[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Thu Feb  8 19:19:01 EST 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv31832/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
revamping test suite for CommonSubs to use only the new methods.  Please God let the deprecated methods die a horrible death.  There's a lot more cleaning-up that could be done in CommonSubs with respect to using 'Local' tags rather than testing whether or not the moby: namespace is there each time, but that can come later.
moby-live/Perl/MOBY CommonSubs.pm,1.94,1.95
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm,v
retrieving revision 1.94
retrieving revision 1.95
diff -u -r1.94 -r1.95
--- /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2007/02/08 23:03:45	1.94
+++ /home/repository/moby/moby-live/Perl/MOBY/CommonSubs.pm	2007/02/09 00:19:01	1.95
@@ -61,12 +61,12 @@
     
     my $responses = serviceResponseParser($resp); # returns MOBY objects
     foreach my $queryID(keys %$responses){  # $inputs is a hashref of $input{queryid}->{articlename} = input object
-        my $this_invocation = $inputs->{$queryID};
+        my $this_invocation = $responses->{$queryID};
         if (my $data = $this_invocation->{'responseArticleName'}){ # $input is a MOBY::Client::Simple|Collection|Parameter object
             my $simples = $data->Simples;
             foreach my $simple(@$simples){
+                my ($ns) = @{$simple->namespaces};
                 my $id = $simple->id;
-                my $id = $simple->namespace;
                 my $XML_LibXML = $input->XML_DOM;  # get access to the DOM 
 
             }
@@ -262,7 +262,7 @@
 		  genericServiceInputParserAsObject
 		  complexServiceInputParser
 		  serviceInputParser
-		  serviceInputParser
+		  serviceResponseParser
 		  whichDeepestParentObject
 		  getServiceNotes
 		  simpleResponse
@@ -387,9 +387,9 @@
   my ( $XML ) = @_;
   my $moby =  _string_to_DOM($XML);
   my @queries;
-  foreach my $querytag qw(mobyData moby:mobyData )
+  foreach my $querytag qw(mobyData )
     {
-      my $x = $moby->getElementsByTagName( $querytag );    # get the mobyData block
+      my $x = $moby->getElementsByLocalName( $querytag );    # get the mobyData block
       for ( 1 .. $x->size() ) {    # there may be more than one mobyData per message
 	push @queries, $x->get_node( $_ );
       }
@@ -667,7 +667,7 @@
 the article's raw XML for simples and secondaries or a reference to an array containing 
 [$articleName, $simpleXML] elements for a collection of simples.
 
-C<$queryID> - (optional, but strongly recommended) the queryID value for
+C<$queryID> - the queryID value for
 the mobyData block to which you are responding
 
 B<notes:> as required by the API you must return a response for every