[MOBY-guts] biomoby commit

[Mark Wilkinson]

Tue Jan 28 19:59:45 EST 2003
Update of /home/repository/moby/moby-live/Perl/Client
In directory dev:/tmp/cvs-serv20152/Perl/Client

Modified Files:
	MOBY-Client.cgi 
Log Message:
amazing!  I think I only needed to modify two or three lines to get the client working from the new API :-)  Okay, go nuts.  Please let me know if you find any errors or feel free to fix them yourself  if youre keen
moby-live/Perl/Client MOBY-Client.cgi,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Client/MOBY-Client.cgi,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /tmp/T0YdaWyN	2003-01-28 19:59:45.270004405 -0500
+++ /tmp/T1ZdaWyN	2003-01-28 19:59:45.280009280 -0500
@@ -76,7 +76,11 @@
     start_html(-title => 'A Simple MOBY Client', -bgcolor => "white"),
     "<table BGCOLOR='#AAAAFF' width = '100%'><TR><TD><center>",
     "<IMG SRC=http://www.biomoby.org/moby1.gif>",
-    h1('MOBY Client Initialization'),"</center></TD></TR></table><p>",
+    h1('MOBY Client Initialization'),"<font color='red'><b>SORRY - MANY SERVICES ARE CURRENTLY OFFLINE DUE TO A CHANGE 
+IN SERVER LOCATION AT NRC.  THIS SHOULD BE RESOLVED SHORTLY</b><br><br>To see examples of functioning services, chose 
+the 'Generic Keyword' namespace, and enter '*brassinosteroid*' in the ID field.  Flybase has a Gene Ontology 
+lookup service that operates on that namespace.  Send <b><i>one</b></i> of the resulting GO terms to the TAIR sequence 
+retrieval service.</font></center></TD></TR></table><p>",
     start_form,
     "<h2>What namespace do you have? ";
     my %nslabels = (%{$NameSpaces});
@@ -177,7 +181,7 @@
         my $obj = $Object->getTagName;
         my $ns = $Object->getAttributeNode("namespace")->getValue();
         my $id = $Object->getAttributeNode("id")->getValue();
-        _LOG("writeCurrentObjects:  Object was $obj namespace was $ns\n");
+        $debug && _LOG("writeCurrentObjects:  Object was $obj namespace was $ns\n");
         $obj = escapeHTML($obj);	# escape the name, namespace, and object XML
         $ns = escapeHTML($ns);
         $id = escapeHTML($id);
@@ -236,16 +240,16 @@
     # EXECUTE SELECTED SERVICE
     my $SelectedService = param('SelectedService');
     my ($URI, $name) = (($SelectedService =~ /(.*?)#(.*)/) && ($1, $2));
-    _LOG("Executing\n");
+    $debug && _LOG("Executing\n");
 
     my $Central = MOBY::Client::Central->new();
 
-    my $wsdl =  $Central->retrieveService($URI, $name);  # get the WSDL for the selected service
-    _LOG("WSDL\n\n___________________________________________________$wsdl\n_______________________________________");
+    my $wsdl =  $Central->retrieveService(authURI => $URI, serviceName => $name);  # get the WSDL for the selected service
+    $debug && _LOG("WSDL\n\n___________________________________________________$wsdl\n_______________________________________");
     my $CurrentObjects = join "\n\n", &extractCurrentObjects(); # get the object XML (in human-readable form if possible for logging purposes)
 
     my $MOBY_Request = "<MOBY>\n".$CurrentObjects."</MOBY>";
-    _LOG("MOBY_REQUEST\n\n___________________________________________________$MOBY_Request\n_______________________________________");
+    $debug && _LOG("MOBY_REQUEST\n\n___________________________________________________$MOBY_Request\n_______________________________________");
 
     my $Service = MOBY::Client::Service->new(service => $wsdl); # create the service
 
@@ -266,7 +270,7 @@
         $success = 1;
         my $Object_text = $Object->toString;
         push @objects,$Object_text;
-        _LOG("Found response object $Object_text .\n");
+        $debug && _LOG("Found response object $Object_text .\n");
     }
 
     unless ($success){$ERROR_FLAG = "MOBY Response Contained No Data"; return};
@@ -327,7 +331,7 @@
 sub extractCurrentObjects {
   # objects are passed as base64 encoded, need to decode them back to XML
   my @objects = param("CurrentObjects");
-  &_LOG("CURRENT_OBJECTS__________________\n at objects\n___________________");
+  $debug && &_LOG("CURRENT_OBJECTS__________________\n at objects\n___________________");
   return map {decode_base64($_)} @objects;
 }
 
@@ -342,7 +346,7 @@
         my $doc = $Parser->parse($_);
         my $Object = $doc->getDocumentElement();
         my $object_name = $Object->getTagName;
-        _LOG("extractObjectTypes:  Object was $object_name\n");
+        $debug && _LOG("extractObjectTypes:  Object was $object_name\n");
         my $CRIB = $Object->getElementsByTagName("CrossReference");
         # should be only one CRIB per object, so...
         if ($CRIB->item(0)){
@@ -370,7 +374,7 @@
 	my $doc = $Parser->parse($_);
 	my $Object = $doc->getDocumentElement();
 	my $ns = $Object->getAttributeNode("namespace");
-    _LOG("extractObjectTypes:  Namespace was ".$ns->getValue."\n");
+    $debug && &_LOG("extractObjectTypes:  Namespace was ".$ns->getValue."\n");
     push @namespaces, $ns->getValue;
   }
   return @namespaces;	
@@ -384,7 +388,7 @@
     # menu* of valid services!!
     my ($objects, $namespace) = @_;
     my @objects = @{$objects};  # has the format @([object_type, \@XREF_XML], [...]...)
-    _LOG("getAllServices:  \n\tInitial Object List @objects\n");
+    $debug && _LOG("getAllServices:  \n\tInitial Object List @objects\n");
 
     my @types;
     foreach (@objects){
@@ -397,8 +401,13 @@
 
     my $Central = MOBY::Client::Central->new();
 
-    _LOG("getAllServices:  \n\tObjects @types\n\tNamespaces @{$namespace}");
-    my @services = $Central->locateServiceByInput(\@types, $namespace);
+    my %searchparams;
+    foreach (@types){
+	$searchparams{$_} = $namespace;
+    }
+    $debug && _LOG("************************************************\n\ngetAllServices:  \n\tObjects @types\n\tNamespaces @{$namespace}\n\n*****************************************");
+    my @services = $Central->locateServiceByInput(
+	input => \%searchparams);
 
     my %popup_services;
     foreach (@services) {