[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Fri Jul 29 13:39:32 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv10893/MOBY

Modified Files:
	Central.pm OntologyServer.pm 
Log Message:
deleting service type failed due to bad lookup of relationships.  Fix reporting of errors from MOBY Central - need to bracket teh (==0) phrase of every test

moby-live/Perl/MOBY Central.pm,1.195,1.196 OntologyServer.pm,1.70,1.71
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.195
retrieving revision 1.196
diff -u -r1.195 -r1.196
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/07/29 15:07:40	1.195
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/07/29 17:39:32	1.196
@@ -313,14 +313,14 @@
 			term     => $reltype,
 			ontology => 'object'
 		  );    # success = 1 if it does
-		$success == 0 && return &_error( $message, $URI );
+		($success == 0) && return &_error( $message, $URI );
 		foreach ( @{$obj} ) {
 			++$ISAs if ( $URI =~ /isa$/i );
 			my ( $objectType, $articleName ) = @{$_};
 			my ( $success, $message, $URI ) =
 			  $OntologyServer->objectExists( term => $objectType )
 			  ;    # success = 1 if it does
-			$success == 0 && return &_error( $message, $URI );
+			($success == 0) && return &_error( $message, $URI );
 		}
 	}
 	return &_error(
@@ -341,12 +341,12 @@
 		if ( $clobber == 1 ) {
 			my ( $success, $message ) =
 			  $OntologyServer->deprecateObject( term => $term );
-			$success == 0 && return &_error( $message, $URI );
+			($success == 0) && return &_error( $message, $URI );
 		}
 		elsif ( $clobber == 2 ) {
 			my ( $success, $message ) =
 			  $OntologyServer->deleteObject( term => $term );
-			$success == 0 && return &_error( $message, $URI );
+			($success == 0) && return &_error( $message, $URI );
 		}
 	}
 	( $success, $message, $URI ) = $OntologyServer->createObject(
@@ -355,7 +355,7 @@
 		authority     => $auth,
 		contact_email => $email
 	);
-	$success == 0 && return &_error( $message, $URI );
+	($success == 0) && return &_error( $message, $URI );
 	my @failures;
 	if ( keys %{$relationships} ) {
 		while ( my ( $reltype, $obj ) = each %{$relationships} ) {
@@ -370,7 +370,7 @@
 					authority     => $auth,
 					contact_email => $email
 				  );
-				$success == 0 && push @failures, $objectType;
+				($success == 0) && push @failures, $objectType;
 			}
 		}
 	}
@@ -378,7 +378,7 @@
 		my ( $success, $message, $deleteURI ) =
 		  $OntologyServer->deleteObject( term => $term )
 		  ;    # hopefully this situation will never happen!
-		$success == 0 && return &_error(
+		($success == 0) && return &_error(
 			"object failed ISA and/or HASA connections,
 		and subsequently failed deletion.  This is a critical error,
 		and may indicate corruption of the MOBY Central registry.", $deleteURI
@@ -635,7 +635,7 @@
 		authority     => $auth,
 		contact_email => $email
 	);
-	$success == 0 && return &_error( $message, $URI );
+	($success == 0) && return &_error( $message, $URI );
 	my @failures;
 	if ( keys %{$relationships} ) {
 		while ( my ( $reltype, $obj ) = each %{$relationships} ) {
@@ -648,7 +648,7 @@
 					authority     => $auth,
 					contact_email => $email
 				  );
-				$success == 0 && push @failures, $serviceType;
+				($success == 0) && push @failures, $serviceType;
 			}
 		}
 	}
@@ -656,7 +656,7 @@
 		my ( $success, $message, $deleteURI ) =
 		  $OntologyServer->deleteServiceType( term => $term )
 		  ;    # hopefully this situation will never happen!
-		$success == 0 && return &_error(
+		($success == 0) && return &_error(
 			"Service registration failed ISA connections,
 		and subsequently failed deletion.  This is a critical error,
 		and may indicate corruption of the MOBY Central registry", $deleteURI
@@ -767,7 +767,7 @@
 	my ( $success2, $message2, $deleteURI ) =
 	  $OntologyServer->deleteServiceType( term => $term )
 	  ;    # hopefully this situation will never happen!
-	$success == 0 && return &_error( $message2, $deleteURI );
+	(($success == 0)) && return &_error( $message2, $deleteURI );
 	return &_success( "Service type $term deleted.", $deleteURI );
 }
 
@@ -855,7 +855,7 @@
 		authority     => $auth,
 		contact_email => $email
 	);
-	$success == 0 && return &_error( $message, $URI );
+	($success == 0) && return &_error( $message, $URI );
 	return &_success( "Namespace type $term registered successfully.", $URI );
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.70
retrieving revision 1.71
diff -u -r1.70 -r1.71
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2005/07/29 15:07:40	1.70
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2005/07/29 17:39:32	1.71
@@ -682,7 +682,7 @@
 	}
 
 	# service1_id ISA service2_id?
-	my $isa = $adaptor->query_service_term2term(service2_id => $lsid);
+	my $isa = $adaptor->query_service_term2term(type => $lsid);
 	my $isas = shift(@$isa);
 	
 	if ( $isas->{service1_id} ) {