[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Wed Jul  9 18:16:47 EDT 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv972/Perl/MOBY

Modified Files:
	Central.pm 
Log Message:
MOBY::Central now is able to discover services with Collection Articles as part of their service signature

moby-live/Perl/MOBY Central.pm,1.92,1.93
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.92
retrieving revision 1.93
diff -u -r1.92 -r1.93
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2003/07/04 16:12:37	1.92
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2003/07/09 22:16:47	1.93
@@ -1646,50 +1646,53 @@
 	return @ids;	
 }
 sub _searchForCollection {
-
 	my ($dbh, $node, $expand, $inout)= @_;  # $node in this case is a Collection object
 	my $query;
-#######################
-#	return; # abort for the moment
-#######################
-		#######################################
-		# MARK START HERE
-		#######################################
-		
+	# luckily, we can return a redundant list of service id's and
+	# this will be cleaned up in the caller
+	
+	my @validservices;   
 	foreach my $simple($node->getChildNodes()){
 		next unless ($simple->getNodeType == ELEMENT_NODE);
 		next unless ($simple->getTagName =~ /simple/i);
 		my ($objectURI, $namespaceURIs) = &_extractObjectTypesAndNamespaces($simple);
 		
-		$query = "select c.service_instance_id, s.namespace_type_uris from simple_input as s, collection_input as c where s.collection_input_id IS NOT NULL and s.collection_input_id = c.collection_input_id AND object_type_uri = '$objectURI' ";
+		$query = "select
+			c.service_instance_id,
+			s.namespace_type_uris
+		from
+			simple_$inout as s,
+			collection_$inout as c
+		where
+			s.collection_${inout}_id IS NOT NULL
+		AND s.collection_${inout}_id = c.collection_${inout}_id
+		AND object_type_uri = '$objectURI' ";
 		
 		my $nsquery;
 		foreach my $ns(@{$namespaceURIs}){ # namespaces are already URI's
 			$nsquery .=" OR namespace_type_uris like '%$ns%' ";
 		}
-		if ($nsquery){$nsquery =~ s/OR//;} # just the first
-		$query .= " AND ($nsquery) ";
+		if ($nsquery){
+			$nsquery =~ s/^\sOR//; # just the first
+			$query .= " AND ($nsquery) ";  # add the AND clause 
+		} 
+		
+		$debug && &_LOG("QUERY: $query");
 		my $sth = $dbh->prepare($query);
 		$sth->execute;
-		my @valid_service_ids;
 		while (my ($id, $nss) = $sth->fetchrow_array){  # get the service instance ID and the namespaces that matched
-			my @ns = split ",", $nss;  # because of the database structure we have to re-test for *identity*, not just like%% similarity
-			my %nshash = map {($_, 1)} @ns,@{$namespaceURIs};  #we're going to test identity by building a hash of namespaces as keys 
-			if (scalar(keys %nshash) < scalar(@ns)+scalar(@{$namespaceURIs})){  # if the number of keys is less than the sum of the number of keys goign into the hash, then one of them was identical
-				push @valid_service_ids, $id;  # and therefore it really is a match, and is valid
+			if (scalar @{$namespaceURIs}){  # if namespaces were specified, then validate the discovered service against this list
+				my @ns = split ",", $nss;  # because of the database structure we have to re-test for *identity*, not just like%% similarity
+				my %nshash = map {($_, 1)} @ns,@{$namespaceURIs};  #we're going to test identity by building a hash of namespaces as keys 
+				if (scalar(keys %nshash) < scalar(@ns)+scalar(@{$namespaceURIs})){  # if the number of keys is less than the sum of the number of keys goign into the hash, then one of them was identical
+					push @validservices, $id;  # and therefore it really is a match, and is valid
+				}
+			} else {  # if no namespace was specified, then all of them are valid
+				push @validservices, $id
 			}
 		}
-		&_LOG("QUERY: $query");
 	}	
-	return;
-#	if ($query){$query =~s/AND//;} # just the first
-#	$debug && &_LOG("_searchForCollectedSimples QUERY = select distinct(collection_$inout"."id from  simple_$inout where collection_$inout"."_id IS NOT NULL AND $query\n\n");
-	#
-	#my $collids = $dbh->selectall_arrayref("create temporary table select distinct(collection_$inout"."id from  simple_$inout where  collection_$inout"."_id IS NOT NULL AND $query");
-	#my @result;	
-	#foreach (@{$collids}){
-	#	push @result, $_->[0];
-	#}
+	return @validservices;
 }
 
 sub _findServicePayload {