[MOBY-guts] biomoby commit

[Dennis Wang]

dwang
Fri Jul 15 12:39:11 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv30067/Perl/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
All subroutines in mysql.pm should take in array of hashes as arguments.
Delete tuple subroutines now returns 0 if successful or 1 if error

moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/13 21:55:36	1.12
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/15 16:39:11	1.13
@@ -228,10 +228,10 @@
 			  undef, @bindvalues );
 	
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}	
 }
 
@@ -278,10 +278,10 @@
 			  undef, @bindvalues );
 	
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}	
 }
 
@@ -342,10 +342,10 @@
 	$dbh->do( $statement,
 			  undef, @bindvalues )
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}			  
 }
 
@@ -405,10 +405,10 @@
 	$dbh->do( $statement,
 			  undef, @bindvalues );
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}	
 }	
 
@@ -463,10 +463,10 @@
 			  undef, @bindvalues );
 	
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}	
 }
 
@@ -526,10 +526,10 @@
 			  undef, @bindvalues );
 	
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}
 }
 
@@ -570,6 +570,24 @@
 	return $dbh->{mysql_insertid};
 }
 
+sub delete_object_term2term{
+	my ($self, @args) = @_;	
+	my $dbh = $self->dbh;
+	
+	my $statement = "delete from object_term2term ";
+	my @bindvalues = ();
+	($statement, @bindvalues) = add_condition($statement, @args); 
+	$dbh->do( $statement,
+			  undef, @bindvalues );
+	
+	if (dbh->err){
+		return (1, dbh->errstr);
+	}
+	else{
+		return 0;
+	}
+}
+
 # selects all the columns from service_instance table
 # where is lsid?
 sub query_service_instance {
@@ -642,10 +660,10 @@
 	$dbh->do( $statement,
 			  undef, @bindvalues );
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}
 }
 	
@@ -742,10 +760,10 @@
 			  undef, @bindvalues );
 	
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}
 }
 
@@ -789,10 +807,10 @@
 			  undef, @bindvalues );
 	
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}
 }
 
@@ -868,10 +886,10 @@
 			  undef, @bindvalues );
 	
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}
 }
 
@@ -906,10 +924,10 @@
 			  undef, @bindvalues );
 	
 	if (dbh->err){
-		return (0, dbh->errstr);
+		return (1, dbh->errstr);
 	}
 	else{
-		return 1;
+		return 0;
 	}				
 }
 
@@ -1163,12 +1181,39 @@
 # relationship query for any table used in Moby::OntologyServer->_doRelationshipQuery()
 # note: returns a reference to an array containing ARRAY references
 sub getRelationship{
-	my ($self, %args) = @_;	
+	my ($self, @args) = @_;	
 	my $dbh = $self->dbh;
+	my $direction = get_value('direction', @args);
+	my $ontology = get_value('ontology', @args);
+	my $term = get_value('term', @args);
+	my $relationship = get_value('relationship', @args);
 	my $defs;
-	my $ontology = $args{ontology};
 	
-	unless ( defined $args{$relationship} ) {
+	if ( $direction eq 'root' ) {
+		unless ( defined $relationship ) {
+			$defs = $self->dbh->selectall_arrayref( "
+            select distinct s2.${ontology}_lsid, relationship_type from
+                ${ontology}_term2term as t2t,
+                $ontology as s1,
+                $ontology as s2  
+            where
+                s1.${ontology}_id = t2t.${ontology}1_id and
+                s2.${ontology}_id = t2t.${ontology}2_id and
+                s1.${ontology}_lsid = ?", undef, $term );    # ")
+		} else {
+			$defs = $self->dbh->selectall_arrayref( "
+            select distinct s2.${ontology}_lsid, relationship_type from
+                ${ontology}_term2term as t2t,
+                $ontology as s1,
+                $ontology as s2  
+            where
+                relationship_type = ? and 
+                s1.${ontology}_id = t2t.${ontology}1_id and
+                s2.${ontology}_id = t2t.${ontology}2_id and
+                s1.${ontology}_lsid = ?", undef, $relationship, $term );    # ")
+		}
+	} else {
+		unless ( defined $relationship ) {
 			$defs = $self->dbh->selectall_arrayref( "
             select distinct s2.${ontology}_lsid, relationship_type from
                 ${ontology}_term2term as t2t,
@@ -1177,7 +1222,7 @@
             where
                 s1.${ontology}_id = t2t.${ontology}1_id and
                 s2.${ontology}_id = t2t.${ontology}2_id and
-                s1.${ontology}_lsid = ?", undef, $args{lsid} );    # ")
+                s2.${ontology}_lsid = ?", undef, $term );                   # ")
 		} else {
 			$defs = $self->dbh->selectall_arrayref( "
             select distinct s2.${ontology}_lsid, relationship_type from
@@ -1188,8 +1233,9 @@
                 relationship_type = ? and 
                 s1.${ontology}_id = t2t.${ontology}1_id and
                 s2.${ontology}_id = t2t.${ontology}2_id and
-                s1.${ontology}_lsid = ?", undef, $args{$relationship}, $args{lsid} );    # ")
+                s2.${ontology}_lsid = ?", undef, $relationship, $term );    # ")
 		}
+	}
 	return $defs;
 }