[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Thu May  8 17:21:36 EDT 2003
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv4445/Perl/MOBY

Modified Files:
	Central.pm 
Log Message:
should be able to register collections now, but not discover them.
moby-live/Perl/MOBY Central.pm,1.44,1.45
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.44
retrieving revision 1.45
diff -u -r1.44 -r1.45
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2003/05/08 20:11:32	1.44
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2003/05/08 21:21:36	1.45
@@ -1114,63 +1114,59 @@
     my ($object_type, @namespaces);
 
     if ($simp_coll eq "Collection"){
-
-        my $table = "collection";
-		#$debug && &_LOG("Collection!\n");  # the following SQl belongs in the service_instance object, but screw it, I'm running out of time!
-		#$dbh->do("insert into collection_$inout (service_instance_id, article_name) values (?,?)", undef, ($SVC->service_instance_id, $article));
-		#my $collection_id=$dbh->{mysql_insertid};
-		#my $Simples = $node->getElementsByTagName('Simple');
-		#my $length = $Simples->getLength;
-		#for (my $x=0; $x<$length; ++$x){
-		#	&_registerArticles($SVC, $inout, $Simples->item($x),$collection_id);
-		#}
-
-
+		$debug && &_LOG("Collection!\n");  # the following SQl belongs in the service_instance object, but screw it, I'm running out of time!
+		$dbh->do("insert into collection_$inout (service_instance_id, article_name) values (?,?)", undef, ($SVC->service_instance_id, $article));
+		my $collection_id=$dbh->{mysql_insertid};
+		my $Simples = $node->getElementsByTagName('Simple');
+		my $length = $Simples->getLength;
+		for (my $x=0; $x<$length; ++$x){
+			&_registerArticles($SVC, $inout, $Simples->item($x),$collection_id);
+		}
     } elsif ($simp_coll eq "Simple")  {
-      my $article = $node->getAttributeNode("articleName");
-      $article = $article->getValue() if $article;
-
-      # get object type and its URI from the ontoogy server
-      my $types =  $node->getElementsByTagName('objectType');
-      my $OE = MOBY::OntologyServer->new(ontology => "object");
-      foreach ($types->item(0)->getChildNodes) { # should only ever be one!
-	($_->getNodeType == TEXT_NODE) && ($object_type = $_->toString);
-      }
-      my ($success, $message, $typeURI) = $OE->objectExists(term => $object_type);
-      unless ($success) {
-	$SVC->DELETE_THYSELF; return (-1,"object: $object_type does not exist");
-      }				# kill it all unless this was successful!
+		my $article = $node->getAttributeNode("articleName");
+		$article = $article->getValue() if $article;
 
-      my $namespace_string;
-      my $namespaces = $node->getElementsByTagName('Namespace');
-      my $num_ns = $namespaces->getLength;
-      $OE = MOBY::OntologyServer->new(ontology => "namespace");
-      for (my $n = 0; $n<$num_ns;++$n) {
-	foreach my $name ($namespaces->item($n)->getChildNodes) {
-	  if ($name->getNodeType == TEXT_NODE) {
-	    my ($success, $message, $URI) = $OE->namespaceExists(term => $name->toString);
-	    unless ($success) {
-	      $SVC->DELETE_THYSELF; return (-1,"namespace: " . $name->toString . " doesn't exist");
-	    }
-	    $namespace_string .=$URI.",";
-	  }
-	}
-      }
-      chop($namespace_string);  # remove trailing comma
-      my $dbh = $SVC->dbh;
-      my $service_instance_id;
-      unless ($collid) {
-	$service_instance_id = $SVC->service_instance_id;
-      }				# one or the other, but not both
-      $dbh->do("insert into simple_".$inout."
+		# get object type and its URI from the ontoogy server
+		my $types =  $node->getElementsByTagName('objectType');
+		my $OE = MOBY::OntologyServer->new(ontology => "object");
+		foreach ($types->item(0)->getChildNodes) { # should only ever be one!
+			($_->getNodeType == TEXT_NODE) && ($object_type = $_->toString);
+		}
+		my ($success, $message, $typeURI) = $OE->objectExists(term => $object_type);
+		unless ($success) {
+			$SVC->DELETE_THYSELF; return (-1,"object: $object_type does not exist");
+		}				# kill it all unless this was successful!
+
+		my $namespace_string;
+		my $namespaces = $node->getElementsByTagName('Namespace');
+		my $num_ns = $namespaces->getLength;
+		$OE = MOBY::OntologyServer->new(ontology => "namespace");
+		for (my $n = 0; $n<$num_ns;++$n) {
+			foreach my $name ($namespaces->item($n)->getChildNodes) {
+				if ($name->getNodeType == TEXT_NODE) {
+					my ($success, $message, $URI) = $OE->namespaceExists(term => $name->toString);
+					unless ($success) {
+					  $SVC->DELETE_THYSELF; return (-1,"namespace: " . $name->toString . " doesn't exist");
+				}
+					$namespace_string .=$URI.",";
+				}
+			}
+		}
+		chop($namespace_string);  # remove trailing comma
+		my $dbh = $SVC->dbh;
+		my $service_instance_id;
+		unless ($collid) {
+			$service_instance_id = $SVC->service_instance_id;
+		}				# one or the other, but not both
+		$dbh->do("insert into simple_".$inout."
 				 (object_type_uri,
 				  namespace_type_uris,
 				  article_name,
 				  service_instance_id,
 				  collection_".$inout."_id)
 				 values (?,?,?,?,?)",
-	       undef,
-	       ($typeURI,
+		undef,
+		($typeURI,
 		$namespace_string,
 		$article,
 		$service_instance_id,