[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Mon Feb  9 20:10:45 EST 2004
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv2100/Services

Modified Files:
	LocalServices.pm 
Log Message:
added two GO traversal routines - get parents and get children

moby-live/Perl/scripts/Services LocalServices.pm,1.59,1.60
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.59
retrieving revision 1.60
diff -u -r1.59 -r1.60
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2004/02/09 23:27:34	1.59
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2004/02/10 01:10:45	1.60
@@ -261,6 +261,81 @@
     return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
 }
 
+sub getSHoundGODBGetParentOf {  # WORKS
+    my ($caller, $data) = @_;
+    my $MOBY_RESPONSE;
+    my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+    return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
+
+    my ($validNS) = validateNamespaces("GO");  # ONLY do this if you are intending to be namespace aware!
+    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+    foreach (@inputs){
+        my ($articleType, $qID, $input) = @{$_};
+        unless (($articleType == SIMPLE) && ($input) ){
+            $MOBY_RESPONSE .= collectionResponse([], "", $qID) ;
+            next;
+        } else {
+            my $namespace = getSimpleArticleNamespaceURI($input);
+			my ($identifier) = getSimpleArticleIDs($input);  # note array output!
+			# GO id's should not, but sometimes may begin with the GO: namespace... get rid of this, and the leading 0's for SeqHound
+			$identifier =~ s/^GO://;
+			$identifier =~ s/^0+//;			
+            (($MOBY_RESPONSE .= collectionResponse([], "", $qID)) && next) unless ($namespace eq $validNS);
+			my $GOs = SHoundGODBGetParentOf($identifier);
+            (($MOBY_RESPONSE .= collectionResponse([], "", $qID)) && next) unless ($GOs);
+			my @GOs = split ",", $GOs;
+			my @simples;
+			foreach my $go (@GOs){
+				next unless $go;
+				$go =~ s/\s//g;
+				my $goacc = sprintf("%07d", $go);
+	            push @simples, "<Object namespace='GO' id='$goacc'/>";
+			}
+			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
+        }
+    }
+	print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+}
+
+sub getSHoundGODBGetChildrenOf {  # WORKS
+    my ($caller, $data) = @_;
+    my $MOBY_RESPONSE;
+    my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
+    return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
+
+    my ($validNS) = validateNamespaces("GO");  # ONLY do this if you are intending to be namespace aware!
+    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+
+    foreach (@inputs){
+        my ($articleType, $qID, $input) = @{$_};
+        unless (($articleType == SIMPLE) && ($input) ){
+            $MOBY_RESPONSE .= collectionResponse([], "", $qID) ;
+            next;
+        } else {
+            my $namespace = getSimpleArticleNamespaceURI($input);
+			my ($identifier) = getSimpleArticleIDs($input);  # note array output!
+			# GO id's should not, but sometimes may begin with the GO: namespace... get rid of this, and the leading 0's for SeqHound
+			$identifier =~ s/^GO://;
+			$identifier =~ s/^0+//;			
+            (($MOBY_RESPONSE .= collectionResponse([], "", $qID)) && next) unless ($namespace eq $validNS);
+			my $GOs = getSHoundGODBGetChildrenOf($identifier);
+            (($MOBY_RESPONSE .= collectionResponse([], "", $qID)) && next) unless ($GOs);
+			my @GOs = split ",", $GOs;
+			my @simples;
+			foreach my $go (@GOs){
+				next unless $go;
+				$go =~ s/\s//g;
+				my $goacc = sprintf("%07d", $go);
+	            push @simples, "<Object namespace='GO' id='$goacc'/>";
+			}
+			$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
+        }
+    }
+	print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
+    return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
+}
 
 sub getSHoundDNAFromOrganism {  # WORKS
     my ($caller, $data) = @_;