args{service_lsid}));
-	$self->_delete_service_term2term;
+	$dbh->do( $statement, undef, ($args{lsid}));
+	$self->_delete_service_term2term(id => $id);
 	if ($dbh->err){
 		return (1, $dbh->errstr);
 	}
@@ -911,12 +909,8 @@
 # NOT BE DOCUMENTED IN THE API.  
 sub _delete_service_term2term{
 	my ($self, %args) = @_;
-	my $type = $args{type};
-	return 0 unless $type;
-	my $result = $self->query_service(type => $type);
-	my $row = shift @$result;
-	my $id = $row->service_id;
-	
+	my $id = $args{id};
+	return 0 unless (defined($id));
 	my $dbh = $self->dbh;	
 	my $statement = "delete from service_term2term where service1_id=?";
 	$dbh->do( $statement,undef, ($id));	
@@ -1006,11 +1000,15 @@
 # pass namesapce_lsid
 sub delete_namespace{
 	my ($self, %args) = @_;	
-	my $lsid = $args{namespace_lsid};
+	my $type = $args{type};
+	my $result = $self->query_namespace(type => $type);
+	my $row = shift(@$result);
+	my $id = $row->{namespace_id};
+	my $lsid = $row->{namespace_lsid};
 	my $dbh = $self->dbh;
 	my $statement = "delete from namespace where namespace_lsid = ?";
 	$dbh->do( $statement, undef, ($lsid));
-	$self->_delete_namespace_term2term;
+	$self->_delete_namespace_term2term(id => $id);
 	if ($dbh->err){
 		return (1, $dbh->errstr);
 	}
@@ -1041,12 +1039,8 @@
 # PRIVATE, NOT PART OF API!
 sub _delete_namespace_term2term{
 	my ($self, %args) = @_;
-	my $type = $args{type};
-	return 0 unless $type;
-	my $result = $self->query_namespace(type => $type);
-	my $row = shift @$result;
-	my $id = $row->namespace_id;
-	
+	my $id = $args{id};
+	return 0 unless defined($id);
 	my $dbh = $self->dbh;	
 	my $statement = "delete from namespace_term2term where namespace1_id=?";
 	$dbh->do( $statement,undef, ($id));