[MOBY-guts] biomoby commit

[Eddie Kawas]

kawas
Fri Jul  8 14:57:00 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv24723

Modified Files:
	Central.pm 
Log Message:
Implemented the check for valid secondary input types.

moby-live/Perl/MOBY Central.pm,1.156,1.157
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.156
retrieving revision 1.157
diff -u -r1.156 -r1.157
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/07/06 15:32:52	1.156
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/07/08 18:57:00	1.157
@@ -185,6 +185,7 @@
 
 
 
+
 =head1 METHODS
 
 
@@ -1409,33 +1410,40 @@
 		);
 	}
 
-  	use MOBY::Client::Central;
-  	my $services         = MOBY::Client::Central::_parseServices( '', '', $si );
-  	my $service_instance = shift @{$services};
-  #	my $storage          = new RDF::Core::Storage::Memory;
-  #	my $model            = new RDF::Core::Model( Storage => $storage );
-  #	my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(
-  #model            => $model,
-  #service_instance => $service_instance );
-  #	my $RDF_XML = $RDF_MODEL->serialize;
-	my $LSID       = $service_instance->LSID;
+	use MOBY::Client::Central;
+	my $services         = MOBY::Client::Central::_parseServices( '', '', $si );
+	my $service_instance = shift @{$services};
+
+	#	my $storage          = new RDF::Core::Storage::Memory;
+	#	my $model            = new RDF::Core::Model( Storage => $storage );
+	#	my $RDF_MODEL = MOBY::RDF::ServiceInstanceRDF->new(
+	#model            => $model,
+	#service_instance => $service_instance );
+	#	my $RDF_XML = $RDF_MODEL->serialize;
+	my $LSID = $service_instance->LSID;
+
 	# my $RDF = _getServiceInstanceRDF($LSID);
-my $RDF="<RDF/>";
-	unless ($RDF){return &_success("Registration successful but LSID resolution error",$SVC->service_instance_id,"" )}
-	unless ($RDF =~ /RDF/){
-		return &_success("Registration successful but LSID resolution error $RDF",$SVC->service_instance_id,"")
+	my $RDF = "<RDF/>";
+	unless ($RDF) {
+		return &_success( "Registration successful but LSID resolution error",
+			$SVC->service_instance_id, "" );
+	}
+	unless ( $RDF =~ /RDF/ ) {
+		return &_success(
+			"Registration successful but LSID resolution error $RDF",
+			$SVC->service_instance_id, "" );
 	}
-	return &_success( "Registration successful",
-		$SVC->service_instance_id, $RDF );
+	return &_success( "Registration successful", $SVC->service_instance_id,
+		$RDF );
 }
 
-
 sub _getServiceInstanceRDF {
-	my ($self, $LSID) = @_;
+	my ( $self, $LSID ) = @_;
 	my $lsid       = LS::ID->new($LSID);
 	my $RDF_XML    = "";
 	my $lsid_error = "";
-	my $lsid_good = 1;
+	my $lsid_good  = 1;
+
 	#use LS::ID;
 	#use LS::Authority::WSDL::Constants;
 	#use LS::Client::BasicResolver;
@@ -1451,13 +1459,14 @@
 	$authority->clean_cache();
 
 	my $resource = $authority->getResource($lsid);
-	unless ($resource) { 
-		$lsid_error .= $authority->error_string. " " ; 
-		return $lsid_error
+	unless ($resource) {
+		$lsid_error .= $authority->error_string . " ";
+		return $lsid_error;
 	}
-	
+
 	my $response = $resource->get_metadata;
 	unless ( ref($response) =~ /LS::Service::Response/ ) {
+
 		#TODO raise an error
 		$lsid_error .= "Metadata response didn't come back";
 		return $lsid_error;
@@ -1471,7 +1480,7 @@
 	}
 	while (<$rsp>) {
 		$RDF_XML .= $_;
-	}    
+	}
 	return $RDF_XML
 
 }
@@ -1614,6 +1623,19 @@
 				( $_->nodeType == TEXT_NODE ) && ( $datatype .= $_->nodeValue );
 			}
 		}
+
+		#ensure that thet type is correct (Integer | String | Float | DateTime)
+		$datatype =~ s/\s//g;
+		my $secondaries = $CONFIG->{valid_secondary_datatypes};
+		my $valid;
+		map { $valid = 1 if $datatype eq $_ } @{$secondaries};
+		unless ($valid) {
+			$SVC->DELETE_THYSELF;
+			return ( -1,
+"Registration failed.  $datatype must be one of type Integer, String, DateTime, or Float."
+			);
+		}
+		
 		my $defs = $parameter->getElementsByTagName('default');
 		if ( $defs->get_node(1) ) {
 			foreach ( $defs->get_node(1)->childNodes )
@@ -2998,20 +3020,26 @@
 =cut
 
 sub DUMP_MySQL {
-	my ( $pkg ) = @_;
-	my $config = MOBY::Config->new();
-	my @dbsections = ('mobycentral', 'mobyobject', 'mobyservice', 'mobynamespace', 'mobyrelationship');
+	my ($pkg)      = @_;
+	my $config     = MOBY::Config->new();
+	my @dbsections = (
+		'mobycentral', 'mobyobject',
+		'mobyservice', 'mobynamespace',
+		'mobyrelationship'
+	);
 	my @response;
-	foreach my $dbsection (@dbsections)	{
-		my $dbname   = ${${$config}{$dbsection}}{'dbname'};
-		my $username = ${${$config}{$dbsection}}{'username'};
-		my $password = ${${$config}{$dbsection}}{'password'};
-		my $host     = ${${$config}{$dbsection}}{'url'};
-		my $port     = ${${$config}{$dbsection}}{'port'};
-		open( IN, "mysqldump -h $host -P $port -u $username --password=$password $dbname|" )
-			|| die "can't open $dbname for dumping";
+	foreach my $dbsection (@dbsections) {
+		my $dbname   = ${ ${$config}{$dbsection} }{'dbname'};
+		my $username = ${ ${$config}{$dbsection} }{'username'};
+		my $password = ${ ${$config}{$dbsection} }{'password'};
+		my $host     = ${ ${$config}{$dbsection} }{'url'};
+		my $port     = ${ ${$config}{$dbsection} }{'port'};
+		open( IN,
+"mysqldump -h $host -P $port -u $username --password=$password $dbname|"
+		  )
+		  || die "can't open $dbname for dumping";
 		my @dbdump;
-		while ( <IN> ) {
+		while (<IN>) {
 			push @dbdump, $_;
 		}
 		my $dbdump = ( join "", @dbdump );
@@ -3067,6 +3095,7 @@
 
 
 
+
 =head1 Internal Object Methods