[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Fri Oct 17 17:29:51 EDT 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv25355/MOBY

Modified Files:
	Central.pm 
Log Message:
bug fixes as per Martins reports

moby-live/Perl/MOBY Central.pm,1.107,1.108
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.107
retrieving revision 1.108
diff -u -r1.107 -r1.108
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2003/10/15 14:02:01	1.107
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2003/10/17 21:29:51	1.108
@@ -1904,7 +1904,7 @@
 	my ($pkg) = shift;
     
 	my $dbh = MOBY::central_db_connection->new()->dbh;
-	my $sth = $dbh->prepare("select authority_uri, servicename from authority natural join service_instance");
+	my $sth = $dbh->prepare("select authority_uri, servicename from authority as a, service_instance as s where s.authority_id = a.authority_id");
 	$sth->execute;
 	my $names = "<serviceNames>\n";
 	while (my ($auth, $name) = $sth->fetchrow_array){
@@ -2261,10 +2261,10 @@
 
 	
 
-=head2 DUMP
+=head2 DUMP_MySQL
 
- Title     :	DUMP
- Usage     :	($central,$object,$service,$namespace,$relat) = $MOBY->DUMP()
+ Title     :	DUMP_MySQL
+ Usage     :	$SQL = $MOBY->DUMP_MySQL; ($central,$object,$service,$namespace,$relat) = @{$SQL};
  Function  :	return a mysql dump of each of the current MOBY Central databases
  Returns   :	an array of SQL strings that can be used to recreate the database locally
  Args      :	none
@@ -2272,7 +2272,7 @@
 =cut
 
 
-sub DUMP {
+sub DUMP_MySQL {
 	my ($pkg) = @_;
 	open (IN, "/usr/local/bin/mysqldump -u mobycentral mobycentral |") || die "can't open mobycentral for dumping";
 	my @response;
@@ -2280,7 +2280,6 @@
 		push @response, $_;
 	}
 	my $mobycentral = (join "", @response);
-	print STDERR "MOBYCENTRAL $mobycentral\n\n\n";
 
 	close IN;
 	open (IN, "/usr/local/bin/mysqldump -u mobycentral mobyobject |") || die "can't open mobyobject for dumping";
@@ -2289,7 +2288,7 @@
 		push @response, $_;
 	}
 	my $mobyobject = (join "", @response);
-	print STDERR "MOBYOBJECT $mobyobject\n\n\n";
+
 	close IN;
 	open (IN, "/usr/local/bin/mysqldump -u mobycentral mobyservice |") || die "can't open mobyservice for dumping";
 	@response = ();
@@ -2313,9 +2312,10 @@
 	}
 	my $mobyrelationship = (join "", @response);
 	close IN;
-	return ($mobycentral, $mobyobject, $mobyservice, $mobynamespace, $mobyrelationship);
+	return [$mobycentral, $mobyobject, $mobyservice, $mobynamespace, $mobyrelationship];
 }
 
+*DUMP = \&DUMP_MySQL;  # alias it for backward compatibility
 
 sub _flatten {
 	# from a given term, traverse the ontology