[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Jul 25 17:13:51 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv21605/MOBY/Adaptor/moby/queryapi

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

moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.33,1.34
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.33
retrieving revision 1.34
diff -u -r1.33 -r1.34
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/25 20:55:35	1.33
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/25 21:13:51	1.34
@@ -482,8 +482,9 @@
 }
 
 # inserts a new tuple into object table
+# pass object_type object_lsid description authority contact_email
 sub insert_object{
-	my ($self, @args) = @_;	
+	my ($self, %args) = @_;	
 	my $dbh = $self->dbh;		
 	$dbh->do("insert into object 
 				 (object_type, 
@@ -493,24 +494,30 @@
 				 contact_email)
 				 values (?,?,?,?,?)",
 		undef,
-		(get_value('object_type', @args),
-		get_value('object_lsid', @args),
-		get_value('description', @args),
-		get_value('authority', @args),
-		get_value('contact_email', @args)));
+		$args{'object_type'},
+		$args{'object_lsid'},
+		$args{'description'},
+		$args{'authority'},
+		$args{'contact_email'});
 	my $id=$dbh->{mysql_insertid};
 	return $id;	
 }
 
+# pass 'type' which is either an LSID or a term
 sub delete_object{
-	my ($self, @args) = @_;	
+	my ($self, %args) = @_;	
 	my $dbh = $self->dbh;
-	my $statement = "delete from object "; #OMG!!  This is a very dangerous thing to start with.........**********
-	# ************** MUST FIX THAT LINE OR WE MAY BE DEAD ONE DAY  ********************
-	my @bindvalues = ();
-	($statement, @bindvalues) =_add_condition($statement, @args); 
-	$dbh->do( $statement,
-			  undef, @bindvalues );
+	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) );
 	
 	if ($dbh->err){
 		return (1, $dbh->errstr);
@@ -520,8 +527,14 @@
 	}
 }
 
+# pass "type" here, should be an LSID, preferably...
 sub query_object_term2term{
-	my ($self, @args) = @_;	
+	my ($self, %args) = @_;
+	my $type = $args{type};
+	my $result = $self->query_object(type => $type);
+	my $row = shift(@$result);
+	my $id = $row->{object_id};
+	return [{}] unless $id;
 	my $dbh = $self->dbh;
 	
 	my $statement = "select
@@ -530,28 +543,33 @@
           object1_id,
           object2_id,
           object2_articlename
-          from object_term2term ";
-    my @bindvalues = (); 
-          
-	if  (@args > 0) 
- 	{
- 		($statement, @bindvalues) =_add_condition($statement, @args);
- 	}
- 	
- 	my $result = do_query($dbh, $statement, @bindvalues);
- 	return $result;			
+          from object_term2term where object2_id = ?";
+ 	my $result2 = do_query($dbh, $statement, ($id));
+ 	return $result2;			
 }
 
+# pass object1_type, object2_type, object2_articlename, relationship_type
 sub insert_object_term2term{
-	my ($self, @args) = @_;	
+	my ($self, %args) = @_;	
+	my $type1 = $args{object1_type};
+	my $result = $self->query_object(type => $type1);
+	my $row = shift(@$result);
+	my $id1 = $row->{object_id};
+	my $type2 = $args{object2_type};
+	$result = $self->query_object(type => $type2);
+	$row = shift(@$result);
+	my $id2 = $row->{object_id};
+	my $relationship_type = $args{relationship_type};
+	my $object2_articlename = $args{object2_articlename};
+
 	my $dbh = $self->dbh;
 	$dbh->do(
-q{insert into object_term2term (relationship_type, object1_id, object2_id, object2_articlename) values (?,?,?,?)},
+	    q{insert into object_term2term (relationship_type, object1_id, object2_id, object2_articlename) values (?,?,?,?)},
 		undef,
-		( get_value('relationship_type', @args), 
-		get_value('object1_id', @args),
-		get_value('object2_id', @args),
-		get_value('object2_articlename', @args) )
+		$relationship_type,
+		$id1,
+		$id2,
+		$object2_articlename
 	);
 	
 	return $dbh->{mysql_insertid};