[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Tue Apr 20 19:19:29 EDT 2004
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory pub.open-bio.org:/tmp/cvs-serv15574/MOBY

Modified Files:
	Central.pm OntologyServer.pm 
Log Message:
done

moby-live/Perl/MOBY Central.pm,1.125,1.126 OntologyServer.pm,1.38,1.39
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.125
retrieving revision 1.126
diff -u -r1.125 -r1.126
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/04/04 19:08:41	1.125
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2004/04/20 23:19:29	1.126
@@ -236,6 +236,7 @@
 	}
 	return &_error("Malformed authURI - must not have an http:// prefix","") if $auth =~ '[/:]';
 	return &_error("Malformed authURI - must take the form NNN.NNN.NNN","") unless $auth =~ /\./;
+print STDERR "\n\nemail was $email\n\n";
 	return &_error("Malformed email - must be a valid email address of the form name\@organization.foo","") unless $email =~ /\S\@\S+\.\S+/;
 
 	# validate that the final ontology will be valid by testing against existing relationships and such
@@ -2329,10 +2330,10 @@
 	return undef unless $term;   # and bail out if we didn't succeed
 
 	$ontology ||="service";   # if we have now succeeded and haven't already taken the ontology then it must be the service ontology
-	&_LOG("Ontology was $ontology; Term was $term\n");
+	&_LOG("Ontology was $ontology; Term was: $term\n");
 	my $OS = MOBY::OntologyServer->new(ontology => $ontology);
 	my %rels = %{$OS->Relationships(term => $term, expand => $expand_relationship)};  # %rels = $rels{relationship} = [lsid, lsid,lsid]
-
+        &_LOG("\nrels ",(keys %rels),"\n");
 	my $response="<Relationships>\n";
 	my $OSrel = MOBY::OntologyServer->new(ontology => 'relationship');
 	foreach (keys %reltypes){  # for each of our desired types
@@ -2340,6 +2341,7 @@
 		delete $reltypes{$_};   # remove the non-LSID version from the hash
 		$reltypes{$rellsid} = 1; # set the LSID as valid
 	}
+        &_LOG("\nvalid rels ",(keys %reltypes),"\n");
 	# now for each of the relationship types that we were returned
 	foreach (keys %rels){
 		my $rellsid = $OSrel->getRelationshipURI($ontology, $_);
@@ -2356,6 +2358,7 @@
 		$response .= "</Relationship>\n";
 	}
 	$response .="</Relationships>\n";
+	&_LOG("returning $response\n");
 	return $response;
 }
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.38
retrieving revision 1.39
diff -u -r1.38 -r1.39
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/04/20 19:12:32	1.38
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2004/04/20 23:19:29	1.39
@@ -593,7 +593,7 @@
     }
         
     if ($term =~ /^urn:lsid:biomoby.org:namespacetype/){
-        $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid = ?");
+        $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_lsid= ?");
     } else {
         $sth = $self->dbh->prepare("select namespace_id, namespace_type, namespace_lsid,description, authority, contact_email from namespace where namespace_type = ?");
     }