[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Jul 25 14:17:44 EDT 2005
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv20619/MOBY

Modified Files:
	Central.pm 
Log Message:
changing the adaptor API to be more perlish. Pass the service LSID rather than the database key to be more generic

moby-live/Perl/MOBY Central.pm,1.179,1.180
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.179
retrieving revision 1.180
diff -u -r1.179 -r1.180
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/07/25 17:50:02	1.179
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2005/07/25 18:17:44	1.180
@@ -3100,120 +3100,6 @@
 	return "<GETstring><![CDATA[$sprintf]]></GETstring>";
 }
 
-#=head2 _traverseServiceDAG
-#
-# Title     :	_traverseServiceDAG
-# Usage     :	@valid = $MOBY->_traverseServiceDAG($dbh, $serviceType, $sth_hash)
-# Function  :	starting from $serviceType, find all child services non-redundantly
-#                by traversing the DAG.
-# Returns   :	list of Service.id database entries.
-# Args      :	none
-#
-#=cut
-#
-#sub _traverseServiceDAG {
-#
-#	$CONFIG ||= MOBY::Config->new;    # exported by Config.pm
-#	my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
-#
-#	my ( $dbh, $serviceType, $sth_hash ) = @_;
-#	my %sth = %{$sth_hash};
-#	my %ServiceIDs;
-#
-#	my $result = $adaptor->general_query({statement => $sth{get_service_type_id}}, {bind_values => [$serviceType]});
-#  	my $row = shift(@$result);
-#	my ($root_id) = @$row;
-#	return undef unless $root_id;
-#
-## we have to do a traversal of the DAG here to get all child nodes...
-## this is one UGLY piece of code written in a hurry!  Please, someone, shoot it and put it out of its misery...
-#	$ServiceIDs{$root_id} = "untested";    # mark the one in-hand as untested
-#	while ( grep /untested/, ( values %ServiceIDs ) )
-#	{    # now, while there are untested services in our list...
-#		foreach my $service ( keys %ServiceIDs )
-#		{    # start parsing through the list
-#			next
-#			  if ( $ServiceIDs{$service} eq "tested" )
-#			  ;    # if it has been tested already then move on
-#
-#			my $result = $adaptor->general_query({statement => $sth{get_service_hierarchy_list}}, {bind_values => [$service]} );
-#			   # execute the query for child nodes
-#			$ServiceIDs{$service} = "tested";    # mark it as tested
-#			foreach my $row (@$result)
-#			{    # now get each of the child nodes
-#				my $new = @$row;
-#				next
-#				  if ( defined $ServiceIDs{$new} )
-#				  ;    # if we have already heard about it then move on
-#				$ServiceIDs{$new} = "untested"
-#				  ;    #otherwise mark it as untested, and start all over again
-#			}
-#		}
-#	}
-#	return keys %ServiceIDs;
-#}
-
-#=head2 _traverseObjectDAG
-#
-# Title     :	_traverseObjectDAG
-# Usage     :	@valid = $MOBY->_traverseObjectDAG( $dbh, $objectType, $sth_hash, "p|c")
-# Function  :	from $objectType, find all parent/child objects non-redundantly
-#                by traversing the DAG.
-# Returns   :	list of Object.id database entries.
-# Args      :	objectType (by name), $statement ahngles, "p" parent, or "c" child
-#
-#=cut
-#
-#sub _traverseObjectDAG {
-#	$CONFIG ||= MOBY::Config->new;    # exported by Config.pm
-#	my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobycentral' );
-#
-#	my ( $dbh, $objectType, $sth_hash, $dir ) = @_;
-#	my %sth = %{$sth_hash};
-#	my %ObjectIDs;
-#
-#	my $result = $adaptor->general_query({statement => $sth{get_object_type_id}}, {bind_values => [$objectType]});
-#
-#	my $row = shift (@$result);
-#	my ($root_id) = @$row;
-#	return undef unless $root_id;
-#	
-## we have to do a traversal of the DAG here to get all child nodes...
-## this is one UGLY piece of code written in a hurry!  Please, someone, shoot it and put it out of its misery...
-#	$ObjectIDs{$root_id} = "untested";    # mark the one in-hand as untested
-#	while ( grep /untested/, ( values %ObjectIDs ) )
-#	{    # now, while there are untested services in our list...
-#		foreach my $object ( keys %ObjectIDs )
-#		{    # start parsing through the list
-#			next
-#			  if ( $ObjectIDs{$object} eq "tested" )
-#			  ;                     # if it has been tested already then move on
-#
-#			my $result;
-#			if ( $dir eq "p" ) {
-#				$debug && &_LOG("getting parents");
-#				$result = $adaptor->general_query({statement => $sth{get_object_parent_list}}, {bind_values => [$object]});
-#			}
-#			else {
-#				$debug && &_LOG("getting children");
-#				$result = $adaptor->general_query({statement => $sth{get_object_child_list}}, {bind_values => [$object]});
-#			}
-#			# execute the query for child nodes
-#
-#			$ObjectIDs{$object} = "tested";    # mark it as tested
-#			foreach my $row (@$result)
-#			{                                  # now get each of the child nodes
-#				my $new = @$row;
-#				next
-#				  if ( defined $ObjectIDs{$new} )
-#				  ;    # if we have already heard about it then move on
-#				$ObjectIDs{$new} = "untested"
-#				  ;    #otherwise mark it as untested, and start all over again
-#			}
-#		}
-#	}
-#	return keys %ObjectIDs;
-#}
 
 #Eddie - converted
 sub _nodeTextContent {