[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Jul 18 18:32:20 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory pub.open-bio.org:/tmp/cvs-serv17143/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
fixing brackets and semicolons

moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/18 16:54:29	1.14
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2005/07/18 22:32:20	1.15
@@ -173,7 +173,7 @@
 	my ($self, @args) = @_;	
 	my $dbh = $self->dbh;
 	my $statement = get_value('statement', @args);
-	my $sth = $dbh->prepare($statement};
+	my $sth = $dbh->prepare($statement);
 	if (@args > 1)
 	{
 		my $bindvalues = get_value('bind_values', @args);
@@ -183,7 +183,7 @@
 		$sth->execute;
 	}
 	my $result = $sth->fetchall_arrayref();
-	return result;
+	return $result;
 }
 	
 sub query_collection_input{
@@ -340,7 +340,7 @@
 	my @bindvalues = ();
 	($statement, @bindvalues) = add_condition($statement, @args); 
 	$dbh->do( $statement,
-			  undef, @bindvalues )
+			  undef, @bindvalues );
 	if (dbh->err){
 		return (1, dbh->errstr);
 	}
@@ -693,8 +693,8 @@
 sub getUniqueAuthorityURI{
 	my ($self, @args) = @_;
 	my $dbh = $self->dbh;
-	$statement = "select distinct authority_uri from authority";
-	$bindvalues = ();
+	my $statement = "select distinct authority_uri from authority";
+	my @bindvalues = ();
 	my $result = do_query($dbh, $statement, @bindvalues);
 	return $result;
 }
@@ -709,7 +709,7 @@
 				 values (?,?,?)",
 		undef,
 		(get_value('authority_common_name', @args),
-		get_value('authority_uri' @args),
+		get_value('authority_uri', @args),
 		get_value('contact_email', @args)));
 	my $id = $dbh->{mysql_insertid};
 	return $id;
@@ -976,9 +976,9 @@
 	my $dbh = $self->dbh;
 	my $existingURI	= get_value('namespace_type_uris', @args);
 	my $term = get_value('term', @args);
+	my $errstr;
 		
-my $sth =
-	  $dbh->prepare(
+        my $sth = $dbh->prepare(
 "select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_input where INSTR(namespace_type_uris,'$existingURI')"
 	  );
 	$sth->execute;
@@ -988,12 +988,11 @@
 		foreach (@nss) {
 			$_ =~ s/\s//g;
 			my $errstr = "Namespace Type $term ($_) is used by a service (service ID number $id) and may not be deregistered";
-			return (1, $errstr);
+			return (1, $errstr)
 			  if ( $_ eq $existingURI );
 		}
 	}
-	$sth =
-	  $dbh->prepare(
+	$sth = $dbh->prepare(
 "select service_instance.service_instance_id, namespace_type_uris from service_instance natural join simple_output where INSTR(namespace_type_uris,'$existingURI')"
 	  );
 	$sth->execute;
@@ -1002,7 +1001,7 @@
 		foreach (@nss) {
 			$_ =~ s/\s//g;
 			my $errstr = "Namespace Type $term ($_) is used by a service (service ID number $id) and may not be deregistered";
-			return (1, $errstr);
+			return (1, $errstr)
 			  if ( $_ eq $existingURI );
 		}
 	}
@@ -1016,7 +1015,7 @@
 		foreach (@nss) {
 			$_ =~ s/\s//g;
 			my $errstr = "Namespace Type $term ($_) is used by a service (service ID number $id) and may not be deregistered";
-			return (1, $errstr);
+			return (1, $errstr)
 			  if ( $_ eq $existingURI );
 		}
 	}
@@ -1030,11 +1029,11 @@
 		foreach (@nss) {
 			$_ =~ s/\s//g;
 			my $errstr = "Namespace Type $term ($_) is used by a service (service ID number $id) and may not be deregistered";
-			return (1, $errstr);
+			return (1, $errstr)
 			  if ( $_ eq $existingURI );
 		}
 	}		
-	return (0, $errstr);
+	return (0, "");
 }
 
 # custom query routine for Moby::Central.pm -> findService()	
@@ -1046,13 +1045,13 @@
 	my $searchstring;
 		
 	foreach my $kw ( @{ $findme{keywords} } ) {
-			$debug && &_LOG("KEYWORD $kw\n");
+#			$debug && &_LOG("KEYWORD $kw\n");
 			$kw =~ s/\*//g;
 			$kw = $dbh->quote("%$kw%");
 			$searchstring .= " OR description like $kw ";
 		}
 		$searchstring =~ s/OR//;    # just the first one
-		$debug && &_LOG("search $searchstring\n");
+#		$debug && &_LOG("search $searchstring\n");
 
 	my $statement = "select service_instance_id from service_instance where $searchstring";
 	my @bindvalues = ();
@@ -1103,7 +1102,7 @@
 		where
 			s.collection_${inout}_id IS NOT NULL
 		AND s.collection_${inout}_id = c.collection_${inout}_id
-		AND object_type_uri = '$objectURI' "
+		AND object_type_uri = '$objectURI' ";
 	my $nsquery;
 		foreach my $ns ( @{$namespaceURIs} ) {    # namespaces are already URI's
 			$nsquery .= " OR INSTR(namespace_type_uris, '$ns') ";