From kawas at dev.open-bio.org  Thu Apr  2 10:53:27 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 10:53:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904021453.n32ErRRb000392@dev.open-bio.org>


kawas
Thu Apr  2 10:53:26 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates
In directory dev.open-bio.org:/tmp/cvs-serv356/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service-cgi-async.tt 
Log Message:
had the method name hard coded; changed it to [% obj.name %]
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service-cgi-async.tt,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt	2009/03/30 13:14:09	1.1
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt	2009/04/02 14:53:26	1.2
@@ -118,7 +118,7 @@
 	# get the data from the 'data' parameter
 	my $data = $q->param('data') || $q->param('POSTDATA') || "";
 	# call the service
-	 __PACKAGE__->getGoTerm($data);
+	 __PACKAGE__->[% obj.name %]($data);
 	
 }
 


From kawas at dev.open-bio.org  Thu Apr  2 11:37:20 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 11:37:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904021537.n32FbKWY000764@dev.open-bio.org>


kawas
Thu Apr  2 11:37:20 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv729/Perl/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
added a -C option for testing asynchronous POST services.
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2008/09/02 17:58:02	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/02 15:37:20	1.8
@@ -10,8 +10,8 @@
 
 	# some command-line options
 	use Getopt::Std;
-	use vars qw/ $opt_h $opt_d $opt_v $opt_l $opt_e $opt_c $opt_a /;
-	getopts('hdvl:e:c:a:');
+	use vars qw/ $opt_h $opt_d $opt_v $opt_l $opt_e $opt_c $opt_a $opt_C /;
+	getopts('hdvl:e:c:C:a:');
 
 	# usage
 	if ( $opt_h or ( @ARGV == 0 and ( not $opt_c ) ) ) {
@@ -32,7 +32,10 @@
        # calling a real service, using cgi
        -c <service-url> [<input-file>]
 
-       # calling a real service, using SOAP
+       # calling a real service, using asynchronous cgi
+       -C <service-url> [<input-file>]
+
+       # calling a real service, using async SOAP
        -a <service-url> <service-name> [<input-file>]
 
     <package-name> is a full name of a called module (service)
@@ -64,6 +67,11 @@
 END_OF_USAGE
 		exit(0);
 	}
+	use HTTP::Request;
+	use LWP::UserAgent;
+	use XML::LibXML;
+	use MOBY::Async::WSRF;
+	use MOBY::Async::LSAE;
 
 	# use MOSES::MOBY::Base;
 	# load modules, depending on the mode of calling
@@ -79,6 +87,19 @@
 		  or die "$@\n";
 		eval "use LWP::UserAgent; 1;"
 		  or die "$@\n";
+	} elsif ($opt_C) {
+
+		# calling a real service, using async cgi
+		eval "use HTTP::Request; 1;"
+		  or die "$@\n";
+		eval "use LWP::UserAgent; 1;"
+		  or die "$@\n";
+		eval "use XML::LibXML; 1;"
+		  or die "$@\n";
+		eval "use MOBY::Async::WSRF; 1;"
+		  or die "$@\n";
+		eval "use MOBY::Async::LSAE; 1;"
+		  or die "$@\n";
 	} else {
 
 		# calling a local service module, without SOAP
@@ -93,12 +114,13 @@
 		$LOG->level('INFO')  if $opt_v;
 		$LOG->level('DEBUG') if $opt_d;
 	}
+
 	# load these modules always to get constants and to avoid warnings
 	eval "use MOBY::Async::LSAE; 1;"
 	  or die "$@\n";
 	eval "use MOBY::Async::WSRF; 1;"
 	  or die "$@\n";
-	
+
 }
 
 use strict;
@@ -114,8 +136,59 @@
 END_OF_XML
 }
 
+sub _check_status {
+	my ( $status, $completed, $queryID, $opt_v ) = @_;
+	if ( $status->type == LSAE_PERCENT_PROGRESS_EVENT ) {
+		if ( $status->percentage >= 100 ) {
+			$completed->{$queryID} = 1;
+		} elsif ( $status->percentage < 100 ) {
+			print "Current percentage: ", $status->percentage, "\n" if $opt_v;
+			sleep(20);
+		} else {
+			die "ERROR:  analysis event block not well formed.\n";
+		}
+
+	} elsif ( $status->type == LSAE_STATE_CHANGED_EVENT ) {
+		if (    ( $status->new_state =~ m"completed"i )
+			 || ( $status->new_state =~ m"terminated_by_request"i )
+			 || ( $status->new_state =~ m"terminated_by_error"i ) )
+		{
+			$completed->{$queryID} = 1;
+		} elsif (    ( $status->new_state =~ m"created"i )
+				  || ( $status->new_state =~ m"running"i ) )
+		{
+			print "Current State: ", $status->new_state, "\n" if $opt_v;
+			sleep(20);
+		} else {
+			die "ERROR:  analysis event block not well formed.\n";
+		}
+
+	} elsif ( $status->type == LSAE_STEP_PROGRESS_EVENT ) {
+		if ( $status->steps_completed >= $status->total_steps ) {
+			$completed->{$queryID} = 1;
+		} elsif ( $status->steps_completed < $status->total_steps ) {
+			print "Steps completed: ", $status->steps_completed, "\n" if $opt_v;
+			sleep(20);
+		} else {
+			die "ERROR:  analysis event block not well formed.\n";
+		}
+
+	} elsif ( $status->type == LSAE_TIME_PROGRESS_EVENT ) {
+		if ( $status->remaining == 0 ) {
+			$completed->{$queryID} = 1;
+		} elsif ( $status->remaining > 0 ) {
+			print "Time remaining: ", $status->remaining, "\n" if $opt_v;
+			sleep(20);
+		} else {
+			die "ERROR:  analysis event block not well formed.\n";
+		}
+	} else {
+		warn "Whilst checking the status of our resource, we entered into a possible infinite loop ...\n";
+	}
+}
+
 sub _get_query_ids {
-	my $input = shift;
+	my $input     = shift;
 	my @query_ids = ();
 	my $parser    = XML::LibXML->new();
 	my $doc       = $parser->parse_string($input);
@@ -124,17 +197,17 @@
 		my $node = $iterator->get_node($_);
 		my $id   = $node->getAttribute("queryID")
 		  || $node->getAttribute(
-				 $node->lookupNamespacePrefix($WSRF::Constants::MOBY_MESSAGE_NS)
-				   . ":queryID" );
+						 $node->lookupNamespacePrefix($WSRF::Constants::MOBY_MESSAGE_NS)
+						   . ":queryID" );
 		push @query_ids, $id;
 	}
 	return @query_ids;
 }
 
 # --- what service to call
-my $module = shift unless $opt_c;    # eg. Service::Mabuhay, or just Mabuhay
+my $module = shift unless $opt_c or $opt_C;    # eg. Service::Mabuhay, or just Mabuhay
 my $service;
-( $service = $module ) =~ s/.*::// unless $opt_c;
+( $service = $module ) =~ s/.*::// unless $opt_c or $opt_C;
 
 # --- call the service
 if ($opt_e) {
@@ -146,12 +219,8 @@
 			my $res  = shift;
 			my $msg =
 			  ref $res
-			  ? "--- SOAP FAULT ---\n"
-			  . $res->faultcode . " "
-			  . $res->faultstring
-			  : "--- TRANSPORT ERROR ---\n"
-			  . $soap->transport->status
-			  . "\n$res\n";
+			  ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring
+			  : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
 			die $msg;
 		}
 	);
@@ -190,6 +259,117 @@
 	$req->content("data=$input");
 	print "\n" . $ua->request($req)->as_string . "\n";
 
+} elsif ($opt_C) {
+
+	my $input = '';
+	if ( @ARGV > 0 ) {
+		my $data = shift;    # a file name
+		open INPUT, "<$data"
+		  or die "Cannot read '$data': $!\n";
+		while (<INPUT>) { $input .= $_; }
+		close INPUT;
+	} else {
+		$input = _empty_input;
+	}
+
+	# extract all of the query ids from $input
+	my @query_ids = _get_query_ids($input);
+	my %completed = ();
+
+	print "Sending the following data to $opt_C\n$input\n";
+
+	# post to the web service
+	my $ua = LWP::UserAgent->new;
+	my $req = HTTP::Request->new( POST => $opt_C );
+	$req->content_type('application/x-www-form-urlencoded');
+	$req->content("data=$input");
+
+	# get the response
+	my $response = $ua->request($req);
+
+	# do we have an error?
+	die "Error calling service: " . $response->status_line
+	  if ( $response->code != 200 );
+
+	my $epr    = $response->header("moby-wsrf");
+	my $parser = XML::LibXML->new();
+	my $doc    = $parser->parse_string($epr);
+	my $ID =
+	  $doc->getElementsByLocalName("ServiceInvocationId")->get_node(1)->textContent;
+	$ID =~ s/ //gi;
+	my $searchTerm = "";
+	$searchTerm .=
+"<wsrf-rp:GetMultipleResourceProperties xmlns:wsrf-rp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
+
+	foreach my $queryID (@query_ids) {
+		$searchTerm .=
+		    "<wsrf-rp:ResourceProperty>mobyws:status_" 
+		  . $queryID
+		  . "</wsrf-rp:ResourceProperty>";
+	}
+	$searchTerm .= "</wsrf-rp:GetMultipleResourceProperties>";
+	my $header = _moby_wsrf_header( $opt_C, $ID );
+	$header =~ s/\n//gi;
+
+	# poll
+	while (1) {
+		foreach my $queryID (@query_ids) {
+
+			# skip poll if current job completed
+			next if $completed{$queryID};
+
+			# poll the service for given query ID
+			$req = HTTP::Request->new( POST => $opt_C . "/status" );
+			$req->header( "moby-wsrf" => $header );
+			$req->content_type('application/x-www-form-urlencoded');
+			$req->content("data=$searchTerm");
+			$response = $ua->request($req);
+			my $xml    = $response->content();
+			my $parser = XML::LibXML->new();
+			my $doc    = $parser->parse_string($xml);
+			$doc = $doc->documentElement()->firstChild()->firstChild();
+
+			my $status = LSAE::AnalysisEventBlock->new( $doc->toString );
+			&_check_status( $status, \%completed, $queryID, $opt_v );
+		}
+		last if scalar keys(%completed) == $#query_ids + 1;
+	}
+
+	# task is finished, obtain the result
+	$searchTerm = "";
+	$searchTerm .=
+"<wsrf-rp:GetMultipleResourceProperties xmlns:wsrf-rp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
+	foreach my $queryID (@query_ids) {
+		$searchTerm .=
+		    "<wsrf-rp:ResourceProperty>mobyws:result_" 
+		  . $queryID
+		  . "</wsrf-rp:ResourceProperty>";
+	}
+	$searchTerm .= "</wsrf-rp:GetMultipleResourceProperties>";
+
+	$header = _moby_wsrf_header( $opt_C, $ID );
+	$header =~ s/\n//gi;
+
+	$req = HTTP::Request->new( POST => $opt_C . "/results" );
+	$req->header( "moby-wsrf" => $header );
+	$req->content_type('application/x-www-form-urlencoded');
+	$req->content("data=$searchTerm");
+	$response = $ua->request($req);
+
+	# create nicely formatted XML
+	$parser = XML::LibXML->new();
+	$doc    = $parser->parse_string( $response->content );
+	print "\n" . $doc->toString(1);
+
+	# destroy the job
+	$searchTerm = '<Destroy xmlns="http://docs.oasis-open.org/wsrf/rl-2"/> ';
+	$req = HTTP::Request->new( POST => $opt_C . "/destroy" );
+	$req->header( "moby-wsrf" => $header );
+	$req->content_type('application/x-www-form-urlencoded');
+	$req->content("data=$searchTerm");
+	$response = $ua->request($req);
+	print "Destroying the resource returned:\n\t" . $response->content . "\n" if $opt_v;
+
 } elsif ($opt_a) {
 
 	# calling a real service, using async soap
@@ -203,12 +383,8 @@
 			my $res  = shift;
 			my $msg =
 			  ref $res
-			  ? "--- SOAP FAULT ---\n"
-			  . $res->faultcode . " "
-			  . $res->faultstring
-			  : "--- TRANSPORT ERROR ---\n"
-			  . $soap->transport->status
-			  . "\n$res\n";
+			  ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring
+			  : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
 			die $msg;
 		}
 	);
@@ -227,13 +403,11 @@
 
 	# extract all of the query ids from $input
 	my @query_ids = _get_query_ids($input);
-	print "\nSending the following data to $service asynchronously:\n",
-	  $input, "\n"
+	print "\nSending the following data to $service asynchronously:\n", $input, "\n"
 	  if $opt_v;
 
 	# submit the job
-	my $epr =
-	  ( $soap->$service( SOAP::Data->type( 'string' => "$input" ) )->result );
+	my $epr = ( $soap->$service( SOAP::Data->type( 'string' => "$input" ) )->result );
 
 	# Get address from the returned Endpoint Reference
 	my $address = $epr->{'EndpointReference'}->{Address};
@@ -265,12 +439,11 @@
 
 			$soap = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
 				sub {
-					sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1],
-					  $_[1];
+					sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
 				}
 			  )->wsaddress($EPR)
 			  ->GetMultipleResourceProperties(
-								  SOAP::Data->value($searchTerm)->type('xml') );
+										  SOAP::Data->value($searchTerm)->type('xml') );
 
 			my $parser = XML::LibXML->new();
 			my $xml    = $soap->raw_xml;
@@ -279,8 +452,7 @@
 			my $prop_name = "status_" . $queryID;
 
 			my ($prop) =
-			  $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY,
-											 $prop_name )
+			     $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
 			  || $soap->getElementsByTagName($prop_name);
 			my $event = $prop->getFirstChild->toString
 			  unless ref $prop eq "XML::LibXML::NodeList";
@@ -338,6 +510,7 @@
 	}
 
 	foreach my $queryID (@query_ids) {
+
 		# get the result
 		my $searchTerm .=
 "<wsrp:ResourceProperty xmlns:wsrp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
@@ -345,21 +518,19 @@
 		$searchTerm .= "</wsrp:ResourceProperty>";
 		my $ans = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
 			sub {
-				sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1],
-				  $_[1];
+				sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
 			}
 		  )->wsaddress($EPR)
 		  ->GetMultipleResourceProperties(
-								  SOAP::Data->value($searchTerm)->type('xml') );
+										  SOAP::Data->value($searchTerm)->type('xml') );
 		die "ERROR:  " . $ans->faultstring if ( $ans->fault );
 
 		my $parser = XML::LibXML->new();
 		my $xml    = $ans->raw_xml;
-		my $doc = $parser->parse_string($xml);
+		my $doc    = $parser->parse_string($xml);
 		$soap = $doc->getDocumentElement();
 		my $prop_name = "result_" . $queryID;
-		my ($prop) =
-		     $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
+		my ($prop) = $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
 		  || $soap->getElementsByTagName($prop_name);
 		my $result = $prop->getFirstChild->toString
 		  unless ref $prop eq "XML::LibXML::NodeList";
@@ -396,4 +567,14 @@
 	} or croak $@;
 }
 
+sub _moby_wsrf_header {
+	my ( $url, $id ) = @_;
+	return <<"END OF XML";
+<moby-wsrf>
+<wsa:Action xmlns:wsa="http://www.w3.org/2005/08/addressing">http://docs.oasis-open.org/wsrf/rpw-2/GetResourceProperty/GetResourcePropertiesRequest</wsa:Action>
+<wsa:To xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd" xmlns:wsa="http://www.w3.org/2005/08/addressing" wsu:Id="To">$url</wsa:To>
+<mobyws:ServiceInvocationId xmlns:mobyws="http://biomoby.org/" xmlns:wsa="http://www.w3.org/2005/08/addressing" wsa:IsReferenceParameter="true">$id</mobyws:ServiceInvocationId>
+</moby-wsrf>
+END OF XML
+}
 __END__


From kawas at dev.open-bio.org  Thu Apr  2 12:10:14 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 12:10:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904021610.n32GAEpU000924@dev.open-bio.org>


kawas
Thu Apr  2 12:10:14 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv889/Perl/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
added some help doc to further explain some of the options
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/02 15:37:20	1.8
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/02 16:10:14	1.9
@@ -21,6 +21,12 @@
        [-vd] [-l <lib-location>] <package-name> [<input-file>]
        or
        [-vd] -c <service-url> [<input-file>]
+       or
+       [-vd] -C <service-url> [<input-file>]
+       or
+       [-vd] -e <service-url> [<input-file>]
+       or
+       [-vd] -a <service-url> [<input-file>]
 
        It also needs a location of a local cache (and potentially a
        BioMoby registry endpoint). It takes it from the
@@ -52,6 +58,10 @@
     -c <cgi-service-url>
         A cgi biomoby service url
         (e.g. http://localhost/cgi-bin/HelloBiomobyWorld.cgi)
+        
+    -C <async-cgi-service-url>
+        An asynchronous cgi biomoby service url
+        (e.g. http://localhost/cgi-bin/HelloBiomobyWorldAsync.cgi)
 
     -a <asynchronous service-url>
         An asynchronous service url


From kawas at dev.open-bio.org  Thu Apr  2 14:33:44 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 14:33:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904021833.n32IXiv9001426@dev.open-bio.org>


kawas
Thu Apr  2 14:33:44 EDT 2009
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv1391/Docs/MOBY-S_API/Perl

Modified Files:
	construct_moses_cgi_async_service.html 
Log Message:
added information on updating event state for a running task
moby-live/Docs/MOBY-S_API/Perl construct_moses_cgi_async_service.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html	2009/03/30 13:12:34	1.1
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html	2009/04/02 18:33:44	1.2
@@ -20,7 +20,7 @@
     <dt><a href="#test">Step 5: Service testing</a> </dt>
     <dt><a href="#deploy">Step 6: Service deployment</a></dt>
     <dt><a href="#test2">Step 7: Service testing using CGI</a></dt>
-    <dt><em>How to update polling status (optional) - coming soon</em></dt>
+    <dt><a href="#poll">How to update polling status (optional)</a></dt>
   </dl>
 </dl>
 <h2><a name="req" id="req"></a>What is needed</h2>
@@ -108,7 +108,7 @@
 <h3>We can update our cache by issuing the following commands:</h3>
 <ol>
   <li> <em>moses-generate-services.pl -u <br />
-  </em></li>
+    </em></li>
   <li><em>moses-generate-datatypes.pl -u</em></li>
 </ol>
 <blockquote>
@@ -128,7 +128,7 @@
 <p>Basically, we used the script <em><strong>moses-generate-services.pl</strong></em> to:</p>
 <ol>
   <li>automatically generate a perl module called <strong>getReverseEchoString.pm</strong> in the directory <strong><em>/your_home_dir/Perl-MoSeS/services/Service</em></strong> (if it already exists, it won't overwrite it).<br />
-  This file contains the implementation for our service and is what we edit to inject our business logic.</li>
+    This file contains the implementation for our service and is what we edit to inject our business logic.</li>
   <li>automatically generates a cgi script called <strong>getReverseEchoString.cgi</strong> in the directory <em><strong>/your_home_dir/Perl-MoSeS/cgi/samples/jmoby/net/</strong></em>.<br />
     This file is what we deploy on our web server that redirects cgi requests to our service to the <em><strong>getReverseEchoString.pm</strong></em> module above.<br />
   </li>
@@ -231,6 +231,105 @@
    &lt;/moby:mobyData&gt;
  &lt;/moby:mobyContent&gt;
 &lt;/moby:MOBY&gt;</pre>
+<h2><a name="poll" id="poll"></a>How to update polling status (optional)</h2>
+<p>If you have a really long running service and would like to ensure that users know exactly how far along the service is to completion, you can create more detailed <em>status</em> messages.</p>
+<p>Before we continue, it would be useful for you to get acquainted with the perl module, <em><strong><a href="http://search.cpan.org/perldoc?MOBY::Async::LSAE" target="_blank">MOBY::Async::LSAE</a>.</strong></em></p>
+<h3>Updating the status of our service</h3>
+<blockquote>
+  <p>There are 2 things that you need to successfully update the status of your service:</p>
+  <ol>
+    <li><em>service invocation id<br />
+      </em></li>
+    <li><em>the job id for the current task</em></li>
+  </ol>
+  <p>The service invocation id is very simple to obtain: </p>
+</blockquote>
+<pre class="script2">my $ID = $ENV{ID};  </pre>
+<blockquote>
+  <p>The job id is equally as easy to obtain!</p>
+</blockquote>
+<pre class="script2">my $jid = $request-&gt;jid;</pre>
+<blockquote>
+  <p>Now that we have those 2 pieces of information, all that is left is for you to choose what type of status update you would like your service to create:</p>
+  <ul>
+    <li>Heartbeat progress event</li>
+    <li>Percent progress event</li>
+    <li>State changed event <em>(default)</em></li>
+    <li>Step progress event</li>
+    <li>Time progress event</li>
+  </ul>
+  <p>We will be using the State changed event in this example.</p>
+  <p>In order to save the state information for our task, we need certain variables like, <em><strong>pid</strong></em>, <em><strong>input</strong></em>, <em><strong>status</strong></em>, and <strong><em>result</em></strong>.</p>
+  <ul>
+    <li><strong><em>pid</em></strong>  is the property id for our service,</li>
+    <li><strong><em>input</em></strong> is the input to our service,</li>
+    <li><strong><em>status</em></strong> is the current event state for our running task, and</li>
+    <li><strong><em>result</em></strong> holds the result for our running task and is obtained once our state is set to completed.</li>
+  </ul>
+</blockquote>
+<pre class="script2"># some variables we need to access/store our event information
+
+my $property_pid    = &quot;pid_$jid&quot;;<br />my $property_input  = &quot;input_$jid&quot;;<br />my $property_status = &quot;status_$jid&quot;;<br />my $property_result = &quot;result_$jid&quot;;</pre>
+<blockquote>
+  <p>To provide updated state information for our event, we need to first remember what our previous state was:</p>
+</blockquote>
+<pre class="script2"># construct an LSAE object based on the old event block
+my $old_status = 
+         LSAE::AnalysisEventBlock-&gt;new(
+                 $WSRF::WSRP::ResourceProperties{$property_status}
+         );</pre>
+<blockquote>
+  <p>We now instantiate a new <em><strong>LSAE::AnalysisEventBlock</strong></em> and set its various fields. For instance, we will take the previous state information from <em><strong>$old_status</strong></em> and then provide new state information for our event:</p>
+</blockquote>
+<pre class="script2"># construct a new state changed event
+my $status = LSAE::AnalysisEventBlock-&gt;new();<br />$status-&gt;type(LSAE_STATE_CHANGED_EVENT);
+# set the previous state<br />$status-&gt;previous_state( $old_status-&gt;new_state() );
+# set the new state<br />$status-&gt;new_state('running');
+# set our job id for this event<br />$status-&gt;id($jid);</pre>
+<blockquote>
+  <p>Once we have created our new analysis event block, we need to save it so that the client that made the job request to our service can access the state information:</p>
+</blockquote>
+<pre class="script2"># create a file based resource that we will store our event information
+my $lock = WSRF::MobyFile-&gt;new( undef, $ID );<br />$WSRF::WSRP::ResourceProperties{$property_status} = $status-&gt;XML();
+# here we leave the result empty since the service is still running<br />$WSRF::WSRP::ResourceProperties{$property_result} = '';
+# save the event so that our clients can access the information
+$lock-&gt;toFile();</pre>
+<blockquote>
+  <p>Here is the complete code that we put into our <em><strong>process_it</strong></em> subroutine where ever you feel like you should update the state of our long running task!</p>
+</blockquote>
+<pre class="script2"># our service invocation id
+my $ID = $ENV{ID};
+
+# our job id
+my $jid = $request-&gt;jid;
+
+
+# some variables we need to access/store our event information
+my $property_pid    = &quot;pid_$jid&quot;;<br />my $property_input  = &quot;input_$jid&quot;;<br />my $property_status = &quot;status_$jid&quot;;<br />my $property_result = &quot;result_$jid&quot;;
+
+
+# construct an LSAE object based on the old event block
+my $old_status = 
+         LSAE::AnalysisEventBlock-&gt;new(
+                 $WSRF::WSRP::ResourceProperties{$property_status}
+         );
+
+
+# construct a new state changed event
+my $status = LSAE::AnalysisEventBlock-&gt;new();<br />$status-&gt;type(LSAE_STATE_CHANGED_EVENT);
+# set the previous state<br />$status-&gt;previous_state( $old_status-&gt;new_state() );
+# set the new state<br />$status-&gt;new_state('running');
+# set our job id for this event<br />$status-&gt;id($jid);
+
+
+# create a file based resource that we will store our event information
+my $lock = WSRF::MobyFile-&gt;new( undef, $ID );<br />$WSRF::WSRP::ResourceProperties{$property_status} = $status-&gt;XML();
+# here we leave the result empty since the service is still running<br />$WSRF::WSRP::ResourceProperties{$property_result} = '';
+# save the event so that our clients can access the information
+$lock-&gt;toFile();</pre>
+<blockquote>
+  <p>&nbsp;</p>
+</blockquote>
 <p>That's all there is to constructing asynchronous CGI based Perl MoSeS services!</p>
 </body>
 </html>


From kawas at dev.open-bio.org  Thu Apr  2 16:07:21 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 16:07:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904022007.n32K7L6N001833@dev.open-bio.org>


kawas
Thu Apr  2 16:07:21 EDT 2009
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv1798/Perl

Modified Files:
	INSTALL 
Log Message:
small documentation update on where to get more information.
moby-live/Perl INSTALL,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/INSTALL	2008/04/23 13:08:11	1.5
+++ /home/repository/moby/moby-live/Perl/INSTALL	2009/04/02 20:07:21	1.6
@@ -33,7 +33,7 @@
 For details on how to configure your own MOBY Central
 registry, should you want to set one up (you DO NOT
 need to set up a registry to access nor serve MOBY-S
-Services) please visit the "Installing a Local Registy"
-link on the biomoby.org homepage.
+Services) please read the documentation on cpan of
+the module MOBY.pm.
 
 Mark


From kawas at dev.open-bio.org  Fri Apr  3 12:35:57 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:35:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031635.n33GZvYx011393@dev.open-bio.org>


kawas
Fri Apr  3 12:35:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv11362/Perl/MOBY-Server/bin/scripts

Added Files:
	moby-s-update-db.pl 
Log Message:
a script to help people update their databases to reflect the new service category cgi-async. 

in the future, any updates to the db can be appended to this script. so if a new change X is made to the db, then all we need to do is add an option to the script and when a user runs the script with that option set, the appropriate update to the db will be made.

for the addition of the additional enum field 'cgi-async', the option to use with the script is -c.
moby-live/Perl/MOBY-Server/bin/scripts moby-s-update-db.pl,NONE,1.1

From kawas at dev.open-bio.org  Fri Apr  3 12:36:36 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:36:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031636.n33Gaa73011454@dev.open-bio.org>


kawas
Fri Apr  3 12:36:35 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv11419/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
addition of the moby-s-update-db.pl file to the manifest
moby-live/Perl/MOBY-Server MANIFEST,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/12/04 15:31:26	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2009/04/03 16:36:35	1.11
@@ -1,5 +1,6 @@
 bin/scripts/moby-s-install.pl
 bin/scripts/moby-s-caching.pl
+bin/scripts/moby-s-update-db.pl
 Changes
 drop_tables.sql
 inc/Module/AutoInstall.pm


From kawas at dev.open-bio.org  Fri Apr  3 12:39:48 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:39:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031639.n33GdmSL011558@dev.open-bio.org>


kawas
Fri Apr  3 12:39:48 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv11523/Perl/MOBY-Server/lib/MOBY

Modified Files:
	MOBY.pm 
Log Message:
added a brief message to say that users should check to see if they need to update their db schema
moby-live/Perl/MOBY-Server/lib/MOBY MOBY.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2008/09/02 13:14:18	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2009/04/03 16:39:48	1.5
@@ -55,6 +55,8 @@
 
 B<Important> if you are upgrading to newer versions, please make sure to remove any files that may be cached by this module! To help you do this, run the script B<moby-s-caching.pl>. For information on using B<moby-s-caching.pl>, use the -h option!
 
+B<Important II> make sure to run C<moby-s-update-db> with the -h option to see if you need to updgrade the db schemas.
+
 =cut
 
 =head2 Installing A Custom MOBY-Central Registry


From kawas at dev.open-bio.org  Fri Apr  3 12:41:36 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:41:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031641.n33Gfars011598@dev.open-bio.org>


kawas
Fri Apr  3 12:41:36 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv11563/Perl/MOBY-Server

Modified Files:
	Changes 
Log Message:
added a message about running the update db script if upgrading your moby installation.
moby-live/Perl/MOBY-Server Changes,1.21,1.22
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/03/30 13:10:19	1.21
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/03 16:41:36	1.22
@@ -1,6 +1,9 @@
 Revision history for Perl extension MOBY.
 
 1.07
+    - Important: run the script moby-s-update-db once you have installed
+      this module if you have *upgraded* an existing installation.
+      
 	- Fix bug in CollectionArticle, SimpleInput, SecondaryArticle, and 
 	  SimpleArticle that caused objects created to have 'memory'.
 	- Updated the MOBY::Client::ServiceInstance module to reflect


From kawas at dev.open-bio.org  Fri Apr  3 12:50:50 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:50:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031650.n33GooYS011703@dev.open-bio.org>


kawas
Fri Apr  3 12:50:50 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv11668/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-update-db.pl 
Log Message:

moby-live/Perl/MOBY-Server/bin/scripts moby-s-update-db.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-update-db.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-update-db.pl	2009/04/03 16:35:56	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-update-db.pl	2009/04/03 16:50:50	1.2
@@ -99,7 +99,7 @@
 	unless ( $category =~ m/cgi\-async/i ) {
 		$go
 		  && $dbh->do(
-" alter table service_instance modify category ENUM('moby','soap','wsdl','cgi','moby-async', 'cgi-async', 'doc-literal', 'doc-literal-async', 'cgi-async') default NULL"
+" alter table service_instance modify category ENUM('moby','soap','wsdl','cgi','moby-async', 'cgi-async', 'doc-literal', 'doc-literal-async') default NULL"
 		  );
 	}
 


From kawas at dev.open-bio.org  Fri Apr  3 12:52:21 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:52:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031652.n33GqL5w011787@dev.open-bio.org>


kawas
Fri Apr  3 12:52:21 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv11752/Perl/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:
specify that we need to install the shared script moby-s-update-db.pl
moby-live/Perl/MOBY-Server Makefile.PL,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/01/28 14:25:29	1.14
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/03 16:52:21	1.15
@@ -70,6 +70,7 @@
 
 	install_script 'bin/scripts/moby-s-install.pl';
 	install_script 'bin/scripts/moby-s-caching.pl';
+	install_script 'bin/scripts/moby-s-update-db.pl';
 
 	install_share 'share';
 


From kawas at dev.open-bio.org  Fri Apr  3 13:01:31 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 13:01:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031701.n33H1Vha012013@dev.open-bio.org>


kawas
Fri Apr  3 13:01:30 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv11978/Perl/MOBY-Client

Modified Files:
	Changes 
Log Message:
updated to reflect recent changes.
moby-live/Perl/MOBY-Client Changes,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes	2009/02/12 19:34:17	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes	2009/04/03 17:01:30	1.8
@@ -14,8 +14,11 @@
 	   *  Added the function 'raw_execute' to MOBY::Async::Service to
 		  allow calling of services with raw XML similarly to the method
 		  in MOBY::Client::Service.
-	   * Fixed typo in MOBY::Client::Service that refered to POST 
+	   *  Fixed typo in MOBY::Client::Service that refered to POST 
 		  services as category 'post' rather than 'cgi'
+	   *  Added the category 'cgi-async' to the list of service
+	      categories that are allowed.
+
 1.03
        * changes to makefile reflecting the cpan addition of wsrf
        * added MOBY/Async.pm to the module


From kawas at dev.open-bio.org  Mon Apr  6 10:16:40 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 6 Apr 2009 10:16:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904061416.n36EGe9s025783@dev.open-bio.org>


kawas
Mon Apr  6 10:16:39 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv25739/Perl/MOBY-Server

Modified Files:
	Makefile.PL META.yml Changes 
Log Message:
had junk  in the cpan version of META.yml so I am generating another version of the module with META.yml fixed
moby-live/Perl/MOBY-Server Makefile.PL,1.15,1.16 META.yml,1.6,1.7 Changes,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/03 16:52:21	1.15
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/06 14:16:39	1.16
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.07';
+	version '1.08';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2009/01/28 14:25:29	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2009/04/06 14:16:39	1.7
@@ -44,4 +44,4 @@
   XML::SemanticCompare: 0
   XML::Simple: 2.18
   WSRF::Lite: 0.8.2.5
-version: 1.07
+version: 1.08

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/03 16:41:36	1.22
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/06 14:16:39	1.23
@@ -1,5 +1,8 @@
 Revision history for Perl extension MOBY.
 
+1.08
+    - Fixed META.yml in the distribution. Please refer to changes for 1.07.
+
 1.07
     - Important: run the script moby-s-update-db once you have installed
       this module if you have *upgraded* an existing installation.


From kawas at dev.open-bio.org  Tue Apr  7 11:33:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 11:33:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071533.n37FXAMY002942@dev.open-bio.org>


kawas
Tue Apr  7 11:33:09 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv2907/src/main/org/biomoby/service/dashboard

Modified Files:
	PerlMoSeSPanel.java 
Log Message:
added an option for generating Async HTTP POST services.
moby-live/Java/src/main/org/biomoby/service/dashboard PerlMoSeSPanel.java,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java	2008/11/03 19:47:45	1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java	2009/04/07 15:33:09	1.15
@@ -79,28 +79,31 @@
     // String: set this for an information message
     static String PM_INFORMATION = "perl-moses-information";
 
-    // boolean - do we over write files
+    // String - do we over write files
     static String PM_OVERWRITE = "perl-moses-overwrite";
 
-    // boolean: do we generate cgi services
+    // String: do we generate cgi services
     static String PM_CGI = "perl-moses-cgi";
     
-    // boolean do we generate soap services
+    // String: do we generate soap services
     static String PM_SOAP = "perl-moses-soap";
     
-    // boolean do we generate async services
+    // String: do we generate async services
     static String PM_ASYNC = "perl-moses-async";
+    
+    // String: do we generate async cgi services
+    static String PM_CGI_ASYNC = "perl-moses-cgi-async";
 
-    // boolean: are we currently updating the datatype cache
+    // String:: are we currently updating the datatype cache
     static String PM_SYNC_DATATYPES = "perl-moses-sync-datatypes";
 
-    // boolean: are we currently updating the services cache
+    // String: are we currently updating the services cache
     static String PM_SYNC_SERVICES = "perl-moses-sync-services";
 
-    // boolean: are we generating services by name
+    // String: are we generating services by name
     static String PM_GENERATING_SPECIFIC_SERVICES = "perl-moses-generating-specific-services";
 
-    // boolean: are we generating services by authority
+    // String: are we generating services by authority
     static String PM_GENERATING_BY_AUTHORITY = "perl-moses-generating-by-authority";
 
     // N/A: set this to make the editor save the current file
@@ -301,6 +304,7 @@
 	propertyChannel.put(PM_SYNC_DATATYPES, new Boolean(false));
 	propertyChannel.put(PM_OVERWRITE, new Boolean(false));
 	propertyChannel.put(PM_CGI, new Boolean(false));
+	propertyChannel.put(PM_CGI_ASYNC, new Boolean(false));
 	propertyChannel.put(PM_ASYNC, new Boolean(false));
 
 	propertyChannel.put(PM_PERL_INSTALL_DIR, getPrefValue(PM_PERL_INSTALL_DIR, ""));
@@ -518,16 +522,18 @@
 		});
 	generateBtn.setEnabled(enable_moses_actions);
 	ButtonGroup group = new ButtonGroup();
-	JRadioButton genCgi, genSoap, genAsync;
+	JRadioButton genCgi, genCgiAsync, genSoap, genAsync;
 	group.add (genCgi      = createHowToButton ("Generate CGI Service", PM_CGI));
+	group.add (genCgiAsync = createHowToButton ("Generate ASYNC CGI Service", PM_CGI_ASYNC));
 	group.add (genSoap     = createHowToButton ("Generate SOAP Service", PM_SOAP));
-	group.add (genAsync     = createHowToButton ("Generate ASYNC Service", PM_ASYNC));
+	group.add (genAsync    = createHowToButton ("Generate ASYNC SOAP Service", PM_ASYNC));
 	
 	SwingUtils.addComponent(bPanel, genOverwrite, 0, 0, 1, 1, NONE, NWEST, 0.0, 0.0);
 	SwingUtils.addComponent(bPanel, genCgi,       0, 1, 2, 1, NONE, NWEST, 0.0, 0.0);
-	SwingUtils.addComponent(bPanel, genSoap,      0, 2, 2, 1, NONE, NWEST, 0.0, 0.0);
-	SwingUtils.addComponent(bPanel, genAsync,     0, 3, 2, 1, NONE, NWEST, 0.0, 0.0);
-	SwingUtils.addComponent(bPanel, generateBtn,  0, 4, 2, 1, HORI, NWEST, 0.0, 0.0);
+	SwingUtils.addComponent(bPanel, genCgiAsync,  0, 2, 2, 1, NONE, NWEST, 0.0, 0.0);
+	SwingUtils.addComponent(bPanel, genSoap,      0, 3, 2, 1, NONE, NWEST, 0.0, 0.0);
+	SwingUtils.addComponent(bPanel, genAsync,     0, 4, 2, 1, NONE, NWEST, 0.0, 0.0);
+	SwingUtils.addComponent(bPanel, generateBtn,  0, 5, 2, 1, HORI, NWEST, 0.0, 0.0);
 
 	// add to the main panel
 	int count = 0;
@@ -826,6 +832,7 @@
 	    radio.setSelected (true);
 	    radio.setEnabled (true);
 	    propertyChannel.put (PM_CGI, false);
+	    propertyChannel.put (PM_CGI_ASYNC, false);
 	    propertyChannel.put (PM_ASYNC, false);
 	}
 	return radio;
@@ -834,6 +841,7 @@
 	    public void actionPerformed (ActionEvent e) {
 		String howTo = e.getActionCommand();
 		propertyChannel.put (PM_CGI, howTo.equals(PM_CGI));
+		propertyChannel.put (PM_CGI_ASYNC, howTo.equals(PM_CGI_ASYNC));
 		propertyChannel.put (PM_ASYNC, howTo.equals(PM_ASYNC));
 		propertyChannel.put (PM_SOAP, howTo.equals(PM_SOAP));
 	    }
@@ -1110,6 +1118,9 @@
 			} else if (Boolean.parseBoolean(propertyChannel
 				.getString(PM_ASYNC))){
 			    command.add("-A");
+			} else if (Boolean.parseBoolean(propertyChannel
+				.getString(PM_CGI_ASYNC))){
+			    command.add("-C");
 			} 
 			command.add(authority);
 			// place command into com
@@ -1205,6 +1216,9 @@
 			} else if (Boolean.parseBoolean(propertyChannel
 				.getString(PM_ASYNC))){
 			    command.add("-A");
+			} else if (Boolean.parseBoolean(propertyChannel
+				.getString(PM_CGI_ASYNC))){
+			    command.add("-C");
 			}
 			command.add(auth);
 			command.add(name);


From kawas at dev.open-bio.org  Tue Apr  7 11:42:39 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 11:42:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071542.n37FgdTG003021@dev.open-bio.org>


kawas
Tue Apr  7 11:42:39 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help
In directory dev.open-bio.org:/tmp/cvs-serv2986/src/main/org/biomoby/service/dashboard/help

Modified Files:
	PerlMoSeSPanel.html 
Log Message:
updated the doc to include both async soap and cgi service generation.
formatted the html for easy reading/writing
moby-live/Java/src/main/org/biomoby/service/dashboard/help PerlMoSeSPanel.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html	2008/06/05 19:46:14	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html	2009/04/07 15:42:39	1.5
@@ -1,98 +1,294 @@
 <h1>Perl MoSeS: Generate &amp; Edit Code</h1>
-<p> This panel is a user-interface to the Perl MoSeS
-  sub-project. <em>MoSeS</em> stands for <em>Moby Services Support</em> and its documentation is available at:<br />
-  	http://search.cpan.org/dist/MOSES-MOBY/lib/MOSES/MOBY.pm</p>
-<p> In order to use this panel, you will have to ensure that you (or your 
-  sys admin) have installed <strong>Perl</strong> and the CPAN module MOSES::MOBY (http://search.cpan.org/dist/MOSES-MOBY/).
-  
-  Once that module has been installed <strong>and</strong> you have performed the 
-  user configuration step (<strong><em>moses-install.pl</em></strong>), 
-  you will be able use this panel! </p>
-<p><font color="#FF0000" size="+1"><strong><em>Once again, this panel is only useful in those situations that you have installed the CPAN module '</em>MOSES::MOBY<em>' and have run the user configuration script </em>'moses-install.pl<em>'!</em></strong></font></p>
-<p> The panel has two different parts - one <b><a href="#gen">generates code</a></b> for the
-  selected services, and one provides you with an <b><a href="#editor">editor</a></b> to aid  
-  in writing the business logic for any service that you generate with this 
-  Perl-MoSeS.  </p>
-<p> For both parts, you need to start by selecting a service, services,
-  or authority in the services tree. Multiple selection is possible using
-  <em><strong>SHIFT</strong></em> or <em><strong>CONTROL</strong></em>. If you select an authority, all services from this
-  authority are considered selected. </p>
-<p> All activities are done in the background using the command line utilities installed by the Perl-MoSeS module. </p>
-<p>&nbsp;</p>
+<p>
+    This panel is a user-interface to the Perl MoSeS 
+    sub-project. <em>MoSeS</em>
+    stands for <em>Moby Services Support</em>
+    and its documentation is available at:
+    <br/>
+    http://search.cpan.org/dist/MOSES-MOBY/lib/MOSES/MOBY.pm
+</p>
+<p>
+    In order to use this panel, you will have to ensure that you (or your 
+    sys admin) have installed <strong>Perl</strong>
+    and the CPAN module MOSES::MOBY (http://search.cpan.org/dist/MOSES-MOBY/).
+    Once that module has been installed <strong>and</strong>
+    you have performed the 
+    user configuration step (<strong><em>moses-install.pl</em></strong>), 
+    you will be able use this panel! 
+</p>
+<p>
+    <font color="#FF0000" size="+1">
+        <strong><em>Once again, this panel is only useful in those situations that you have installed the CPAN module '</em>MOSES::MOBY<em>' and have run the user configuration script </em>'moses-install.pl<em>'!</em></strong>
+    </font>
+</p>
+<p>
+    The panel has two different parts - one <b><a href="#gen">generates code</a></b>
+    for the 
+    selected services, and one provides you with an <b><a href="#editor">editor</a></b>
+    to aid 
+    in writing the business logic for any service that you generate with this  
+    Perl-MoSeS. 
+</p>
+<p>
+    For both parts, you need to start by selecting a service, services,
+    or authority in the services tree. Multiple selection is possible using<em><strong>SHIFT</strong></em>
+    or <em><strong>CONTROL</strong></em>. If you select an authority, all services from this 
+    authority are considered selected. 
+</p>
+<p>
+    All activities are done in the background using the command line utilities installed by the Perl-MoSeS module. 
+</p>
+<p>
+    &nbsp;
+</p>
 <h2>Perl-MoSeS sub panel</h2>
-<p>The Perl-MoSeS sub panel allows you to:</p>
-<ul><li><strong><a href="#gen">Generate</a></strong> -  generate perl modules for services that you select,</li>
-  <li><a href="#local_user_config"><strong>Local User Config</strong></a> - for those users without root access when they installed Perl-MoSeS<em><strong>*</strong></em></li>
+<p>
+    The Perl-MoSeS sub panel allows you to:
+</p>
+<ul>
+    <li>
+        <strong><a href="#gen">Generate</a></strong>
+        -  generate perl modules for services that you select,
+    </li>
+    <li>
+        <a href="#local_user_config"><strong>Local User Config</strong></a>
+        - for those users without root access when they installed Perl-MoSeS<em><strong>*</strong></em>
+    </li>
 </ul>
 <blockquote>
-  <p><em><strong>* when the panel is created, it makes a best attempt to determine whether or not the cpan module MOSES-MOBY was installed as root. If it was not, this sub panel is visible.</strong></em></p>
+    <p>
+        <em><strong>* when the panel is created, it makes a best attempt to determine whether or not the cpan module MOSES-MOBY was installed as root. If it was not, this sub panel is visible.</strong></em>
+    </p>
 </blockquote>
-<p><em><strong>Possible caveats:</strong></em></p>
+<p>
+    <em><strong>Possible caveats:</strong></em>
+</p>
 <ul>
-  <li> The actions in this panel depend on the availability of certain command line tools (installed by MOSES-MOBY, when you did <em><strong>'make install'</strong></em> of the cpan module) being available on the system PATH.</li>
+    <li>
+        The actions in this panel depend on the availability of certain command line tools (installed by MOSES-MOBY, when you did <em><strong>'make install'</strong></em>
+        of the cpan module) being available on the system PATH.
+    </li>
 </ul>
 <h3><a name="gen" id="gen"></a>Generate</h3>
-<p> There is one <em><strong>generator</strong></em> in this panel for creating services, with a couple of options.</p>
+<p>
+    There is one <em><strong>generator</strong></em>
+    in this panel for creating services, with a couple of options.
+</p>
 <ul>
-  <li><strong>Overwrite Existing Code</strong> - use this to overwrite any service code that has already been generated with MoSeS</li>
-  <li><strong>Generate CGI Service</strong> - use this to generate a category '<em><strong>cgi</strong></em>' BioMOBY web service.</li>
-  <li><strong>Generate SOAP Service</strong> - use this to generate a category '<em><strong>moby</strong></em>' BioMOBY web service.</li>
-</ul>
-<p>Once you have chosen your desired options, you can click on the <strong>Generate Skeletons</strong> button. This will go through and generate perl modules that represent the services that you selected in the '<em><strong>Service Browser</strong></em>'.</p>
-<p>All files are generated into your local <strong><em>Perl-MoSeS/</em></strong> installation. For instance, <em><strong>assuming</strong></em> that your <strong>username</strong> is <em><strong>moby_user</strong></em> and that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em>, then you could <strong>find</strong> your <strong>service skeletons</strong> in <em><strong>/home/moby_user/Perl-MoSeS/services/Service/</strong></em> directory.</p>
-<p>When you generate CGI based moby services, an additional file is generated into <em><strong>/Perl-MoSeS/cgi/</strong></em>. In order to <strong>implement the business logic</strong>, only the <strong>skeletons mentioned above</strong> are required. The files in the c<em><strong>gi/</strong></em> directory are only used for <strong>deploying your services</strong>.</p>
+    <li>
+        <strong>Overwrite Existing Code</strong>
+        - use this to overwrite any service code that has already been generated with MoSeS
+    </li>
+    <li>
+        <strong>Generate CGI Service</strong>
+        - use this to generate a category '<em><strong>cgi</strong></em>' BioMOBY web service.
+    </li>
+	<li>
+        <strong>Generate ASYNC CGI Service</strong>
+        - use this to generate a category '<em><strong>cgi-async</strong></em>' BioMOBY web service.
+    </li>
+    <li>
+        <strong>Generate SOAP Service</strong>
+        - use this to generate a category '<em><strong>moby</strong></em>' BioMOBY web service.
+    </li>
+	<li>
+        <strong>Generate ASYNC SOAP Service</strong>
+        - use this to generate a category '<em><strong>moby-async</strong></em>' BioMOBY web service.
+    </li>
+</ul>
+<p>
+    Once you have chosen your desired options, you can click on the <strong>Generate Skeletons</strong>
+    button. This will go through and generate perl modules that represent the services that you selected in the '<em><strong>Service Browser</strong></em>'.
+</p>
+<p>
+    All files are generated into your local <strong><em>Perl-MoSeS/</em></strong>
+    installation. For instance, <em><strong>assuming</strong></em>
+    that your <strong>username</strong>
+    is <em><strong>moby_user</strong></em>
+    and that your <strong>home directory</strong>
+    is <em><strong>/home/moby_user/</strong></em>, then you could <strong>find</strong>
+    your <strong>service skeletons</strong>
+    in <em><strong>/home/moby_user/Perl-MoSeS/services/Service/</strong></em>
+    directory.
+</p>
+<p>
+    When you generate CGI based moby services, an additional file is generated into <em><strong>/Perl-MoSeS/cgi/</strong></em>. In order to <strong>implement the business logic</strong>, only the <strong>skeletons mentioned above</strong>
+    are required. The files in the c<em><strong>gi/</strong></em>
+    directory are only used for <strong>deploying your services</strong>.
+</p>
 <h3><a name="local_user_config" id="local_user_config"></a>Local User Config</h3>
-<p>The configuration sub panel allows you to specify:</p>
+<p>
+    The configuration sub panel allows you to specify:
+</p>
 <ul>
-  <li><strong>Perl Install Path</strong> - this is the path to the PERL executable, for instance, /usr/bin/perl <strong><em>[required]</em></strong></li>
-  <li><strong>PERL5LIB dir</strong> - a directory to add to Perls' <strong>@INC <em>[required]</em></strong></li>
-  <li><strong>PERL5LIB dir(2)</strong> - another directory to add to Perls' <strong>@INC</strong> <strong><em>[optional]</em></strong></li>
-  <li><strong>MoSeS Scripts Dir </strong>- the directory that contains the moses-*.pl scripts <em><strong>[required]</strong></em></li>
+    <li>
+        <strong>Perl Install Path</strong>
+        - this is the path to the PERL executable, for instance, /usr/bin/perl <strong><em>[required]</em></strong>
+    </li>
+    <li>
+        <strong>PERL5LIB dir</strong>
+        - a directory to add to Perls' <strong>@INC <em>[required]</em></strong>
+    </li>
+    <li>
+        <strong>PERL5LIB dir(2)</strong>
+        - another directory to add to Perls' <strong>@INC</strong>
+        <strong><em>[optional]</em></strong>
+    </li>
+    <li>
+        <strong>MoSeS Scripts Dir </strong>- the directory that contains the moses-*.pl scripts <em><strong>[required]</strong></em>
+    </li>
 </ul>
-<p>Once this information is entered, and the <em><strong>'Confirm values are correct'</strong></em> is clicked, we check whether the required MOSES scripts are accessible. If everything is deemed to be fine, the other sub panels are enabled. Otherwise, you will be prompted to check your values.</p>
+<p>
+    Once this information is entered, and the <em><strong>'Confirm values are correct'</strong></em>
+    is clicked, we check whether the required MOSES scripts are accessible. If everything is deemed to be fine, the other sub panels are enabled. Otherwise, you will be prompted to check your values.
+</p>
 <h4>Help on setting your local user configuration</h4>
-<p>Some users find this information hard to obtain. One trick that I use, is to enter 'perl -V' at the command prompt. Among other things, one of the last things that you will see displayed is something like:</p>
+<p>
+    Some users find this information hard to obtain. One trick that I use, is to enter 'perl -V' at the command prompt. Among other things, one of the last things that you will see displayed is something like:
+</p>
 <pre>Built under linux<br />  Compiled at Nov 27 2007 10:44:36<br />  @INC:<br />    /etc/perl<br />    /usr/local/lib/perl/5.8.8<br />    /usr/local/share/perl/5.8.8<br />    /usr/lib/perl5<br />    /usr/share/perl5<br />    /usr/lib/perl/5.8<br />    /usr/share/perl/5.8<br />    /usr/local/lib/site_perl<br />    .</pre>
-<p>Keeping the above in mind and remembering that when you installed (locally for just you and not system wide!) MOSES-MOBY from the command prompt, you specified a <strong>PREFIX</strong>=/some/path/, similar to the following:</p>
+<p>
+    Keeping the above in mind and remembering that when you installed (locally for just you and not system wide!) MOSES-MOBY from the command prompt, you specified a <strong>PREFIX</strong>=/some/path/, similar to the following:
+</p>
 <pre>   perl Makefile.PL <strong>PREFIX</strong>=/home/ekawas/usr/local</pre>
-<p>The values that you would then enter for <strong>PERL5LIB</strong> are:</p>
+<p>
+    The values that you would then enter for <strong>PERL5LIB</strong>
+    are:
+</p>
 <ul>
-  <li>/home/ekawas/usr/local/lib/perl/5.8.8</li>
-  <li>/home/ekawas/usr/local/lib/site_perl</li>
+    <li>
+        /home/ekawas/usr/local/lib/perl/5.8.8
+    </li>
+    <li>
+        /home/ekawas/usr/local/lib/site_perl
+    </li>
 </ul>
-<p>In other words, you are interested in using the <strong>PREFIX</strong><em><strong>/lib/</strong></em> directories. </p>
-<p>The value that you should set for the <strong>'MoSeS Scripts Directory'</strong> are usually located in the <strong>PREFIX<em>/bin/</em></strong> directory.</p>
-<p>&nbsp;</p>
+<p>
+    In other words, you are interested in using the <strong>PREFIX</strong>
+    <em><strong>/lib/</strong></em>
+    directories. 
+</p>
+<p>
+    The value that you should set for the <strong>'MoSeS Scripts Directory'</strong>
+    are usually located in the <strong>PREFIX<em>/bin/</em></strong>
+    directory.
+</p>
+<p>
+    &nbsp;
+</p>
 <h2>Perl-MoSeS: Editor sub panel</h2>
-<p>This sub panel consists of an editor pane with various tools that will allow you to open and edit perl scripts generated by Perl-MoSeS. One of the nicer features of this editor, is the syntax highlighing that it performs on perl scripts.</p>
+<p>
+    This sub panel consists of an editor pane with various tools that will allow you to open and edit perl scripts generated by Perl-MoSeS. One of the nicer features of this editor, is the syntax highlighing that it performs on perl scripts.
+</p>
 <h3><a name="editor" id="editor"></a>Editor</h3>
-<p>The editor allows you to open and easily edit perl scripts that you generate with MoSeS.</p>
-<p>The editor has a really simple interface:</p>
+<p>
+    The editor allows you to open and easily edit perl scripts that you generate with MoSeS.
+</p>
+<p>
+    The editor has a really simple interface:
+</p>
 <ul>
-  <li><strong>Open</strong> - used to open a perl script.</li>
-  <li><strong>Save</strong> - used to save an open script.</li>
-  <li><strong>Close</strong> - used to remove the script from view.</li>
-  <li><strong>Font</strong> - used to select a font for the editor.</li>
+    <li>
+        <strong>Open</strong>
+        - used to open a perl script.
+    </li>
+    <li>
+        <strong>Save</strong>
+        - used to save an open script.
+    </li>
+    <li>
+        <strong>Close</strong>
+        - used to remove the script from view.
+    </li>
+    <li>
+        <strong>Font</strong>
+        - used to select a font for the editor.
+    </li>
 </ul>
-<p>There are also a two buttons for enlarging or shrinking the text in the editor. All of these buttons are located on a toolbar that you can detach from the panel.</p>
+<p>
+    There are also a two buttons for enlarging or shrinking the text in the editor. All of these buttons are located on a toolbar that you can detach from the panel.
+</p>
 <h2>&nbsp;</h2>
 <h2>Service deployment</h2>
-<p>Once you have created your service, you will want to deploy it. Depending on whether you have generated a SOAP service or a CGI based service, the steps to involved to deploy your service.</p>
+<p>
+    Once you have created your service, you will want to deploy it. Depending on whether you have generated a SOAP service or a CGI based service, the steps to involved to deploy your service.
+</p>
 <h3>Deploying a SOAP Service</h3>
-<p>Deploying a SOAP based service is both easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.</p>
-<p>An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong> is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em> and that your <strong>cgi-bin directory</strong> is located at <em><strong>/usr/lib/cgi-bin</strong></em>.</p>
-<p></p>
+<p>
+    Deploying a SOAP based service is both easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.
+</p>
+<p>
+    An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong>
+    is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+    is <em><strong>/home/moby_user/</strong></em>
+    and that your <strong>cgi-bin directory</strong>
+    is located at <em><strong>/usr/lib/cgi-bin</strong></em>.
+</p>
+<p>
+</p>
 <pre>   cd /usr/lib/cgi-bin
    sudo ln -s /home/moby_user/Perl-MoSeS/MobyServer.cgi .</pre>
-<p><strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong></p>
-<p>That is all there is to it. Now you can use <em>Dashboard's</em> <em><strong>Simple Client</strong></em> panel to test your service!</p>
+<p>
+    <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+    That is all there is to it. Now you can use <em>Dashboard's</em>
+    <em><strong>Simple Client</strong></em>
+    panel to test your service!
+</p>
+<h3>Deploying an ASYNC SOAP Service</h3>
+<p>
+    Deploying asynchronous SOAP based service is also easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.
+</p>
+<p>
+    An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong>
+    is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+    is <em><strong>/home/moby_user/</strong></em>
+    and that your <strong>cgi-bin directory</strong>
+    is located at <em><strong>/usr/lib/cgi-bin</strong></em>.
+</p>
+<p>
+</p>
+<pre>   cd /usr/lib/cgi-bin
+   sudo ln -s /home/moby_user/Perl-MoSeS/AsyncMobyServer.cgi .</pre>
+<p>
+    <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+    That is all there is to it. Now you can use <em>Dashboard's</em>
+    <em><strong>Simple Client</strong></em>
+    panel to test your service!
+</p>
 <h3>Deploying a CGI Service</h3>
-<p>Deploying a CGI based service is a lot like deploying a SOAP based one. Unfortunately, every CGI based service that you generate requires you to deploy it onto your web server. This is in constrast to the SOAP services mentioned above.</p>
-<p>When you generate CGI services, Perl-MoSeS generates 2 files. Your implementation file and a cgi script to be placed on your web server. Perl-MoSeS only requires you to place a symbolic link to this cgi script in your web servers cgi-bin directory.</p>
-<p>You might ask, where is this cgi script? All cgi scripts generated by Perl-MoSeS are placed in the <strong>Perl-MoSeS/cgi/</strong> directory.</p>
-<p>An example of how to deploy your CGI service is shown below. The example assumes that your <strong>username</strong> is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em> and that your <strong>cgi-bin directory</strong> is located at <em><strong>/usr/lib/cgi-bin</strong></em>. Moreover, we will be deploying the <strong>CGI service</strong> <em><strong>HelloBiomobyWorld</strong></em> that is <strong>provided by</strong> <em><strong>samples.jmoby.net</strong></em>.</p>
-<p></p>
+<p>
+    Deploying a CGI based service is a lot like deploying a SOAP based one. Unfortunately, every CGI based service that you generate requires you to deploy it onto your web server. This is in constrast to the SOAP services mentioned above.
+</p>
+<p>
+    When you generate CGI services, Perl-MoSeS generates 2 files. Your implementation file and a cgi script to be placed on your web server. Perl-MoSeS only requires you to place a symbolic link to this cgi script in your web servers cgi-bin directory.
+</p>
+<p>
+    You might ask, where is this cgi script? All cgi scripts generated by Perl-MoSeS are placed in the <strong>Perl-MoSeS/cgi/</strong>
+    directory.
+</p>
+<p>
+    An example of how to deploy your CGI service is shown below. The example assumes that your <strong>username</strong>
+    is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+    is <em><strong>/home/moby_user/</strong></em>
+    and that your <strong>cgi-bin directory</strong>
+    is located at <em><strong>/usr/lib/cgi-bin</strong></em>. Moreover, we will be deploying the <strong>CGI service</strong>
+    <em><strong>HelloBiomobyWorld</strong></em>
+    that is <strong>provided by</strong>
+    <em><strong>samples.jmoby.net</strong></em>.
+</p>
+<p>
+</p>
 <pre>   cd /usr/lib/cgi-bin
    sudo ln -s /home/moby_user/Perl-MoSeS/cgi/samples/jmoby/net/HelloBiomobyWorld.cgi .</pre>
-<p><strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong></p>
-<p>That is all there is to it. Now you can use <em>Dashboard's</em> <em><strong>Simple Client</strong></em> panel to test your service!</p>
+<p>
+    <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+    That is all there is to it. Now you can use <em>Dashboard's</em>
+    <em><strong>Simple Client</strong></em>
+    panel to test your service!
+</p>


From kawas at dev.open-bio.org  Tue Apr  7 12:21:25 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 12:21:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071621.n37GLP0i003153@dev.open-bio.org>


kawas
Tue Apr  7 12:21:25 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES
In directory dev.open-bio.org:/tmp/cvs-serv3118/MOSES-MOBY/lib/MOSES

Modified Files:
	MOBY.pm 
Log Message:
added some references to async cgi documentation
moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/01/13 19:41:01	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/07 16:21:25	1.8
@@ -123,6 +123,8 @@
 
 =over 4
 
+=item * Support for Asynchronous CGI based moby services
+
 =item * Support for CGI based moby services
 
 =item * Support for Asynchronous based moby services
@@ -2054,6 +2056,7 @@
 
 	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_soap_service.html' target='_blank'>Tutorial for creating SOAP based Biomoby Services</a><br/>
 	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_service.html' target='_blank'>Tutorial for creating CGI based Biomoby Services</a>
+	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html' target='_blank'>Tutorial for creating Asynchronous CGI based Biomoby Services</a>
 	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html' target='_blank'>Tutorial for creating Asynchronous SOAP based Biomoby Services</a>
 
 =end html


From kawas at dev.open-bio.org  Tue Apr  7 12:21:49 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 12:21:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071621.n37GLnkH003211@dev.open-bio.org>


kawas
Tue Apr  7 12:21:49 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv3176/MOSES-MOBY

Modified Files:
	Makefile.PL 
Log Message:
updated version for cpan release
moby-live/Perl/MOSES-MOBY Makefile.PL,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/03/30 13:18:33	1.13
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/07 16:21:49	1.14
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.87';
+	version '0.88';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';


From kawas at dev.open-bio.org  Tue Apr  7 12:29:47 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 12:29:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071629.n37GTlWF003330@dev.open-bio.org>


kawas
Tue Apr  7 12:29:47 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv3295/MOSES-MOBY

Modified Files:
	META.yml 
Log Message:
updated META.yml to include up to date dependencies and to update the modules' version number
moby-live/Perl/MOSES-MOBY META.yml,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2008/05/07 17:26:15	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/07 16:29:47	1.6
@@ -21,18 +21,23 @@
     - t
 requires:
   Carp: 0
+  CGI: 0
   Class::Inspector: 1.17
   Config::Simple: 4.58
   File::HomeDir: 0.65
   File::ShareDir: 0.05
   File::Spec: 0.8
+  HTTP::Date: 5.81
   IO::Prompt: 0.99.2
   IO::Stringy: 2.11
   Log::Log4perl: 1.12
+  MOBY::Client::Central: 1.06
   Params::Util: 0.28
   SOAP::Lite: 0.69
   Template: 1.11
   Unicode::String: 2.09
+  Want: 0.18
+  WSRF::Lite: 0.8.2.5
   XML::LibXML: 1.62
-version: 0.85
+version: 0.88
 


From kawas at dev.open-bio.org  Tue Apr  7 14:13:12 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 14:13:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071813.n37IDCBP003600@dev.open-bio.org>


kawas
Tue Apr  7 14:13:11 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES
In directory dev.open-bio.org:/tmp/cvs-serv3565/MOSES-MOBY/lib/MOSES

Modified Files:
	MOBY.pm 
Log Message:
links to tutorials appear on only one line ... added line breaks to the links
moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/07 16:21:25	1.8
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/07 18:13:11	1.9
@@ -2055,9 +2055,9 @@
 =begin html
 
 	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_soap_service.html' target='_blank'>Tutorial for creating SOAP based Biomoby Services</a><br/>
-	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_service.html' target='_blank'>Tutorial for creating CGI based Biomoby Services</a>
-	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html' target='_blank'>Tutorial for creating Asynchronous CGI based Biomoby Services</a>
-	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html' target='_blank'>Tutorial for creating Asynchronous SOAP based Biomoby Services</a>
+	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_service.html' target='_blank'>Tutorial for creating CGI based Biomoby Services</a><br/>
+	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html' target='_blank'>Tutorial for creating Asynchronous CGI based Biomoby Services</a><br/>
+	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html' target='_blank'>Tutorial for creating Asynchronous SOAP based Biomoby Services</a><br/>
 
 =end html
 


From kawas at dev.open-bio.org  Tue Apr  7 14:48:24 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 14:48:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071848.n37ImO81003683@dev.open-bio.org>


kawas
Tue Apr  7 14:48:24 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t
In directory dev.open-bio.org:/tmp/cvs-serv3648/MOSES-MOBY/t

Modified Files:
	MOSES-MOBY-Cache.t 
Log Message:
changed test to look for != '' rather than a hard coded string because people may be using a non-default registry
moby-live/Perl/MOSES-MOBY/t MOSES-MOBY-Cache.t,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Cache.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Cache.t	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Cache.t	2009/04/07 18:48:24	1.4
@@ -38,7 +38,7 @@
 $cache = new MOSES::MOBY::Cache::Central( );
 ok($cachedir ne $cache->cachedir, "cachedir - default during constructor") 
 	or diag('cachedir was not set properly.');
-ok('default' eq $cache->registry, "registry - default during constructor") 
+ok('' ne $cache->registry, "registry - default during constructor") 
 	or diag('registry was not set properly.');
 ok('' ne $cache->_namespace, "namespace - set during default constructor") 
 	or diag($cache->_namespace . " is not the same as $namespace");


From kawas at dev.open-bio.org  Wed Apr  8 10:51:50 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 10:51:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904081451.n38EpoUE008297@dev.open-bio.org>


kawas
Wed Apr  8 10:51:50 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv8262/MOBY-Server/lib/MOBY

Modified Files:
	Central.pm 
Log Message:
fixed regex that checks datatype name when registering a datatype.
moby-live/Perl/MOBY-Server/lib/MOBY Central.pm,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2009/03/26 18:41:41	1.8
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2009/04/08 14:51:50	1.9
@@ -318,7 +318,7 @@
 	return &_error("Object name may not contain spaces or other characters invalid in a URN",
 		""
 	  )
-	  if $term =~ /\s\"\&\<\>\[\]\^\`\{\|\}\~/;
+	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~]/;
 	if ( $term =~ m"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?" )
 	{    # matches a URI
 		return &_error( "Object name may not be an URN or URI", "" ) if $1;


From kawas at dev.open-bio.org  Wed Apr  8 11:39:40 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 11:39:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904081539.n38FdetE008425@dev.open-bio.org>


kawas
Wed Apr  8 11:39:40 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv8390/MOBY-Server

Modified Files:
	Changes 
Log Message:

moby-live/Perl/MOBY-Server Changes,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/06 14:16:39	1.23
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/08 15:39:40	1.24
@@ -1,5 +1,9 @@
 Revision history for Perl extension MOBY.
 
+1.09
+    - Fixed bug where data types registered into registry could contain
+      illegal characters.
+    
 1.08
     - Fixed META.yml in the distribution. Please refer to changes for 1.07.
 


From kawas at dev.open-bio.org  Wed Apr  8 12:16:49 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 12:16:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904081616.n38GGnsC008587@dev.open-bio.org>


kawas
Wed Apr  8 12:16:48 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/t
In directory dev.open-bio.org:/tmp/cvs-serv8552/MOBY-Server/t

Modified Files:
	Client-Central.t 
Log Message:
added some tests to test registration of datatypes with characters that break things in their names.
moby-live/Perl/MOBY-Server/t Client-Central.t,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/t/Client-Central.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/t/Client-Central.t	2009/03/26 18:42:20	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/t/Client-Central.t	2009/04/08 16:16:48	1.4
@@ -218,6 +218,94 @@
 $r = $C->deregisterObjectClass( objectType => "Rubbish_Art" );
 
 
+# confirm that we cannot register a datatype with odd characters in its name
+$r = $C->registerObjectClass(
+	(
+	   objectType    => "Rubbish_'Art",
+	   description   => "a human-readable description of the object",
+	   contactEmail  => 'your at email.address',
+	   authURI       => "test.suite.com",
+	   Relationships => {
+						  ISA => [
+								   {
+									 object      => 'Object',
+									 articleName => 'article1'
+								   }
+						  ],
+						  HASA => [
+									{
+									  object      => 'Object',
+									  articleName => 'articleName3'
+									},
+						  ]
+	   }
+	)
+);
+ok( !$r->success, "Object registration correctly failed" )
+  or diag(
+	"Shouldn't be possible to register Object with an invalid character in its name!"
+	  . $r->message );
+$r = $C->deregisterObjectClass( objectType => "Rubbish_'Art" );
+
+# confirm that we cannot register a datatype with odd characters in its name
+$r = $C->registerObjectClass(
+	(
+	   objectType    => "Rubbish_\"Art",
+	   description   => "a human-readable description of the object",
+	   contactEmail  => 'your at email.address',
+	   authURI       => "test.suite.com",
+	   Relationships => {
+						  ISA => [
+								   {
+									 object      => 'Object',
+									 articleName => 'article1'
+								   }
+						  ],
+						  HASA => [
+									{
+									  object      => 'Object',
+									  articleName => 'articleName3'
+									},
+						  ]
+	   }
+	)
+);
+ok( !$r->success, "Object registration correctly failed" )
+  or diag(
+	"Shouldn't be possible to register Object with an invalid character in its name!"
+	  . $r->message );
+$r = $C->deregisterObjectClass( objectType => "Rubbish_\"Art" );
+
+# confirm that we cannot register a datatype with odd characters in its name
+$r = $C->registerObjectClass(
+	(
+	   objectType    => "Rubbish_/Art",
+	   description   => "a human-readable description of the object",
+	   contactEmail  => 'your at email.address',
+	   authURI       => "test.suite.com",
+	   Relationships => {
+						  ISA => [
+								   {
+									 object      => 'Object',
+									 articleName => 'article1'
+								   }
+						  ],
+						  HASA => [
+									{
+									  object      => 'Object',
+									  articleName => 'articleName3'
+									},
+						  ]
+	   }
+	)
+);
+ok( !$r->success, "Object registration correctly failed" )
+  or diag(
+	"Shouldn't be possible to register Object with an invalid character in its name!"
+	  . $r->message );
+$r = $C->deregisterObjectClass( objectType => "Rubbish_/Art" );
+
+
 ##############     NAMESPACE REGISTRATION     ##############
 # Register a new namespace
 my %Namespace = (


From kawas at dev.open-bio.org  Wed Apr  8 16:46:23 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 16:46:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082046.n38KkNM1009086@dev.open-bio.org>


kawas
Wed Apr  8 16:46:23 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv9050/MOSES-MOBY/lib/MOSES/MOBY

Modified Files:
	Async.pm 
Log Message:
MOBY tag was missing from the response.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Async.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm	2009/03/30 13:16:00	1.1
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm	2009/04/08 20:46:23	1.2
@@ -296,7 +296,8 @@
 		$WSRF::WSRP::Private{$property_pid}               = '';
 		$WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
 		$WSRF::WSRP::ResourceProperties{$property_result} =
-		  $out_package_for_this_job->job_by_id( $job->jid )->toXML->toString(0);
+		  #$out_package_for_this_job->job_by_id( $job->jid )->toXML->toString(0);
+		  $out_package_for_this_job->toXML->toString(0);
 		$lock->toFile();
 
 		# Exits the child process


From kawas at dev.open-bio.org  Wed Apr  8 18:40:12 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:40:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082240.n38MeCUO009531@dev.open-bio.org>


kawas
Wed Apr  8 18:40:11 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES
In directory dev.open-bio.org:/tmp/cvs-serv9496/MOSES-MOBY/lib/MOSES

Modified Files:
	MOBY.pm 
Log Message:
updated doc
moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/07 18:13:11	1.9
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/08 22:40:11	1.10
@@ -907,6 +907,8 @@
    rather than load the base" enabled.<p/>
    Option <strong>-c</strong> generates both a <a href="#perl_modules_representing_bases_of_service_implementations">service implementation</a> 
      as well as a CGI dispatcher script.<p/>
+   Option <strong>-C</strong> generates both a <a href="#perl_modules_representing_bases_of_service_implementations">service implementation</a> 
+     as well as an Asynchronous CGI dispatcher script.<p/>
    Option <strong>-A</strong> generates both a <a href="#perl_modules_representing_bases_of_service_implementations">service implementation</a> 
      as well as an asynchronous module (and it updates the dispatcher table, as well).<p/>
    Option <strong>-u</strong> updates the service cache.<p/>
@@ -949,11 +951,11 @@
 IRRI, MIPS, default, iCAPTURE, testing
 $Registries = {
    'testing' => {
-      'namespace' => 'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central',
+      'namespace' => 'http://bioinfo.icapture.ubc.ca/MOBY/Central',
       'public' => 'yes',
       'name' => 'Testing BioMoby registry',
       'contact' => 'Edward Kawas (edward.kawas at gmail.com)',
-      'endpoint' => 'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl'
+      'endpoint' => 'http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl'
       },
    'IRRI' => {
       'namespace' => 'http://cropwiki.irri.org/MOBY/Central',
@@ -967,12 +969,12 @@
        'endpoint' => 'http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl'
        },
    'iCAPTURE' => {
-       'namespace' => 'http://mobycentral.icapture.ubc.ca/MOBY/Central',
+       'namespace' => 'http://moby.ucalgary.ca/MOBY/Central',
        'text' => 'A curated public registry hosted at the iCAPTURE Centre, Vancouver',
        'public' => 'yes',
        'name' => 'iCAPTURE Centre, Vancouver',
        'contact' => 'Edward Kawas (edward.kawas at gmail.com)',
-       'endpoint' => 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'
+       'endpoint' => 'http://moby.ucalgary.ca/moby/MOBY-Central.pl'
        },
    'default' => $Registries->{'iCAPTURE'},
    'MIPS' => {


From kawas at dev.open-bio.org  Wed Apr  8 18:41:26 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:41:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082241.n38MfQnH009592@dev.open-bio.org>


kawas
Wed Apr  8 18:41:26 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv9557/MOBY-Server

Modified Files:
	Changes 
Log Message:
updated changes
moby-live/Perl/MOBY-Server Changes,1.24,1.25
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/08 15:39:40	1.24
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/08 22:41:26	1.25
@@ -3,6 +3,7 @@
 1.09
     - Fixed bug where data types registered into registry could contain
       illegal characters.
+    	* added some tests to Client-Central.t to test for this condition 
     
 1.08
     - Fixed META.yml in the distribution. Please refer to changes for 1.07.


From kawas at dev.open-bio.org  Wed Apr  8 18:41:39 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:41:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082241.n38MfdHA009632@dev.open-bio.org>


kawas
Wed Apr  8 18:41:39 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv9597/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:

moby-live/Perl/MOBY-Server Makefile.PL,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/06 14:16:39	1.16
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/08 22:41:39	1.17
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.08';
+	version '1.09';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';


From kawas at dev.open-bio.org  Wed Apr  8 18:42:51 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:42:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082242.n38MgpDN009728@dev.open-bio.org>


kawas
Wed Apr  8 18:42:51 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv9693/MOSES-MOBY/bin/scripts

Modified Files:
	moses-install.pl 
Log Message:
updated the 'Help' for this script
moby-live/Perl/MOSES-MOBY/bin/scripts moses-install.pl,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-install.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-install.pl	2009/03/30 13:17:04	1.6
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-install.pl	2009/04/08 22:42:51	1.7
@@ -24,6 +24,7 @@
        services.log
        parser.log
        MobyServer.cgi
+       AsyncMobyServer.cgi
     The existing files are not overwritten - unless an option -F
     has been used.
 
@@ -66,7 +67,7 @@
 		check_module ($module);
     }
     # check for async libraries if user wants to ....
-    print STDOUT "Shall we check for the moby-async libraries\n\t(do this only if you plan on creating async moby services)? y/n [n]";
+    print STDOUT "Shall we check for the moby-async libraries\n\t(do this only if you plan on creating soap based\n\t async moby services)? y/n [n]";
     my $tmp = <STDIN>;
     $tmp =~ s/\s//g; 
     if ($tmp =~ /y/i) {


From kawas at dev.open-bio.org  Wed Apr  8 18:43:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:43:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082243.n38MhAwW009830@dev.open-bio.org>


kawas
Wed Apr  8 18:43:10 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv9787/MOSES-MOBY

Modified Files:
	META.yml Changes Makefile.PL 
Log Message:
updated version numbers and history
moby-live/Perl/MOSES-MOBY META.yml,1.6,1.7 Changes,1.11,1.12 Makefile.PL,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/07 16:29:47	1.6
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/08 22:43:10	1.7
@@ -39,5 +39,5 @@
   Want: 0.18
   WSRF::Lite: 0.8.2.5
   XML::LibXML: 1.62
-version: 0.88
+version: 0.89
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/03/30 13:18:33	1.11
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/08 22:43:10	1.12
@@ -1,11 +1,15 @@
 Revision history for Perl extension MOSES::MOBY.
 
+.89 
+	- The tag MOBY was missing in the async cgi
+	  response for 'results'.
+	- updated some documentation
+
 .88 
 	- Added support for Asynchronous POST services.
 	  moses-service-tester, moses-generate-services,
 	  and moses-install all have been updated.
 	  
-
 .87 
 	- fixed a string append bug where '+' was used
 	  instead of '.'

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/07 16:21:49	1.14
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/08 22:43:10	1.15
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.88';
+	version '0.89';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';


From kawas at dev.open-bio.org  Thu Apr  9 09:01:15 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 9 Apr 2009 09:01:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904091301.n39D1Fbl012449@dev.open-bio.org>


kawas
Thu Apr  9 09:01:15 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv12414/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
noticed that one of the 'Actions' was incorrectly labeled, so I fixed it. This should have no effect to MOSES services because we dont really validate this message (psst ... dont tell anyone)
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/02 16:10:14	1.9
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/09 13:01:15	1.10
@@ -581,7 +581,7 @@
 	my ( $url, $id ) = @_;
 	return <<"END OF XML";
 <moby-wsrf>
-<wsa:Action xmlns:wsa="http://www.w3.org/2005/08/addressing">http://docs.oasis-open.org/wsrf/rpw-2/GetResourceProperty/GetResourcePropertiesRequest</wsa:Action>
+<wsa:Action xmlns:wsa="http://www.w3.org/2005/08/addressing">http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest</wsa:Action>
 <wsa:To xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd" xmlns:wsa="http://www.w3.org/2005/08/addressing" wsu:Id="To">$url</wsa:To>
 <mobyws:ServiceInvocationId xmlns:mobyws="http://biomoby.org/" xmlns:wsa="http://www.w3.org/2005/08/addressing" wsa:IsReferenceParameter="true">$id</mobyws:ServiceInvocationId>
 </moby-wsrf>


From kawas at dev.open-bio.org  Wed Apr 15 12:38:57 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:38:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151638.n3FGcvHe021303@dev.open-bio.org>


kawas
Wed Apr 15 12:38:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv21256/MOBY-Server

Modified Files:
	META.yml Changes Makefile.PL MANIFEST 
Log Message:
Added a cgi script that obtains WSDL for services in a RESTful manner. Thank you to Jos? Manuel Rodr?guez Carrasco!
moby-live/Perl/MOBY-Server META.yml,1.7,1.8 Changes,1.25,1.26 Makefile.PL,1.17,1.18 MANIFEST,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2009/04/06 14:16:39	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2009/04/15 16:38:57	1.8
@@ -44,4 +44,4 @@
   XML::SemanticCompare: 0
   XML::Simple: 2.18
   WSRF::Lite: 0.8.2.5
-version: 1.08
+version: 1.10

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/08 22:41:26	1.25
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/15 16:38:57	1.26
@@ -1,5 +1,11 @@
 Revision history for Perl extension MOBY.
 
+1.10
+    - Added a RESTful WSDL page to the installation. Basically, you do
+      a GET on BioMobyWSDL/authURI/servicename/ and a WSDL for that service
+      is returned. 
+      ** Thanks to Jos? Manuel Rodr?guez Carrasco ** 
+
 1.09
     - Fixed bug where data types registered into registry could contain
       illegal characters.

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/08 22:41:39	1.17
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/15 16:38:57	1.18
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.09';
+	version '1.10';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2009/04/03 16:36:35	1.11
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2009/04/15 16:38:57	1.12
@@ -91,6 +91,7 @@
 README
 share/cgi/AgentRDFValidator
 share/cgi/authority.pl
+share/cgi/BioMobyWSDL
 share/cgi/GenerateRDF.cgi
 share/cgi/Moby
 share/cgi/MOBY-Admin.pl


From kawas at dev.open-bio.org  Wed Apr 15 12:38:57 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:38:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151638.n3FGcvpo021339@dev.open-bio.org>


kawas
Wed Apr 15 12:38:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv21256/MOBY-Server/bin/scripts

Modified Files:
	moby-s-install.pl 
Log Message:
Added a cgi script that obtains WSDL for services in a RESTful manner. Thank you to Jos? Manuel Rodr?guez Carrasco!
moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/11/25 19:47:23	1.14
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2009/04/15 16:38:57	1.15
@@ -1481,6 +1481,12 @@
 	    { '#!/usr/bin/perl -w' => "#!$perl_exec", }
 	    );
 	file_from_template(
+	    "$apache_cgi/BioMobyWSDL",
+	    File::ShareDir::dist_file( 'MOBY', 'cgi/BioMobyWSDL' ),
+	    'MOBY-Central RESTful WSDL generator',
+	    { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	    );
+	file_from_template(
 	    "$apache_cgi/ServicePingerValidator",
 	    File::ShareDir::dist_file(
 		'MOBY', 'cgi/ServicePingerValidator'


From kawas at dev.open-bio.org  Wed Apr 15 12:38:57 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:38:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151638.n3FGcvND021318@dev.open-bio.org>


kawas
Wed Apr 15 12:38:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv21256/MOBY-Server/share/cgi

Added Files:
	BioMobyWSDL 
Log Message:
Added a cgi script that obtains WSDL for services in a RESTful manner. Thank you to Jos? Manuel Rodr?guez Carrasco!
moby-live/Perl/MOBY-Server/share/cgi BioMobyWSDL,NONE,1.1

From kawas at dev.open-bio.org  Wed Apr 15 12:54:25 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:54:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151654.n3FGsP4w021422@dev.open-bio.org>


kawas
Wed Apr 15 12:54:25 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv21387/MOBY-Server/share/cgi

Modified Files:
	Moby 
Log Message:
Added an example for BioMobyWSDL to the list of installed scripts.
moby-live/Perl/MOBY-Server/share/cgi Moby,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/Moby,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/Moby	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/Moby	2009/04/15 16:54:25	1.2
@@ -277,6 +277,18 @@
 target="_blank">click here.</a><br/>
   </p>
 </blockquote>
+<p><a href="http://$location/cgi-bin/BioMobyWSDL/">BioMobyWSDL 
+</a> - RESTful app that returns WSDL for a given service. 
+</p>
+<blockquote>
+  <p>For example,</p>
+  <ol>
+    <li><a href="http://$location/cgi-bin/BioMobyWSDL/bioinfo.icapture.ubc.ca/getGoTerm">WSDL for getGoTerm, 
+    by the authority bioinfo.icapture.ubc.ca </a></li>
+  </ol>
+  <p>All that you have to do is append <strong><em>authURI/servicename</em></strong> to the path of the script. <br/>
+  The WSDL for that service, if it exists, will be returned!</p>
+</blockquote>
 <p><a href="http://$location/cgi-bin/RESOURCES/">The Resources 'Scripts' 
 </a> - Servlets that return the RDF representations of the BioMOBY 
 ontologies. </p>


From kawas at dev.open-bio.org  Wed Apr 15 12:56:01 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:56:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151656.n3FGu12b021462@dev.open-bio.org>


kawas
Wed Apr 15 12:56:01 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv21427/MOBY-Server/share/cgi

Modified Files:
	BioMobyWSDL 
Log Message:
fixed the $id: $ portion of the script at the top to correctly display script name and version
moby-live/Perl/MOBY-Server/share/cgi BioMobyWSDL,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL	2009/04/15 16:38:57	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL	2009/04/15 16:56:01	1.2
@@ -1,6 +1,6 @@
 #!/usr/bin/perl -W
 # _________________________________________________________________
-#$Id: getMOBYWSDL,v 1.0
+# $Id$
 # Developed by: Jose Manuel Rodriguez Carrasco -jmrodriguez at cnio.es-
 # Created: 13-April-2009
 # Updated: 14-April-2009


From kawas at dev.open-bio.org  Wed Apr 15 13:45:23 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 13:45:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151745.n3FHjN5u021811@dev.open-bio.org>


kawas
Wed Apr 15 13:45:23 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv21776/MOBY-Server/lib/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
got fed up of seeing a warning from CommonSubs, so I fixed the underlying problem
moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm	2008/09/22 15:42:27	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm	2009/04/15 17:45:23	1.7
@@ -1171,7 +1171,17 @@
       . "\n called from line $line";
     return '';
   }
-  return ( $xref->getAttributeNode($attr) || $xref->getAttributeNode( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr" ) );
+  # check for just the attribute by name
+  return $xref->getAttributeNode($attr)
+    if $xref->getAttributeNode($attr);
+  # check for a namespaced attribute by name
+  return $xref->getAttributeNodeNS('http://www.biomoby.org/moby', $attr)
+  	if $xref->getAttributeNodeNS('http://www.biomoby.org/moby', $attr);
+  # check for a namespaced attribute with a prefix ... this is probably redundant!
+  return $xref->getAttributeNode( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") 
+  	if $xref->lookupNamespacePrefix('http://www.biomoby.org/moby');
+  # cant find it ...
+  return '';
 }
 
 sub _moby_getAttribute {
@@ -1191,7 +1201,18 @@
     . "\n called from line $line";
     return '';
   }
-  return (   $xref->getAttribute($attr) || $xref->getAttribute( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") );
+  
+  # check for just the attribute by name
+  return $xref->getAttribute($attr)
+    if $xref->getAttribute($attr);
+  # check for a namespaced attribute by name
+  return $xref->getAttributeNS('http://www.biomoby.org/moby', $attr)
+  	if $xref->getAttributeNS('http://www.biomoby.org/moby', $attr);
+  # check for a namespaced attribute with a prefix ... this is probably redundant!
+  return $xref->getAttribute( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") 
+  	if $xref->lookupNamespacePrefix('http://www.biomoby.org/moby');
+  # cant find it ...
+  return '';
 }
 
 sub _makeXrefType {


From kawas at dev.open-bio.org  Wed Apr 15 13:45:23 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 13:45:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151745.n3FHjNln021829@dev.open-bio.org>


kawas
Wed Apr 15 13:45:23 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv21776/MOBY-Server

Modified Files:
	Changes 
Log Message:
got fed up of seeing a warning from CommonSubs, so I fixed the underlying problem
moby-live/Perl/MOBY-Server Changes,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/15 16:38:57	1.26
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/15 17:45:23	1.27
@@ -5,6 +5,9 @@
       a GET on BioMobyWSDL/authURI/servicename/ and a WSDL for that service
       is returned. 
       ** Thanks to Jos? Manuel Rodr?guez Carrasco ** 
+    - Updated _moby_getAttribute and _moby_getAttributeNode so that the
+      warning regarding unitialized value is no longer given when running
+      t/CommonSubs.t or using CommonSubs.pm.
 
 1.09
     - Fixed bug where data types registered into registry could contain


From kawas at dev.open-bio.org  Thu Apr 16 14:13:03 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Apr 2009 14:13:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904161813.n3GID3hI029989@dev.open-bio.org>


kawas
Thu Apr 16 14:13:03 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates
In directory dev.open-bio.org:/tmp/cvs-serv29954/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service-cgi-async.tt 
Log Message:
added a check for \r because our service message was been misinterpreted ...
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service-cgi-async.tt,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt	2009/04/02 14:53:26	1.2
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt	2009/04/16 18:13:03	1.3
@@ -117,8 +117,10 @@
 sub call_service {
 	# get the data from the 'data' parameter
 	my $data = $q->param('data') || $q->param('POSTDATA') || "";
+	# remove any \r because these cause errors in our messages with newlines
+	$data =~ s/\r//gi;
 	# call the service
-	 __PACKAGE__->[% obj.name %]($data);
+	__PACKAGE__->[% obj.name %]($data);
 	
 }
 


From kawas at dev.open-bio.org  Thu Apr 16 14:14:34 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Apr 2009 14:14:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904161814.n3GIEYoT030047@dev.open-bio.org>


kawas
Thu Apr 16 14:14:34 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30012/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent changes.
moby-live/Perl/MOSES-MOBY Changes,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/08 22:43:10	1.12
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/16 18:14:34	1.13
@@ -1,5 +1,10 @@
 Revision history for Perl extension MOSES::MOBY.
 
+.90
+	- bug fix: when sending data with newlines on
+	  a WinOS, \r was causing problems with the
+	  incoming message.
+
 .89 
 	- The tag MOBY was missing in the async cgi
 	  response for 'results'.


From kawas at dev.open-bio.org  Thu Apr 16 14:17:24 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Apr 2009 14:17:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904161817.n3GIHOGU030089@dev.open-bio.org>


kawas
Thu Apr 16 14:17:24 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv30054/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
message for asynchronous post was being truncated (sometimes ...). update how we post the data.
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/09 13:01:15	1.10
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/16 18:17:24	1.11
@@ -14,7 +14,7 @@
 	getopts('hdvl:e:c:C:a:');
 
 	# usage
-	if ( $opt_h or ( @ARGV == 0 and ( not $opt_c ) ) ) {
+	if ( $opt_h or ( @ARGV == 0 and ( not $opt_c or not $opt_C ) ) ) {
 		print STDOUT <<'END_OF_USAGE';
 Calling a BioMoby services (without using SOAP, just locally).
 Usage: # calling a local module representing a service, without using SOAP
@@ -291,8 +291,8 @@
 	# post to the web service
 	my $ua = LWP::UserAgent->new;
 	my $req = HTTP::Request->new( POST => $opt_C );
-	$req->content_type('application/x-www-form-urlencoded');
-	$req->content("data=$input");
+	$req->content_type('text/xml');
+	$req->content("$input");
 
 	# get the response
 	my $response = $ua->request($req);


From kawas at dev.open-bio.org  Thu Apr 16 14:18:25 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Apr 2009 14:18:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904161818.n3GIIPvL030149@dev.open-bio.org>


kawas
Thu Apr 16 14:18:25 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30114/MOSES-MOBY

Modified Files:
	Changes 
Log Message:

moby-live/Perl/MOSES-MOBY Changes,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/16 18:14:34	1.13
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/16 18:18:25	1.14
@@ -4,6 +4,8 @@
 	- bug fix: when sending data with newlines on
 	  a WinOS, \r was causing problems with the
 	  incoming message.
+	- bug fix: moses-testing-service.pl was truncating
+	  the message sent to an async POST service.
 
 .89 
 	- The tag MOBY was missing in the async cgi


From kawas at dev.open-bio.org  Mon Apr 20 10:32:27 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 20 Apr 2009 10:32:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904201432.n3KEWRA4019539@dev.open-bio.org>


kawas
Mon Apr 20 10:32:26 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv19504/MOSES-MOBY

Modified Files:
	META.yml 
Log Message:
updated the version number
moby-live/Perl/MOSES-MOBY META.yml,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/08 22:43:10	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/20 14:32:26	1.8
@@ -39,5 +39,5 @@
   Want: 0.18
   WSRF::Lite: 0.8.2.5
   XML::LibXML: 1.62
-version: 0.89
+version: 0.90
 


From kawas at dev.open-bio.org  Mon Apr 20 10:32:55 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 20 Apr 2009 10:32:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904201432.n3KEWtLR019633@dev.open-bio.org>


kawas
Mon Apr 20 10:32:55 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv19598/MOSES-MOBY

Modified Files:
	Makefile.PL 
Log Message:
updated the version number
moby-live/Perl/MOSES-MOBY Makefile.PL,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/08 22:43:10	1.15
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/20 14:32:55	1.16
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.89';
+	version '0.90';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';


From kawas at dev.open-bio.org  Mon Apr 20 10:34:00 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 20 Apr 2009 10:34:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904201434.n3KEY0UX019745@dev.open-bio.org>


kawas
Mon Apr 20 10:34:00 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv19710/MOBY-Server/share/cgi

Modified Files:
	BioMobyWSDL 
Log Message:

moby-live/Perl/MOBY-Server/share/cgi BioMobyWSDL,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL	2009/04/15 16:56:01	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL	2009/04/20 14:34:00	1.3
@@ -1,5 +1,6 @@
 #!/usr/bin/perl -W
 # _________________________________________________________________
+# 
 # $Id$
 # Developed by: Jose Manuel Rodriguez Carrasco -jmrodriguez at cnio.es-
 # Created: 13-April-2009


From kawas at dev.open-bio.org  Thu Apr  2 14:53:27 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 10:53:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904021453.n32ErRRb000392@dev.open-bio.org>


kawas
Thu Apr  2 10:53:26 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates
In directory dev.open-bio.org:/tmp/cvs-serv356/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service-cgi-async.tt 
Log Message:
had the method name hard coded; changed it to [% obj.name %]
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service-cgi-async.tt,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt	2009/03/30 13:14:09	1.1
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt	2009/04/02 14:53:26	1.2
@@ -118,7 +118,7 @@
 	# get the data from the 'data' parameter
 	my $data = $q->param('data') || $q->param('POSTDATA') || "";
 	# call the service
-	 __PACKAGE__->getGoTerm($data);
+	 __PACKAGE__->[% obj.name %]($data);
 	
 }
 



From kawas at dev.open-bio.org  Thu Apr  2 15:37:20 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 11:37:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904021537.n32FbKWY000764@dev.open-bio.org>


kawas
Thu Apr  2 11:37:20 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv729/Perl/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
added a -C option for testing asynchronous POST services.
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2008/09/02 17:58:02	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/02 15:37:20	1.8
@@ -10,8 +10,8 @@
 
 	# some command-line options
 	use Getopt::Std;
-	use vars qw/ $opt_h $opt_d $opt_v $opt_l $opt_e $opt_c $opt_a /;
-	getopts('hdvl:e:c:a:');
+	use vars qw/ $opt_h $opt_d $opt_v $opt_l $opt_e $opt_c $opt_a $opt_C /;
+	getopts('hdvl:e:c:C:a:');
 
 	# usage
 	if ( $opt_h or ( @ARGV == 0 and ( not $opt_c ) ) ) {
@@ -32,7 +32,10 @@
        # calling a real service, using cgi
        -c <service-url> [<input-file>]
 
-       # calling a real service, using SOAP
+       # calling a real service, using asynchronous cgi
+       -C <service-url> [<input-file>]
+
+       # calling a real service, using async SOAP
        -a <service-url> <service-name> [<input-file>]
 
     <package-name> is a full name of a called module (service)
@@ -64,6 +67,11 @@
 END_OF_USAGE
 		exit(0);
 	}
+	use HTTP::Request;
+	use LWP::UserAgent;
+	use XML::LibXML;
+	use MOBY::Async::WSRF;
+	use MOBY::Async::LSAE;
 
 	# use MOSES::MOBY::Base;
 	# load modules, depending on the mode of calling
@@ -79,6 +87,19 @@
 		  or die "$@\n";
 		eval "use LWP::UserAgent; 1;"
 		  or die "$@\n";
+	} elsif ($opt_C) {
+
+		# calling a real service, using async cgi
+		eval "use HTTP::Request; 1;"
+		  or die "$@\n";
+		eval "use LWP::UserAgent; 1;"
+		  or die "$@\n";
+		eval "use XML::LibXML; 1;"
+		  or die "$@\n";
+		eval "use MOBY::Async::WSRF; 1;"
+		  or die "$@\n";
+		eval "use MOBY::Async::LSAE; 1;"
+		  or die "$@\n";
 	} else {
 
 		# calling a local service module, without SOAP
@@ -93,12 +114,13 @@
 		$LOG->level('INFO')  if $opt_v;
 		$LOG->level('DEBUG') if $opt_d;
 	}
+
 	# load these modules always to get constants and to avoid warnings
 	eval "use MOBY::Async::LSAE; 1;"
 	  or die "$@\n";
 	eval "use MOBY::Async::WSRF; 1;"
 	  or die "$@\n";
-	
+
 }
 
 use strict;
@@ -114,8 +136,59 @@
 END_OF_XML
 }
 
+sub _check_status {
+	my ( $status, $completed, $queryID, $opt_v ) = @_;
+	if ( $status->type == LSAE_PERCENT_PROGRESS_EVENT ) {
+		if ( $status->percentage >= 100 ) {
+			$completed->{$queryID} = 1;
+		} elsif ( $status->percentage < 100 ) {
+			print "Current percentage: ", $status->percentage, "\n" if $opt_v;
+			sleep(20);
+		} else {
+			die "ERROR:  analysis event block not well formed.\n";
+		}
+
+	} elsif ( $status->type == LSAE_STATE_CHANGED_EVENT ) {
+		if (    ( $status->new_state =~ m"completed"i )
+			 || ( $status->new_state =~ m"terminated_by_request"i )
+			 || ( $status->new_state =~ m"terminated_by_error"i ) )
+		{
+			$completed->{$queryID} = 1;
+		} elsif (    ( $status->new_state =~ m"created"i )
+				  || ( $status->new_state =~ m"running"i ) )
+		{
+			print "Current State: ", $status->new_state, "\n" if $opt_v;
+			sleep(20);
+		} else {
+			die "ERROR:  analysis event block not well formed.\n";
+		}
+
+	} elsif ( $status->type == LSAE_STEP_PROGRESS_EVENT ) {
+		if ( $status->steps_completed >= $status->total_steps ) {
+			$completed->{$queryID} = 1;
+		} elsif ( $status->steps_completed < $status->total_steps ) {
+			print "Steps completed: ", $status->steps_completed, "\n" if $opt_v;
+			sleep(20);
+		} else {
+			die "ERROR:  analysis event block not well formed.\n";
+		}
+
+	} elsif ( $status->type == LSAE_TIME_PROGRESS_EVENT ) {
+		if ( $status->remaining == 0 ) {
+			$completed->{$queryID} = 1;
+		} elsif ( $status->remaining > 0 ) {
+			print "Time remaining: ", $status->remaining, "\n" if $opt_v;
+			sleep(20);
+		} else {
+			die "ERROR:  analysis event block not well formed.\n";
+		}
+	} else {
+		warn "Whilst checking the status of our resource, we entered into a possible infinite loop ...\n";
+	}
+}
+
 sub _get_query_ids {
-	my $input = shift;
+	my $input     = shift;
 	my @query_ids = ();
 	my $parser    = XML::LibXML->new();
 	my $doc       = $parser->parse_string($input);
@@ -124,17 +197,17 @@
 		my $node = $iterator->get_node($_);
 		my $id   = $node->getAttribute("queryID")
 		  || $node->getAttribute(
-				 $node->lookupNamespacePrefix($WSRF::Constants::MOBY_MESSAGE_NS)
-				   . ":queryID" );
+						 $node->lookupNamespacePrefix($WSRF::Constants::MOBY_MESSAGE_NS)
+						   . ":queryID" );
 		push @query_ids, $id;
 	}
 	return @query_ids;
 }
 
 # --- what service to call
-my $module = shift unless $opt_c;    # eg. Service::Mabuhay, or just Mabuhay
+my $module = shift unless $opt_c or $opt_C;    # eg. Service::Mabuhay, or just Mabuhay
 my $service;
-( $service = $module ) =~ s/.*::// unless $opt_c;
+( $service = $module ) =~ s/.*::// unless $opt_c or $opt_C;
 
 # --- call the service
 if ($opt_e) {
@@ -146,12 +219,8 @@
 			my $res  = shift;
 			my $msg =
 			  ref $res
-			  ? "--- SOAP FAULT ---\n"
-			  . $res->faultcode . " "
-			  . $res->faultstring
-			  : "--- TRANSPORT ERROR ---\n"
-			  . $soap->transport->status
-			  . "\n$res\n";
+			  ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring
+			  : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
 			die $msg;
 		}
 	);
@@ -190,6 +259,117 @@
 	$req->content("data=$input");
 	print "\n" . $ua->request($req)->as_string . "\n";
 
+} elsif ($opt_C) {
+
+	my $input = '';
+	if ( @ARGV > 0 ) {
+		my $data = shift;    # a file name
+		open INPUT, "<$data"
+		  or die "Cannot read '$data': $!\n";
+		while (<INPUT>) { $input .= $_; }
+		close INPUT;
+	} else {
+		$input = _empty_input;
+	}
+
+	# extract all of the query ids from $input
+	my @query_ids = _get_query_ids($input);
+	my %completed = ();
+
+	print "Sending the following data to $opt_C\n$input\n";
+
+	# post to the web service
+	my $ua = LWP::UserAgent->new;
+	my $req = HTTP::Request->new( POST => $opt_C );
+	$req->content_type('application/x-www-form-urlencoded');
+	$req->content("data=$input");
+
+	# get the response
+	my $response = $ua->request($req);
+
+	# do we have an error?
+	die "Error calling service: " . $response->status_line
+	  if ( $response->code != 200 );
+
+	my $epr    = $response->header("moby-wsrf");
+	my $parser = XML::LibXML->new();
+	my $doc    = $parser->parse_string($epr);
+	my $ID =
+	  $doc->getElementsByLocalName("ServiceInvocationId")->get_node(1)->textContent;
+	$ID =~ s/ //gi;
+	my $searchTerm = "";
+	$searchTerm .=
+"<wsrf-rp:GetMultipleResourceProperties xmlns:wsrf-rp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
+
+	foreach my $queryID (@query_ids) {
+		$searchTerm .=
+		    "<wsrf-rp:ResourceProperty>mobyws:status_" 
+		  . $queryID
+		  . "</wsrf-rp:ResourceProperty>";
+	}
+	$searchTerm .= "</wsrf-rp:GetMultipleResourceProperties>";
+	my $header = _moby_wsrf_header( $opt_C, $ID );
+	$header =~ s/\n//gi;
+
+	# poll
+	while (1) {
+		foreach my $queryID (@query_ids) {
+
+			# skip poll if current job completed
+			next if $completed{$queryID};
+
+			# poll the service for given query ID
+			$req = HTTP::Request->new( POST => $opt_C . "/status" );
+			$req->header( "moby-wsrf" => $header );
+			$req->content_type('application/x-www-form-urlencoded');
+			$req->content("data=$searchTerm");
+			$response = $ua->request($req);
+			my $xml    = $response->content();
+			my $parser = XML::LibXML->new();
+			my $doc    = $parser->parse_string($xml);
+			$doc = $doc->documentElement()->firstChild()->firstChild();
+
+			my $status = LSAE::AnalysisEventBlock->new( $doc->toString );
+			&_check_status( $status, \%completed, $queryID, $opt_v );
+		}
+		last if scalar keys(%completed) == $#query_ids + 1;
+	}
+
+	# task is finished, obtain the result
+	$searchTerm = "";
+	$searchTerm .=
+"<wsrf-rp:GetMultipleResourceProperties xmlns:wsrf-rp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
+	foreach my $queryID (@query_ids) {
+		$searchTerm .=
+		    "<wsrf-rp:ResourceProperty>mobyws:result_" 
+		  . $queryID
+		  . "</wsrf-rp:ResourceProperty>";
+	}
+	$searchTerm .= "</wsrf-rp:GetMultipleResourceProperties>";
+
+	$header = _moby_wsrf_header( $opt_C, $ID );
+	$header =~ s/\n//gi;
+
+	$req = HTTP::Request->new( POST => $opt_C . "/results" );
+	$req->header( "moby-wsrf" => $header );
+	$req->content_type('application/x-www-form-urlencoded');
+	$req->content("data=$searchTerm");
+	$response = $ua->request($req);
+
+	# create nicely formatted XML
+	$parser = XML::LibXML->new();
+	$doc    = $parser->parse_string( $response->content );
+	print "\n" . $doc->toString(1);
+
+	# destroy the job
+	$searchTerm = '<Destroy xmlns="http://docs.oasis-open.org/wsrf/rl-2"/> ';
+	$req = HTTP::Request->new( POST => $opt_C . "/destroy" );
+	$req->header( "moby-wsrf" => $header );
+	$req->content_type('application/x-www-form-urlencoded');
+	$req->content("data=$searchTerm");
+	$response = $ua->request($req);
+	print "Destroying the resource returned:\n\t" . $response->content . "\n" if $opt_v;
+
 } elsif ($opt_a) {
 
 	# calling a real service, using async soap
@@ -203,12 +383,8 @@
 			my $res  = shift;
 			my $msg =
 			  ref $res
-			  ? "--- SOAP FAULT ---\n"
-			  . $res->faultcode . " "
-			  . $res->faultstring
-			  : "--- TRANSPORT ERROR ---\n"
-			  . $soap->transport->status
-			  . "\n$res\n";
+			  ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring
+			  : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
 			die $msg;
 		}
 	);
@@ -227,13 +403,11 @@
 
 	# extract all of the query ids from $input
 	my @query_ids = _get_query_ids($input);
-	print "\nSending the following data to $service asynchronously:\n",
-	  $input, "\n"
+	print "\nSending the following data to $service asynchronously:\n", $input, "\n"
 	  if $opt_v;
 
 	# submit the job
-	my $epr =
-	  ( $soap->$service( SOAP::Data->type( 'string' => "$input" ) )->result );
+	my $epr = ( $soap->$service( SOAP::Data->type( 'string' => "$input" ) )->result );
 
 	# Get address from the returned Endpoint Reference
 	my $address = $epr->{'EndpointReference'}->{Address};
@@ -265,12 +439,11 @@
 
 			$soap = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
 				sub {
-					sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1],
-					  $_[1];
+					sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
 				}
 			  )->wsaddress($EPR)
 			  ->GetMultipleResourceProperties(
-								  SOAP::Data->value($searchTerm)->type('xml') );
+										  SOAP::Data->value($searchTerm)->type('xml') );
 
 			my $parser = XML::LibXML->new();
 			my $xml    = $soap->raw_xml;
@@ -279,8 +452,7 @@
 			my $prop_name = "status_" . $queryID;
 
 			my ($prop) =
-			  $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY,
-											 $prop_name )
+			     $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
 			  || $soap->getElementsByTagName($prop_name);
 			my $event = $prop->getFirstChild->toString
 			  unless ref $prop eq "XML::LibXML::NodeList";
@@ -338,6 +510,7 @@
 	}
 
 	foreach my $queryID (@query_ids) {
+
 		# get the result
 		my $searchTerm .=
 "<wsrp:ResourceProperty xmlns:wsrp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
@@ -345,21 +518,19 @@
 		$searchTerm .= "</wsrp:ResourceProperty>";
 		my $ans = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
 			sub {
-				sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1],
-				  $_[1];
+				sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
 			}
 		  )->wsaddress($EPR)
 		  ->GetMultipleResourceProperties(
-								  SOAP::Data->value($searchTerm)->type('xml') );
+										  SOAP::Data->value($searchTerm)->type('xml') );
 		die "ERROR:  " . $ans->faultstring if ( $ans->fault );
 
 		my $parser = XML::LibXML->new();
 		my $xml    = $ans->raw_xml;
-		my $doc = $parser->parse_string($xml);
+		my $doc    = $parser->parse_string($xml);
 		$soap = $doc->getDocumentElement();
 		my $prop_name = "result_" . $queryID;
-		my ($prop) =
-		     $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
+		my ($prop) = $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
 		  || $soap->getElementsByTagName($prop_name);
 		my $result = $prop->getFirstChild->toString
 		  unless ref $prop eq "XML::LibXML::NodeList";
@@ -396,4 +567,14 @@
 	} or croak $@;
 }
 
+sub _moby_wsrf_header {
+	my ( $url, $id ) = @_;
+	return <<"END OF XML";
+<moby-wsrf>
+<wsa:Action xmlns:wsa="http://www.w3.org/2005/08/addressing">http://docs.oasis-open.org/wsrf/rpw-2/GetResourceProperty/GetResourcePropertiesRequest</wsa:Action>
+<wsa:To xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd" xmlns:wsa="http://www.w3.org/2005/08/addressing" wsu:Id="To">$url</wsa:To>
+<mobyws:ServiceInvocationId xmlns:mobyws="http://biomoby.org/" xmlns:wsa="http://www.w3.org/2005/08/addressing" wsa:IsReferenceParameter="true">$id</mobyws:ServiceInvocationId>
+</moby-wsrf>
+END OF XML
+}
 __END__



From kawas at dev.open-bio.org  Thu Apr  2 16:10:14 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 12:10:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904021610.n32GAEpU000924@dev.open-bio.org>


kawas
Thu Apr  2 12:10:14 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv889/Perl/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
added some help doc to further explain some of the options
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/02 15:37:20	1.8
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/02 16:10:14	1.9
@@ -21,6 +21,12 @@
        [-vd] [-l <lib-location>] <package-name> [<input-file>]
        or
        [-vd] -c <service-url> [<input-file>]
+       or
+       [-vd] -C <service-url> [<input-file>]
+       or
+       [-vd] -e <service-url> [<input-file>]
+       or
+       [-vd] -a <service-url> [<input-file>]
 
        It also needs a location of a local cache (and potentially a
        BioMoby registry endpoint). It takes it from the
@@ -52,6 +58,10 @@
     -c <cgi-service-url>
         A cgi biomoby service url
         (e.g. http://localhost/cgi-bin/HelloBiomobyWorld.cgi)
+        
+    -C <async-cgi-service-url>
+        An asynchronous cgi biomoby service url
+        (e.g. http://localhost/cgi-bin/HelloBiomobyWorldAsync.cgi)
 
     -a <asynchronous service-url>
         An asynchronous service url



From kawas at dev.open-bio.org  Thu Apr  2 18:33:44 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 14:33:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904021833.n32IXiv9001426@dev.open-bio.org>


kawas
Thu Apr  2 14:33:44 EDT 2009
Update of /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl
In directory dev.open-bio.org:/tmp/cvs-serv1391/Docs/MOBY-S_API/Perl

Modified Files:
	construct_moses_cgi_async_service.html 
Log Message:
added information on updating event state for a running task
moby-live/Docs/MOBY-S_API/Perl construct_moses_cgi_async_service.html,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html	2009/03/30 13:12:34	1.1
+++ /home/repository/moby/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html	2009/04/02 18:33:44	1.2
@@ -20,7 +20,7 @@
     <dt><a href="#test">Step 5: Service testing</a> </dt>
     <dt><a href="#deploy">Step 6: Service deployment</a></dt>
     <dt><a href="#test2">Step 7: Service testing using CGI</a></dt>
-    <dt><em>How to update polling status (optional) - coming soon</em></dt>
+    <dt><a href="#poll">How to update polling status (optional)</a></dt>
   </dl>
 </dl>
 <h2><a name="req" id="req"></a>What is needed</h2>
@@ -108,7 +108,7 @@
 <h3>We can update our cache by issuing the following commands:</h3>
 <ol>
   <li> <em>moses-generate-services.pl -u <br />
-  </em></li>
+    </em></li>
   <li><em>moses-generate-datatypes.pl -u</em></li>
 </ol>
 <blockquote>
@@ -128,7 +128,7 @@
 <p>Basically, we used the script <em><strong>moses-generate-services.pl</strong></em> to:</p>
 <ol>
   <li>automatically generate a perl module called <strong>getReverseEchoString.pm</strong> in the directory <strong><em>/your_home_dir/Perl-MoSeS/services/Service</em></strong> (if it already exists, it won't overwrite it).<br />
-  This file contains the implementation for our service and is what we edit to inject our business logic.</li>
+    This file contains the implementation for our service and is what we edit to inject our business logic.</li>
   <li>automatically generates a cgi script called <strong>getReverseEchoString.cgi</strong> in the directory <em><strong>/your_home_dir/Perl-MoSeS/cgi/samples/jmoby/net/</strong></em>.<br />
     This file is what we deploy on our web server that redirects cgi requests to our service to the <em><strong>getReverseEchoString.pm</strong></em> module above.<br />
   </li>
@@ -231,6 +231,105 @@
    &lt;/moby:mobyData&gt;
  &lt;/moby:mobyContent&gt;
 &lt;/moby:MOBY&gt;</pre>
+<h2><a name="poll" id="poll"></a>How to update polling status (optional)</h2>
+<p>If you have a really long running service and would like to ensure that users know exactly how far along the service is to completion, you can create more detailed <em>status</em> messages.</p>
+<p>Before we continue, it would be useful for you to get acquainted with the perl module, <em><strong><a href="http://search.cpan.org/perldoc?MOBY::Async::LSAE" target="_blank">MOBY::Async::LSAE</a>.</strong></em></p>
+<h3>Updating the status of our service</h3>
+<blockquote>
+  <p>There are 2 things that you need to successfully update the status of your service:</p>
+  <ol>
+    <li><em>service invocation id<br />
+      </em></li>
+    <li><em>the job id for the current task</em></li>
+  </ol>
+  <p>The service invocation id is very simple to obtain: </p>
+</blockquote>
+<pre class="script2">my $ID = $ENV{ID};  </pre>
+<blockquote>
+  <p>The job id is equally as easy to obtain!</p>
+</blockquote>
+<pre class="script2">my $jid = $request-&gt;jid;</pre>
+<blockquote>
+  <p>Now that we have those 2 pieces of information, all that is left is for you to choose what type of status update you would like your service to create:</p>
+  <ul>
+    <li>Heartbeat progress event</li>
+    <li>Percent progress event</li>
+    <li>State changed event <em>(default)</em></li>
+    <li>Step progress event</li>
+    <li>Time progress event</li>
+  </ul>
+  <p>We will be using the State changed event in this example.</p>
+  <p>In order to save the state information for our task, we need certain variables like, <em><strong>pid</strong></em>, <em><strong>input</strong></em>, <em><strong>status</strong></em>, and <strong><em>result</em></strong>.</p>
+  <ul>
+    <li><strong><em>pid</em></strong>  is the property id for our service,</li>
+    <li><strong><em>input</em></strong> is the input to our service,</li>
+    <li><strong><em>status</em></strong> is the current event state for our running task, and</li>
+    <li><strong><em>result</em></strong> holds the result for our running task and is obtained once our state is set to completed.</li>
+  </ul>
+</blockquote>
+<pre class="script2"># some variables we need to access/store our event information
+
+my $property_pid    = &quot;pid_$jid&quot;;<br />my $property_input  = &quot;input_$jid&quot;;<br />my $property_status = &quot;status_$jid&quot;;<br />my $property_result = &quot;result_$jid&quot;;</pre>
+<blockquote>
+  <p>To provide updated state information for our event, we need to first remember what our previous state was:</p>
+</blockquote>
+<pre class="script2"># construct an LSAE object based on the old event block
+my $old_status = 
+         LSAE::AnalysisEventBlock-&gt;new(
+                 $WSRF::WSRP::ResourceProperties{$property_status}
+         );</pre>
+<blockquote>
+  <p>We now instantiate a new <em><strong>LSAE::AnalysisEventBlock</strong></em> and set its various fields. For instance, we will take the previous state information from <em><strong>$old_status</strong></em> and then provide new state information for our event:</p>
+</blockquote>
+<pre class="script2"># construct a new state changed event
+my $status = LSAE::AnalysisEventBlock-&gt;new();<br />$status-&gt;type(LSAE_STATE_CHANGED_EVENT);
+# set the previous state<br />$status-&gt;previous_state( $old_status-&gt;new_state() );
+# set the new state<br />$status-&gt;new_state('running');
+# set our job id for this event<br />$status-&gt;id($jid);</pre>
+<blockquote>
+  <p>Once we have created our new analysis event block, we need to save it so that the client that made the job request to our service can access the state information:</p>
+</blockquote>
+<pre class="script2"># create a file based resource that we will store our event information
+my $lock = WSRF::MobyFile-&gt;new( undef, $ID );<br />$WSRF::WSRP::ResourceProperties{$property_status} = $status-&gt;XML();
+# here we leave the result empty since the service is still running<br />$WSRF::WSRP::ResourceProperties{$property_result} = '';
+# save the event so that our clients can access the information
+$lock-&gt;toFile();</pre>
+<blockquote>
+  <p>Here is the complete code that we put into our <em><strong>process_it</strong></em> subroutine where ever you feel like you should update the state of our long running task!</p>
+</blockquote>
+<pre class="script2"># our service invocation id
+my $ID = $ENV{ID};
+
+# our job id
+my $jid = $request-&gt;jid;
+
+
+# some variables we need to access/store our event information
+my $property_pid    = &quot;pid_$jid&quot;;<br />my $property_input  = &quot;input_$jid&quot;;<br />my $property_status = &quot;status_$jid&quot;;<br />my $property_result = &quot;result_$jid&quot;;
+
+
+# construct an LSAE object based on the old event block
+my $old_status = 
+         LSAE::AnalysisEventBlock-&gt;new(
+                 $WSRF::WSRP::ResourceProperties{$property_status}
+         );
+
+
+# construct a new state changed event
+my $status = LSAE::AnalysisEventBlock-&gt;new();<br />$status-&gt;type(LSAE_STATE_CHANGED_EVENT);
+# set the previous state<br />$status-&gt;previous_state( $old_status-&gt;new_state() );
+# set the new state<br />$status-&gt;new_state('running');
+# set our job id for this event<br />$status-&gt;id($jid);
+
+
+# create a file based resource that we will store our event information
+my $lock = WSRF::MobyFile-&gt;new( undef, $ID );<br />$WSRF::WSRP::ResourceProperties{$property_status} = $status-&gt;XML();
+# here we leave the result empty since the service is still running<br />$WSRF::WSRP::ResourceProperties{$property_result} = '';
+# save the event so that our clients can access the information
+$lock-&gt;toFile();</pre>
+<blockquote>
+  <p>&nbsp;</p>
+</blockquote>
 <p>That's all there is to constructing asynchronous CGI based Perl MoSeS services!</p>
 </body>
 </html>



From kawas at dev.open-bio.org  Thu Apr  2 20:07:21 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 2 Apr 2009 16:07:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904022007.n32K7L6N001833@dev.open-bio.org>


kawas
Thu Apr  2 16:07:21 EDT 2009
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv1798/Perl

Modified Files:
	INSTALL 
Log Message:
small documentation update on where to get more information.
moby-live/Perl INSTALL,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/INSTALL,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/INSTALL	2008/04/23 13:08:11	1.5
+++ /home/repository/moby/moby-live/Perl/INSTALL	2009/04/02 20:07:21	1.6
@@ -33,7 +33,7 @@
 For details on how to configure your own MOBY Central
 registry, should you want to set one up (you DO NOT
 need to set up a registry to access nor serve MOBY-S
-Services) please visit the "Installing a Local Registy"
-link on the biomoby.org homepage.
+Services) please read the documentation on cpan of
+the module MOBY.pm.
 
 Mark



From kawas at dev.open-bio.org  Fri Apr  3 16:35:57 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:35:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031635.n33GZvYx011393@dev.open-bio.org>


kawas
Fri Apr  3 12:35:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv11362/Perl/MOBY-Server/bin/scripts

Added Files:
	moby-s-update-db.pl 
Log Message:
a script to help people update their databases to reflect the new service category cgi-async. 

in the future, any updates to the db can be appended to this script. so if a new change X is made to the db, then all we need to do is add an option to the script and when a user runs the script with that option set, the appropriate update to the db will be made.

for the addition of the additional enum field 'cgi-async', the option to use with the script is -c.
moby-live/Perl/MOBY-Server/bin/scripts moby-s-update-db.pl,NONE,1.1


From kawas at dev.open-bio.org  Fri Apr  3 16:36:36 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:36:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031636.n33Gaa73011454@dev.open-bio.org>


kawas
Fri Apr  3 12:36:35 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv11419/Perl/MOBY-Server

Modified Files:
	MANIFEST 
Log Message:
addition of the moby-s-update-db.pl file to the manifest
moby-live/Perl/MOBY-Server MANIFEST,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2008/12/04 15:31:26	1.10
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2009/04/03 16:36:35	1.11
@@ -1,5 +1,6 @@
 bin/scripts/moby-s-install.pl
 bin/scripts/moby-s-caching.pl
+bin/scripts/moby-s-update-db.pl
 Changes
 drop_tables.sql
 inc/Module/AutoInstall.pm



From kawas at dev.open-bio.org  Fri Apr  3 16:39:48 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:39:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031639.n33GdmSL011558@dev.open-bio.org>


kawas
Fri Apr  3 12:39:48 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv11523/Perl/MOBY-Server/lib/MOBY

Modified Files:
	MOBY.pm 
Log Message:
added a brief message to say that users should check to see if they need to update their db schema
moby-live/Perl/MOBY-Server/lib/MOBY MOBY.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2008/09/02 13:14:18	1.4
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/MOBY.pm	2009/04/03 16:39:48	1.5
@@ -55,6 +55,8 @@
 
 B<Important> if you are upgrading to newer versions, please make sure to remove any files that may be cached by this module! To help you do this, run the script B<moby-s-caching.pl>. For information on using B<moby-s-caching.pl>, use the -h option!
 
+B<Important II> make sure to run C<moby-s-update-db> with the -h option to see if you need to updgrade the db schemas.
+
 =cut
 
 =head2 Installing A Custom MOBY-Central Registry



From kawas at dev.open-bio.org  Fri Apr  3 16:41:36 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:41:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031641.n33Gfars011598@dev.open-bio.org>


kawas
Fri Apr  3 12:41:36 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv11563/Perl/MOBY-Server

Modified Files:
	Changes 
Log Message:
added a message about running the update db script if upgrading your moby installation.
moby-live/Perl/MOBY-Server Changes,1.21,1.22
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/03/30 13:10:19	1.21
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/03 16:41:36	1.22
@@ -1,6 +1,9 @@
 Revision history for Perl extension MOBY.
 
 1.07
+    - Important: run the script moby-s-update-db once you have installed
+      this module if you have *upgraded* an existing installation.
+      
 	- Fix bug in CollectionArticle, SimpleInput, SecondaryArticle, and 
 	  SimpleArticle that caused objects created to have 'memory'.
 	- Updated the MOBY::Client::ServiceInstance module to reflect



From kawas at dev.open-bio.org  Fri Apr  3 16:50:50 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:50:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031650.n33GooYS011703@dev.open-bio.org>


kawas
Fri Apr  3 12:50:50 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv11668/Perl/MOBY-Server/bin/scripts

Modified Files:
	moby-s-update-db.pl 
Log Message:

moby-live/Perl/MOBY-Server/bin/scripts moby-s-update-db.pl,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-update-db.pl,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-update-db.pl	2009/04/03 16:35:56	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-update-db.pl	2009/04/03 16:50:50	1.2
@@ -99,7 +99,7 @@
 	unless ( $category =~ m/cgi\-async/i ) {
 		$go
 		  && $dbh->do(
-" alter table service_instance modify category ENUM('moby','soap','wsdl','cgi','moby-async', 'cgi-async', 'doc-literal', 'doc-literal-async', 'cgi-async') default NULL"
+" alter table service_instance modify category ENUM('moby','soap','wsdl','cgi','moby-async', 'cgi-async', 'doc-literal', 'doc-literal-async') default NULL"
 		  );
 	}
 



From kawas at dev.open-bio.org  Fri Apr  3 16:52:21 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 12:52:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031652.n33GqL5w011787@dev.open-bio.org>


kawas
Fri Apr  3 12:52:21 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv11752/Perl/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:
specify that we need to install the shared script moby-s-update-db.pl
moby-live/Perl/MOBY-Server Makefile.PL,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/01/28 14:25:29	1.14
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/03 16:52:21	1.15
@@ -70,6 +70,7 @@
 
 	install_script 'bin/scripts/moby-s-install.pl';
 	install_script 'bin/scripts/moby-s-caching.pl';
+	install_script 'bin/scripts/moby-s-update-db.pl';
 
 	install_share 'share';
 



From kawas at dev.open-bio.org  Fri Apr  3 17:01:31 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 3 Apr 2009 13:01:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904031701.n33H1Vha012013@dev.open-bio.org>


kawas
Fri Apr  3 13:01:30 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Client
In directory dev.open-bio.org:/tmp/cvs-serv11978/Perl/MOBY-Client

Modified Files:
	Changes 
Log Message:
updated to reflect recent changes.
moby-live/Perl/MOBY-Client Changes,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Client/Changes,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Client/Changes	2009/02/12 19:34:17	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Client/Changes	2009/04/03 17:01:30	1.8
@@ -14,8 +14,11 @@
 	   *  Added the function 'raw_execute' to MOBY::Async::Service to
 		  allow calling of services with raw XML similarly to the method
 		  in MOBY::Client::Service.
-	   * Fixed typo in MOBY::Client::Service that refered to POST 
+	   *  Fixed typo in MOBY::Client::Service that refered to POST 
 		  services as category 'post' rather than 'cgi'
+	   *  Added the category 'cgi-async' to the list of service
+	      categories that are allowed.
+
 1.03
        * changes to makefile reflecting the cpan addition of wsrf
        * added MOBY/Async.pm to the module



From kawas at dev.open-bio.org  Mon Apr  6 14:16:40 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 6 Apr 2009 10:16:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904061416.n36EGe9s025783@dev.open-bio.org>


kawas
Mon Apr  6 10:16:39 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv25739/Perl/MOBY-Server

Modified Files:
	Makefile.PL META.yml Changes 
Log Message:
had junk  in the cpan version of META.yml so I am generating another version of the module with META.yml fixed
moby-live/Perl/MOBY-Server Makefile.PL,1.15,1.16 META.yml,1.6,1.7 Changes,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/03 16:52:21	1.15
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/06 14:16:39	1.16
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.07';
+	version '1.08';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2009/01/28 14:25:29	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2009/04/06 14:16:39	1.7
@@ -44,4 +44,4 @@
   XML::SemanticCompare: 0
   XML::Simple: 2.18
   WSRF::Lite: 0.8.2.5
-version: 1.07
+version: 1.08

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/03 16:41:36	1.22
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/06 14:16:39	1.23
@@ -1,5 +1,8 @@
 Revision history for Perl extension MOBY.
 
+1.08
+    - Fixed META.yml in the distribution. Please refer to changes for 1.07.
+
 1.07
     - Important: run the script moby-s-update-db once you have installed
       this module if you have *upgraded* an existing installation.



From kawas at dev.open-bio.org  Tue Apr  7 15:33:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 11:33:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071533.n37FXAMY002942@dev.open-bio.org>


kawas
Tue Apr  7 11:33:09 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard
In directory dev.open-bio.org:/tmp/cvs-serv2907/src/main/org/biomoby/service/dashboard

Modified Files:
	PerlMoSeSPanel.java 
Log Message:
added an option for generating Async HTTP POST services.
moby-live/Java/src/main/org/biomoby/service/dashboard PerlMoSeSPanel.java,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java	2008/11/03 19:47:45	1.14
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/PerlMoSeSPanel.java	2009/04/07 15:33:09	1.15
@@ -79,28 +79,31 @@
     // String: set this for an information message
     static String PM_INFORMATION = "perl-moses-information";
 
-    // boolean - do we over write files
+    // String - do we over write files
     static String PM_OVERWRITE = "perl-moses-overwrite";
 
-    // boolean: do we generate cgi services
+    // String: do we generate cgi services
     static String PM_CGI = "perl-moses-cgi";
     
-    // boolean do we generate soap services
+    // String: do we generate soap services
     static String PM_SOAP = "perl-moses-soap";
     
-    // boolean do we generate async services
+    // String: do we generate async services
     static String PM_ASYNC = "perl-moses-async";
+    
+    // String: do we generate async cgi services
+    static String PM_CGI_ASYNC = "perl-moses-cgi-async";
 
-    // boolean: are we currently updating the datatype cache
+    // String:: are we currently updating the datatype cache
     static String PM_SYNC_DATATYPES = "perl-moses-sync-datatypes";
 
-    // boolean: are we currently updating the services cache
+    // String: are we currently updating the services cache
     static String PM_SYNC_SERVICES = "perl-moses-sync-services";
 
-    // boolean: are we generating services by name
+    // String: are we generating services by name
     static String PM_GENERATING_SPECIFIC_SERVICES = "perl-moses-generating-specific-services";
 
-    // boolean: are we generating services by authority
+    // String: are we generating services by authority
     static String PM_GENERATING_BY_AUTHORITY = "perl-moses-generating-by-authority";
 
     // N/A: set this to make the editor save the current file
@@ -301,6 +304,7 @@
 	propertyChannel.put(PM_SYNC_DATATYPES, new Boolean(false));
 	propertyChannel.put(PM_OVERWRITE, new Boolean(false));
 	propertyChannel.put(PM_CGI, new Boolean(false));
+	propertyChannel.put(PM_CGI_ASYNC, new Boolean(false));
 	propertyChannel.put(PM_ASYNC, new Boolean(false));
 
 	propertyChannel.put(PM_PERL_INSTALL_DIR, getPrefValue(PM_PERL_INSTALL_DIR, ""));
@@ -518,16 +522,18 @@
 		});
 	generateBtn.setEnabled(enable_moses_actions);
 	ButtonGroup group = new ButtonGroup();
-	JRadioButton genCgi, genSoap, genAsync;
+	JRadioButton genCgi, genCgiAsync, genSoap, genAsync;
 	group.add (genCgi      = createHowToButton ("Generate CGI Service", PM_CGI));
+	group.add (genCgiAsync = createHowToButton ("Generate ASYNC CGI Service", PM_CGI_ASYNC));
 	group.add (genSoap     = createHowToButton ("Generate SOAP Service", PM_SOAP));
-	group.add (genAsync     = createHowToButton ("Generate ASYNC Service", PM_ASYNC));
+	group.add (genAsync    = createHowToButton ("Generate ASYNC SOAP Service", PM_ASYNC));
 	
 	SwingUtils.addComponent(bPanel, genOverwrite, 0, 0, 1, 1, NONE, NWEST, 0.0, 0.0);
 	SwingUtils.addComponent(bPanel, genCgi,       0, 1, 2, 1, NONE, NWEST, 0.0, 0.0);
-	SwingUtils.addComponent(bPanel, genSoap,      0, 2, 2, 1, NONE, NWEST, 0.0, 0.0);
-	SwingUtils.addComponent(bPanel, genAsync,     0, 3, 2, 1, NONE, NWEST, 0.0, 0.0);
-	SwingUtils.addComponent(bPanel, generateBtn,  0, 4, 2, 1, HORI, NWEST, 0.0, 0.0);
+	SwingUtils.addComponent(bPanel, genCgiAsync,  0, 2, 2, 1, NONE, NWEST, 0.0, 0.0);
+	SwingUtils.addComponent(bPanel, genSoap,      0, 3, 2, 1, NONE, NWEST, 0.0, 0.0);
+	SwingUtils.addComponent(bPanel, genAsync,     0, 4, 2, 1, NONE, NWEST, 0.0, 0.0);
+	SwingUtils.addComponent(bPanel, generateBtn,  0, 5, 2, 1, HORI, NWEST, 0.0, 0.0);
 
 	// add to the main panel
 	int count = 0;
@@ -826,6 +832,7 @@
 	    radio.setSelected (true);
 	    radio.setEnabled (true);
 	    propertyChannel.put (PM_CGI, false);
+	    propertyChannel.put (PM_CGI_ASYNC, false);
 	    propertyChannel.put (PM_ASYNC, false);
 	}
 	return radio;
@@ -834,6 +841,7 @@
 	    public void actionPerformed (ActionEvent e) {
 		String howTo = e.getActionCommand();
 		propertyChannel.put (PM_CGI, howTo.equals(PM_CGI));
+		propertyChannel.put (PM_CGI_ASYNC, howTo.equals(PM_CGI_ASYNC));
 		propertyChannel.put (PM_ASYNC, howTo.equals(PM_ASYNC));
 		propertyChannel.put (PM_SOAP, howTo.equals(PM_SOAP));
 	    }
@@ -1110,6 +1118,9 @@
 			} else if (Boolean.parseBoolean(propertyChannel
 				.getString(PM_ASYNC))){
 			    command.add("-A");
+			} else if (Boolean.parseBoolean(propertyChannel
+				.getString(PM_CGI_ASYNC))){
+			    command.add("-C");
 			} 
 			command.add(authority);
 			// place command into com
@@ -1205,6 +1216,9 @@
 			} else if (Boolean.parseBoolean(propertyChannel
 				.getString(PM_ASYNC))){
 			    command.add("-A");
+			} else if (Boolean.parseBoolean(propertyChannel
+				.getString(PM_CGI_ASYNC))){
+			    command.add("-C");
 			}
 			command.add(auth);
 			command.add(name);



From kawas at dev.open-bio.org  Tue Apr  7 15:42:39 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 11:42:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071542.n37FgdTG003021@dev.open-bio.org>


kawas
Tue Apr  7 11:42:39 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help
In directory dev.open-bio.org:/tmp/cvs-serv2986/src/main/org/biomoby/service/dashboard/help

Modified Files:
	PerlMoSeSPanel.html 
Log Message:
updated the doc to include both async soap and cgi service generation.
formatted the html for easy reading/writing
moby-live/Java/src/main/org/biomoby/service/dashboard/help PerlMoSeSPanel.html,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html	2008/06/05 19:46:14	1.4
+++ /home/repository/moby/moby-live/Java/src/main/org/biomoby/service/dashboard/help/PerlMoSeSPanel.html	2009/04/07 15:42:39	1.5
@@ -1,98 +1,294 @@
 <h1>Perl MoSeS: Generate &amp; Edit Code</h1>
-<p> This panel is a user-interface to the Perl MoSeS
-  sub-project. <em>MoSeS</em> stands for <em>Moby Services Support</em> and its documentation is available at:<br />
-  	http://search.cpan.org/dist/MOSES-MOBY/lib/MOSES/MOBY.pm</p>
-<p> In order to use this panel, you will have to ensure that you (or your 
-  sys admin) have installed <strong>Perl</strong> and the CPAN module MOSES::MOBY (http://search.cpan.org/dist/MOSES-MOBY/).
-  
-  Once that module has been installed <strong>and</strong> you have performed the 
-  user configuration step (<strong><em>moses-install.pl</em></strong>), 
-  you will be able use this panel! </p>
-<p><font color="#FF0000" size="+1"><strong><em>Once again, this panel is only useful in those situations that you have installed the CPAN module '</em>MOSES::MOBY<em>' and have run the user configuration script </em>'moses-install.pl<em>'!</em></strong></font></p>
-<p> The panel has two different parts - one <b><a href="#gen">generates code</a></b> for the
-  selected services, and one provides you with an <b><a href="#editor">editor</a></b> to aid  
-  in writing the business logic for any service that you generate with this 
-  Perl-MoSeS.  </p>
-<p> For both parts, you need to start by selecting a service, services,
-  or authority in the services tree. Multiple selection is possible using
-  <em><strong>SHIFT</strong></em> or <em><strong>CONTROL</strong></em>. If you select an authority, all services from this
-  authority are considered selected. </p>
-<p> All activities are done in the background using the command line utilities installed by the Perl-MoSeS module. </p>
-<p>&nbsp;</p>
+<p>
+    This panel is a user-interface to the Perl MoSeS 
+    sub-project. <em>MoSeS</em>
+    stands for <em>Moby Services Support</em>
+    and its documentation is available at:
+    <br/>
+    http://search.cpan.org/dist/MOSES-MOBY/lib/MOSES/MOBY.pm
+</p>
+<p>
+    In order to use this panel, you will have to ensure that you (or your 
+    sys admin) have installed <strong>Perl</strong>
+    and the CPAN module MOSES::MOBY (http://search.cpan.org/dist/MOSES-MOBY/).
+    Once that module has been installed <strong>and</strong>
+    you have performed the 
+    user configuration step (<strong><em>moses-install.pl</em></strong>), 
+    you will be able use this panel! 
+</p>
+<p>
+    <font color="#FF0000" size="+1">
+        <strong><em>Once again, this panel is only useful in those situations that you have installed the CPAN module '</em>MOSES::MOBY<em>' and have run the user configuration script </em>'moses-install.pl<em>'!</em></strong>
+    </font>
+</p>
+<p>
+    The panel has two different parts - one <b><a href="#gen">generates code</a></b>
+    for the 
+    selected services, and one provides you with an <b><a href="#editor">editor</a></b>
+    to aid 
+    in writing the business logic for any service that you generate with this  
+    Perl-MoSeS. 
+</p>
+<p>
+    For both parts, you need to start by selecting a service, services,
+    or authority in the services tree. Multiple selection is possible using<em><strong>SHIFT</strong></em>
+    or <em><strong>CONTROL</strong></em>. If you select an authority, all services from this 
+    authority are considered selected. 
+</p>
+<p>
+    All activities are done in the background using the command line utilities installed by the Perl-MoSeS module. 
+</p>
+<p>
+    &nbsp;
+</p>
 <h2>Perl-MoSeS sub panel</h2>
-<p>The Perl-MoSeS sub panel allows you to:</p>
-<ul><li><strong><a href="#gen">Generate</a></strong> -  generate perl modules for services that you select,</li>
-  <li><a href="#local_user_config"><strong>Local User Config</strong></a> - for those users without root access when they installed Perl-MoSeS<em><strong>*</strong></em></li>
+<p>
+    The Perl-MoSeS sub panel allows you to:
+</p>
+<ul>
+    <li>
+        <strong><a href="#gen">Generate</a></strong>
+        -  generate perl modules for services that you select,
+    </li>
+    <li>
+        <a href="#local_user_config"><strong>Local User Config</strong></a>
+        - for those users without root access when they installed Perl-MoSeS<em><strong>*</strong></em>
+    </li>
 </ul>
 <blockquote>
-  <p><em><strong>* when the panel is created, it makes a best attempt to determine whether or not the cpan module MOSES-MOBY was installed as root. If it was not, this sub panel is visible.</strong></em></p>
+    <p>
+        <em><strong>* when the panel is created, it makes a best attempt to determine whether or not the cpan module MOSES-MOBY was installed as root. If it was not, this sub panel is visible.</strong></em>
+    </p>
 </blockquote>
-<p><em><strong>Possible caveats:</strong></em></p>
+<p>
+    <em><strong>Possible caveats:</strong></em>
+</p>
 <ul>
-  <li> The actions in this panel depend on the availability of certain command line tools (installed by MOSES-MOBY, when you did <em><strong>'make install'</strong></em> of the cpan module) being available on the system PATH.</li>
+    <li>
+        The actions in this panel depend on the availability of certain command line tools (installed by MOSES-MOBY, when you did <em><strong>'make install'</strong></em>
+        of the cpan module) being available on the system PATH.
+    </li>
 </ul>
 <h3><a name="gen" id="gen"></a>Generate</h3>
-<p> There is one <em><strong>generator</strong></em> in this panel for creating services, with a couple of options.</p>
+<p>
+    There is one <em><strong>generator</strong></em>
+    in this panel for creating services, with a couple of options.
+</p>
 <ul>
-  <li><strong>Overwrite Existing Code</strong> - use this to overwrite any service code that has already been generated with MoSeS</li>
-  <li><strong>Generate CGI Service</strong> - use this to generate a category '<em><strong>cgi</strong></em>' BioMOBY web service.</li>
-  <li><strong>Generate SOAP Service</strong> - use this to generate a category '<em><strong>moby</strong></em>' BioMOBY web service.</li>
-</ul>
-<p>Once you have chosen your desired options, you can click on the <strong>Generate Skeletons</strong> button. This will go through and generate perl modules that represent the services that you selected in the '<em><strong>Service Browser</strong></em>'.</p>
-<p>All files are generated into your local <strong><em>Perl-MoSeS/</em></strong> installation. For instance, <em><strong>assuming</strong></em> that your <strong>username</strong> is <em><strong>moby_user</strong></em> and that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em>, then you could <strong>find</strong> your <strong>service skeletons</strong> in <em><strong>/home/moby_user/Perl-MoSeS/services/Service/</strong></em> directory.</p>
-<p>When you generate CGI based moby services, an additional file is generated into <em><strong>/Perl-MoSeS/cgi/</strong></em>. In order to <strong>implement the business logic</strong>, only the <strong>skeletons mentioned above</strong> are required. The files in the c<em><strong>gi/</strong></em> directory are only used for <strong>deploying your services</strong>.</p>
+    <li>
+        <strong>Overwrite Existing Code</strong>
+        - use this to overwrite any service code that has already been generated with MoSeS
+    </li>
+    <li>
+        <strong>Generate CGI Service</strong>
+        - use this to generate a category '<em><strong>cgi</strong></em>' BioMOBY web service.
+    </li>
+	<li>
+        <strong>Generate ASYNC CGI Service</strong>
+        - use this to generate a category '<em><strong>cgi-async</strong></em>' BioMOBY web service.
+    </li>
+    <li>
+        <strong>Generate SOAP Service</strong>
+        - use this to generate a category '<em><strong>moby</strong></em>' BioMOBY web service.
+    </li>
+	<li>
+        <strong>Generate ASYNC SOAP Service</strong>
+        - use this to generate a category '<em><strong>moby-async</strong></em>' BioMOBY web service.
+    </li>
+</ul>
+<p>
+    Once you have chosen your desired options, you can click on the <strong>Generate Skeletons</strong>
+    button. This will go through and generate perl modules that represent the services that you selected in the '<em><strong>Service Browser</strong></em>'.
+</p>
+<p>
+    All files are generated into your local <strong><em>Perl-MoSeS/</em></strong>
+    installation. For instance, <em><strong>assuming</strong></em>
+    that your <strong>username</strong>
+    is <em><strong>moby_user</strong></em>
+    and that your <strong>home directory</strong>
+    is <em><strong>/home/moby_user/</strong></em>, then you could <strong>find</strong>
+    your <strong>service skeletons</strong>
+    in <em><strong>/home/moby_user/Perl-MoSeS/services/Service/</strong></em>
+    directory.
+</p>
+<p>
+    When you generate CGI based moby services, an additional file is generated into <em><strong>/Perl-MoSeS/cgi/</strong></em>. In order to <strong>implement the business logic</strong>, only the <strong>skeletons mentioned above</strong>
+    are required. The files in the c<em><strong>gi/</strong></em>
+    directory are only used for <strong>deploying your services</strong>.
+</p>
 <h3><a name="local_user_config" id="local_user_config"></a>Local User Config</h3>
-<p>The configuration sub panel allows you to specify:</p>
+<p>
+    The configuration sub panel allows you to specify:
+</p>
 <ul>
-  <li><strong>Perl Install Path</strong> - this is the path to the PERL executable, for instance, /usr/bin/perl <strong><em>[required]</em></strong></li>
-  <li><strong>PERL5LIB dir</strong> - a directory to add to Perls' <strong>@INC <em>[required]</em></strong></li>
-  <li><strong>PERL5LIB dir(2)</strong> - another directory to add to Perls' <strong>@INC</strong> <strong><em>[optional]</em></strong></li>
-  <li><strong>MoSeS Scripts Dir </strong>- the directory that contains the moses-*.pl scripts <em><strong>[required]</strong></em></li>
+    <li>
+        <strong>Perl Install Path</strong>
+        - this is the path to the PERL executable, for instance, /usr/bin/perl <strong><em>[required]</em></strong>
+    </li>
+    <li>
+        <strong>PERL5LIB dir</strong>
+        - a directory to add to Perls' <strong>@INC <em>[required]</em></strong>
+    </li>
+    <li>
+        <strong>PERL5LIB dir(2)</strong>
+        - another directory to add to Perls' <strong>@INC</strong>
+        <strong><em>[optional]</em></strong>
+    </li>
+    <li>
+        <strong>MoSeS Scripts Dir </strong>- the directory that contains the moses-*.pl scripts <em><strong>[required]</strong></em>
+    </li>
 </ul>
-<p>Once this information is entered, and the <em><strong>'Confirm values are correct'</strong></em> is clicked, we check whether the required MOSES scripts are accessible. If everything is deemed to be fine, the other sub panels are enabled. Otherwise, you will be prompted to check your values.</p>
+<p>
+    Once this information is entered, and the <em><strong>'Confirm values are correct'</strong></em>
+    is clicked, we check whether the required MOSES scripts are accessible. If everything is deemed to be fine, the other sub panels are enabled. Otherwise, you will be prompted to check your values.
+</p>
 <h4>Help on setting your local user configuration</h4>
-<p>Some users find this information hard to obtain. One trick that I use, is to enter 'perl -V' at the command prompt. Among other things, one of the last things that you will see displayed is something like:</p>
+<p>
+    Some users find this information hard to obtain. One trick that I use, is to enter 'perl -V' at the command prompt. Among other things, one of the last things that you will see displayed is something like:
+</p>
 <pre>Built under linux<br />  Compiled at Nov 27 2007 10:44:36<br />  @INC:<br />    /etc/perl<br />    /usr/local/lib/perl/5.8.8<br />    /usr/local/share/perl/5.8.8<br />    /usr/lib/perl5<br />    /usr/share/perl5<br />    /usr/lib/perl/5.8<br />    /usr/share/perl/5.8<br />    /usr/local/lib/site_perl<br />    .</pre>
-<p>Keeping the above in mind and remembering that when you installed (locally for just you and not system wide!) MOSES-MOBY from the command prompt, you specified a <strong>PREFIX</strong>=/some/path/, similar to the following:</p>
+<p>
+    Keeping the above in mind and remembering that when you installed (locally for just you and not system wide!) MOSES-MOBY from the command prompt, you specified a <strong>PREFIX</strong>=/some/path/, similar to the following:
+</p>
 <pre>   perl Makefile.PL <strong>PREFIX</strong>=/home/ekawas/usr/local</pre>
-<p>The values that you would then enter for <strong>PERL5LIB</strong> are:</p>
+<p>
+    The values that you would then enter for <strong>PERL5LIB</strong>
+    are:
+</p>
 <ul>
-  <li>/home/ekawas/usr/local/lib/perl/5.8.8</li>
-  <li>/home/ekawas/usr/local/lib/site_perl</li>
+    <li>
+        /home/ekawas/usr/local/lib/perl/5.8.8
+    </li>
+    <li>
+        /home/ekawas/usr/local/lib/site_perl
+    </li>
 </ul>
-<p>In other words, you are interested in using the <strong>PREFIX</strong><em><strong>/lib/</strong></em> directories. </p>
-<p>The value that you should set for the <strong>'MoSeS Scripts Directory'</strong> are usually located in the <strong>PREFIX<em>/bin/</em></strong> directory.</p>
-<p>&nbsp;</p>
+<p>
+    In other words, you are interested in using the <strong>PREFIX</strong>
+    <em><strong>/lib/</strong></em>
+    directories. 
+</p>
+<p>
+    The value that you should set for the <strong>'MoSeS Scripts Directory'</strong>
+    are usually located in the <strong>PREFIX<em>/bin/</em></strong>
+    directory.
+</p>
+<p>
+    &nbsp;
+</p>
 <h2>Perl-MoSeS: Editor sub panel</h2>
-<p>This sub panel consists of an editor pane with various tools that will allow you to open and edit perl scripts generated by Perl-MoSeS. One of the nicer features of this editor, is the syntax highlighing that it performs on perl scripts.</p>
+<p>
+    This sub panel consists of an editor pane with various tools that will allow you to open and edit perl scripts generated by Perl-MoSeS. One of the nicer features of this editor, is the syntax highlighing that it performs on perl scripts.
+</p>
 <h3><a name="editor" id="editor"></a>Editor</h3>
-<p>The editor allows you to open and easily edit perl scripts that you generate with MoSeS.</p>
-<p>The editor has a really simple interface:</p>
+<p>
+    The editor allows you to open and easily edit perl scripts that you generate with MoSeS.
+</p>
+<p>
+    The editor has a really simple interface:
+</p>
 <ul>
-  <li><strong>Open</strong> - used to open a perl script.</li>
-  <li><strong>Save</strong> - used to save an open script.</li>
-  <li><strong>Close</strong> - used to remove the script from view.</li>
-  <li><strong>Font</strong> - used to select a font for the editor.</li>
+    <li>
+        <strong>Open</strong>
+        - used to open a perl script.
+    </li>
+    <li>
+        <strong>Save</strong>
+        - used to save an open script.
+    </li>
+    <li>
+        <strong>Close</strong>
+        - used to remove the script from view.
+    </li>
+    <li>
+        <strong>Font</strong>
+        - used to select a font for the editor.
+    </li>
 </ul>
-<p>There are also a two buttons for enlarging or shrinking the text in the editor. All of these buttons are located on a toolbar that you can detach from the panel.</p>
+<p>
+    There are also a two buttons for enlarging or shrinking the text in the editor. All of these buttons are located on a toolbar that you can detach from the panel.
+</p>
 <h2>&nbsp;</h2>
 <h2>Service deployment</h2>
-<p>Once you have created your service, you will want to deploy it. Depending on whether you have generated a SOAP service or a CGI based service, the steps to involved to deploy your service.</p>
+<p>
+    Once you have created your service, you will want to deploy it. Depending on whether you have generated a SOAP service or a CGI based service, the steps to involved to deploy your service.
+</p>
 <h3>Deploying a SOAP Service</h3>
-<p>Deploying a SOAP based service is both easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.</p>
-<p>An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong> is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em> and that your <strong>cgi-bin directory</strong> is located at <em><strong>/usr/lib/cgi-bin</strong></em>.</p>
-<p></p>
+<p>
+    Deploying a SOAP based service is both easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.
+</p>
+<p>
+    An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong>
+    is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+    is <em><strong>/home/moby_user/</strong></em>
+    and that your <strong>cgi-bin directory</strong>
+    is located at <em><strong>/usr/lib/cgi-bin</strong></em>.
+</p>
+<p>
+</p>
 <pre>   cd /usr/lib/cgi-bin
    sudo ln -s /home/moby_user/Perl-MoSeS/MobyServer.cgi .</pre>
-<p><strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong></p>
-<p>That is all there is to it. Now you can use <em>Dashboard's</em> <em><strong>Simple Client</strong></em> panel to test your service!</p>
+<p>
+    <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+    That is all there is to it. Now you can use <em>Dashboard's</em>
+    <em><strong>Simple Client</strong></em>
+    panel to test your service!
+</p>
+<h3>Deploying an ASYNC SOAP Service</h3>
+<p>
+    Deploying asynchronous SOAP based service is also easy and straightforward. Best of all, you only need to worry about deploying your service once (all subsequent services that you generate dont require you to do anything!). The reason for this is that SOAP based services utilize a dispatcher file that maps client requests to an appropriate Perl module. Perl-MoSeS only requires you to place a symbolic link to this dispatcher in your web servers cgi-bin directory. Once this is complete, Perl-MoSeS takes care of the rest each and every time you generate new services.
+</p>
+<p>
+    An example of how to deploy your service is shown below. The example assumes that your <strong>username</strong>
+    is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+    is <em><strong>/home/moby_user/</strong></em>
+    and that your <strong>cgi-bin directory</strong>
+    is located at <em><strong>/usr/lib/cgi-bin</strong></em>.
+</p>
+<p>
+</p>
+<pre>   cd /usr/lib/cgi-bin
+   sudo ln -s /home/moby_user/Perl-MoSeS/AsyncMobyServer.cgi .</pre>
+<p>
+    <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+    That is all there is to it. Now you can use <em>Dashboard's</em>
+    <em><strong>Simple Client</strong></em>
+    panel to test your service!
+</p>
 <h3>Deploying a CGI Service</h3>
-<p>Deploying a CGI based service is a lot like deploying a SOAP based one. Unfortunately, every CGI based service that you generate requires you to deploy it onto your web server. This is in constrast to the SOAP services mentioned above.</p>
-<p>When you generate CGI services, Perl-MoSeS generates 2 files. Your implementation file and a cgi script to be placed on your web server. Perl-MoSeS only requires you to place a symbolic link to this cgi script in your web servers cgi-bin directory.</p>
-<p>You might ask, where is this cgi script? All cgi scripts generated by Perl-MoSeS are placed in the <strong>Perl-MoSeS/cgi/</strong> directory.</p>
-<p>An example of how to deploy your CGI service is shown below. The example assumes that your <strong>username</strong> is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong> is <em><strong>/home/moby_user/</strong></em> and that your <strong>cgi-bin directory</strong> is located at <em><strong>/usr/lib/cgi-bin</strong></em>. Moreover, we will be deploying the <strong>CGI service</strong> <em><strong>HelloBiomobyWorld</strong></em> that is <strong>provided by</strong> <em><strong>samples.jmoby.net</strong></em>.</p>
-<p></p>
+<p>
+    Deploying a CGI based service is a lot like deploying a SOAP based one. Unfortunately, every CGI based service that you generate requires you to deploy it onto your web server. This is in constrast to the SOAP services mentioned above.
+</p>
+<p>
+    When you generate CGI services, Perl-MoSeS generates 2 files. Your implementation file and a cgi script to be placed on your web server. Perl-MoSeS only requires you to place a symbolic link to this cgi script in your web servers cgi-bin directory.
+</p>
+<p>
+    You might ask, where is this cgi script? All cgi scripts generated by Perl-MoSeS are placed in the <strong>Perl-MoSeS/cgi/</strong>
+    directory.
+</p>
+<p>
+    An example of how to deploy your CGI service is shown below. The example assumes that your <strong>username</strong>
+    is <em><strong>moby_user</strong></em>, that your <strong>home directory</strong>
+    is <em><strong>/home/moby_user/</strong></em>
+    and that your <strong>cgi-bin directory</strong>
+    is located at <em><strong>/usr/lib/cgi-bin</strong></em>. Moreover, we will be deploying the <strong>CGI service</strong>
+    <em><strong>HelloBiomobyWorld</strong></em>
+    that is <strong>provided by</strong>
+    <em><strong>samples.jmoby.net</strong></em>.
+</p>
+<p>
+</p>
 <pre>   cd /usr/lib/cgi-bin
    sudo ln -s /home/moby_user/Perl-MoSeS/cgi/samples/jmoby/net/HelloBiomobyWorld.cgi .</pre>
-<p><strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong></p>
-<p>That is all there is to it. Now you can use <em>Dashboard's</em> <em><strong>Simple Client</strong></em> panel to test your service!</p>
+<p>
+    <strong><em>Please make sure that the complete path the /home/moby_user/Perl-MoSeS is readable by your web server's process.</em></strong>
+</p>
+<p>
+    That is all there is to it. Now you can use <em>Dashboard's</em>
+    <em><strong>Simple Client</strong></em>
+    panel to test your service!
+</p>



From kawas at dev.open-bio.org  Tue Apr  7 16:21:25 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 12:21:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071621.n37GLP0i003153@dev.open-bio.org>


kawas
Tue Apr  7 12:21:25 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES
In directory dev.open-bio.org:/tmp/cvs-serv3118/MOSES-MOBY/lib/MOSES

Modified Files:
	MOBY.pm 
Log Message:
added some references to async cgi documentation
moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/01/13 19:41:01	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/07 16:21:25	1.8
@@ -123,6 +123,8 @@
 
 =over 4
 
+=item * Support for Asynchronous CGI based moby services
+
 =item * Support for CGI based moby services
 
 =item * Support for Asynchronous based moby services
@@ -2054,6 +2056,7 @@
 
 	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_soap_service.html' target='_blank'>Tutorial for creating SOAP based Biomoby Services</a><br/>
 	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_service.html' target='_blank'>Tutorial for creating CGI based Biomoby Services</a>
+	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html' target='_blank'>Tutorial for creating Asynchronous CGI based Biomoby Services</a>
 	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html' target='_blank'>Tutorial for creating Asynchronous SOAP based Biomoby Services</a>
 
 =end html



From kawas at dev.open-bio.org  Tue Apr  7 16:21:49 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 12:21:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071621.n37GLnkH003211@dev.open-bio.org>


kawas
Tue Apr  7 12:21:49 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv3176/MOSES-MOBY

Modified Files:
	Makefile.PL 
Log Message:
updated version for cpan release
moby-live/Perl/MOSES-MOBY Makefile.PL,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/03/30 13:18:33	1.13
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/07 16:21:49	1.14
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.87';
+	version '0.88';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';



From kawas at dev.open-bio.org  Tue Apr  7 16:29:47 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 12:29:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071629.n37GTlWF003330@dev.open-bio.org>


kawas
Tue Apr  7 12:29:47 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv3295/MOSES-MOBY

Modified Files:
	META.yml 
Log Message:
updated META.yml to include up to date dependencies and to update the modules' version number
moby-live/Perl/MOSES-MOBY META.yml,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2008/05/07 17:26:15	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/07 16:29:47	1.6
@@ -21,18 +21,23 @@
     - t
 requires:
   Carp: 0
+  CGI: 0
   Class::Inspector: 1.17
   Config::Simple: 4.58
   File::HomeDir: 0.65
   File::ShareDir: 0.05
   File::Spec: 0.8
+  HTTP::Date: 5.81
   IO::Prompt: 0.99.2
   IO::Stringy: 2.11
   Log::Log4perl: 1.12
+  MOBY::Client::Central: 1.06
   Params::Util: 0.28
   SOAP::Lite: 0.69
   Template: 1.11
   Unicode::String: 2.09
+  Want: 0.18
+  WSRF::Lite: 0.8.2.5
   XML::LibXML: 1.62
-version: 0.85
+version: 0.88
 



From kawas at dev.open-bio.org  Tue Apr  7 18:13:12 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 14:13:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071813.n37IDCBP003600@dev.open-bio.org>


kawas
Tue Apr  7 14:13:11 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES
In directory dev.open-bio.org:/tmp/cvs-serv3565/MOSES-MOBY/lib/MOSES

Modified Files:
	MOBY.pm 
Log Message:
links to tutorials appear on only one line ... added line breaks to the links
moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/07 16:21:25	1.8
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/07 18:13:11	1.9
@@ -2055,9 +2055,9 @@
 =begin html
 
 	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_soap_service.html' target='_blank'>Tutorial for creating SOAP based Biomoby Services</a><br/>
-	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_service.html' target='_blank'>Tutorial for creating CGI based Biomoby Services</a>
-	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html' target='_blank'>Tutorial for creating Asynchronous CGI based Biomoby Services</a>
-	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html' target='_blank'>Tutorial for creating Asynchronous SOAP based Biomoby Services</a>
+	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_service.html' target='_blank'>Tutorial for creating CGI based Biomoby Services</a><br/>
+	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_cgi_async_service.html' target='_blank'>Tutorial for creating Asynchronous CGI based Biomoby Services</a><br/>
+	<a href='http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/MOBY-S_API/Perl/construct_moses_async_service.html' target='_blank'>Tutorial for creating Asynchronous SOAP based Biomoby Services</a><br/>
 
 =end html
 



From kawas at dev.open-bio.org  Tue Apr  7 18:48:24 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 7 Apr 2009 14:48:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904071848.n37ImO81003683@dev.open-bio.org>


kawas
Tue Apr  7 14:48:24 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/t
In directory dev.open-bio.org:/tmp/cvs-serv3648/MOSES-MOBY/t

Modified Files:
	MOSES-MOBY-Cache.t 
Log Message:
changed test to look for != '' rather than a hard coded string because people may be using a non-default registry
moby-live/Perl/MOSES-MOBY/t MOSES-MOBY-Cache.t,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Cache.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Cache.t	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/t/MOSES-MOBY-Cache.t	2009/04/07 18:48:24	1.4
@@ -38,7 +38,7 @@
 $cache = new MOSES::MOBY::Cache::Central( );
 ok($cachedir ne $cache->cachedir, "cachedir - default during constructor") 
 	or diag('cachedir was not set properly.');
-ok('default' eq $cache->registry, "registry - default during constructor") 
+ok('' ne $cache->registry, "registry - default during constructor") 
 	or diag('registry was not set properly.');
 ok('' ne $cache->_namespace, "namespace - set during default constructor") 
 	or diag($cache->_namespace . " is not the same as $namespace");



From kawas at dev.open-bio.org  Wed Apr  8 14:51:50 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 10:51:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904081451.n38EpoUE008297@dev.open-bio.org>


kawas
Wed Apr  8 10:51:50 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv8262/MOBY-Server/lib/MOBY

Modified Files:
	Central.pm 
Log Message:
fixed regex that checks datatype name when registering a datatype.
moby-live/Perl/MOBY-Server/lib/MOBY Central.pm,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2009/03/26 18:41:41	1.8
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/Central.pm	2009/04/08 14:51:50	1.9
@@ -318,7 +318,7 @@
 	return &_error("Object name may not contain spaces or other characters invalid in a URN",
 		""
 	  )
-	  if $term =~ /\s\"\&\<\>\[\]\^\`\{\|\}\~/;
+	  if $term =~ /[\/\'\\\s\"\&\<\>\[\]\^\`\{\|\}\~]/;
 	if ( $term =~ m"^(([^:/?#]+):)?(//([^/?#]*))?([^?#]*)(\?([^#]*))?(#(.*))?" )
 	{    # matches a URI
 		return &_error( "Object name may not be an URN or URI", "" ) if $1;



From kawas at dev.open-bio.org  Wed Apr  8 15:39:40 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 11:39:40 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904081539.n38FdetE008425@dev.open-bio.org>


kawas
Wed Apr  8 11:39:40 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv8390/MOBY-Server

Modified Files:
	Changes 
Log Message:

moby-live/Perl/MOBY-Server Changes,1.23,1.24
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/06 14:16:39	1.23
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/08 15:39:40	1.24
@@ -1,5 +1,9 @@
 Revision history for Perl extension MOBY.
 
+1.09
+    - Fixed bug where data types registered into registry could contain
+      illegal characters.
+    
 1.08
     - Fixed META.yml in the distribution. Please refer to changes for 1.07.
 



From kawas at dev.open-bio.org  Wed Apr  8 16:16:49 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 12:16:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904081616.n38GGnsC008587@dev.open-bio.org>


kawas
Wed Apr  8 12:16:48 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/t
In directory dev.open-bio.org:/tmp/cvs-serv8552/MOBY-Server/t

Modified Files:
	Client-Central.t 
Log Message:
added some tests to test registration of datatypes with characters that break things in their names.
moby-live/Perl/MOBY-Server/t Client-Central.t,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/t/Client-Central.t,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY-Server/t/Client-Central.t	2009/03/26 18:42:20	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/t/Client-Central.t	2009/04/08 16:16:48	1.4
@@ -218,6 +218,94 @@
 $r = $C->deregisterObjectClass( objectType => "Rubbish_Art" );
 
 
+# confirm that we cannot register a datatype with odd characters in its name
+$r = $C->registerObjectClass(
+	(
+	   objectType    => "Rubbish_'Art",
+	   description   => "a human-readable description of the object",
+	   contactEmail  => 'your at email.address',
+	   authURI       => "test.suite.com",
+	   Relationships => {
+						  ISA => [
+								   {
+									 object      => 'Object',
+									 articleName => 'article1'
+								   }
+						  ],
+						  HASA => [
+									{
+									  object      => 'Object',
+									  articleName => 'articleName3'
+									},
+						  ]
+	   }
+	)
+);
+ok( !$r->success, "Object registration correctly failed" )
+  or diag(
+	"Shouldn't be possible to register Object with an invalid character in its name!"
+	  . $r->message );
+$r = $C->deregisterObjectClass( objectType => "Rubbish_'Art" );
+
+# confirm that we cannot register a datatype with odd characters in its name
+$r = $C->registerObjectClass(
+	(
+	   objectType    => "Rubbish_\"Art",
+	   description   => "a human-readable description of the object",
+	   contactEmail  => 'your at email.address',
+	   authURI       => "test.suite.com",
+	   Relationships => {
+						  ISA => [
+								   {
+									 object      => 'Object',
+									 articleName => 'article1'
+								   }
+						  ],
+						  HASA => [
+									{
+									  object      => 'Object',
+									  articleName => 'articleName3'
+									},
+						  ]
+	   }
+	)
+);
+ok( !$r->success, "Object registration correctly failed" )
+  or diag(
+	"Shouldn't be possible to register Object with an invalid character in its name!"
+	  . $r->message );
+$r = $C->deregisterObjectClass( objectType => "Rubbish_\"Art" );
+
+# confirm that we cannot register a datatype with odd characters in its name
+$r = $C->registerObjectClass(
+	(
+	   objectType    => "Rubbish_/Art",
+	   description   => "a human-readable description of the object",
+	   contactEmail  => 'your at email.address',
+	   authURI       => "test.suite.com",
+	   Relationships => {
+						  ISA => [
+								   {
+									 object      => 'Object',
+									 articleName => 'article1'
+								   }
+						  ],
+						  HASA => [
+									{
+									  object      => 'Object',
+									  articleName => 'articleName3'
+									},
+						  ]
+	   }
+	)
+);
+ok( !$r->success, "Object registration correctly failed" )
+  or diag(
+	"Shouldn't be possible to register Object with an invalid character in its name!"
+	  . $r->message );
+$r = $C->deregisterObjectClass( objectType => "Rubbish_/Art" );
+
+
 ##############     NAMESPACE REGISTRATION     ##############
 # Register a new namespace
 my %Namespace = (



From kawas at dev.open-bio.org  Wed Apr  8 20:46:23 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 16:46:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082046.n38KkNM1009086@dev.open-bio.org>


kawas
Wed Apr  8 16:46:23 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv9050/MOSES-MOBY/lib/MOSES/MOBY

Modified Files:
	Async.pm 
Log Message:
MOBY tag was missing from the response.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Async.pm,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm	2009/03/30 13:16:00	1.1
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Async.pm	2009/04/08 20:46:23	1.2
@@ -296,7 +296,8 @@
 		$WSRF::WSRP::Private{$property_pid}               = '';
 		$WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
 		$WSRF::WSRP::ResourceProperties{$property_result} =
-		  $out_package_for_this_job->job_by_id( $job->jid )->toXML->toString(0);
+		  #$out_package_for_this_job->job_by_id( $job->jid )->toXML->toString(0);
+		  $out_package_for_this_job->toXML->toString(0);
 		$lock->toFile();
 
 		# Exits the child process



From kawas at dev.open-bio.org  Wed Apr  8 22:40:12 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:40:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082240.n38MeCUO009531@dev.open-bio.org>


kawas
Wed Apr  8 18:40:11 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES
In directory dev.open-bio.org:/tmp/cvs-serv9496/MOSES-MOBY/lib/MOSES

Modified Files:
	MOBY.pm 
Log Message:
updated doc
moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/07 18:13:11	1.9
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/08 22:40:11	1.10
@@ -907,6 +907,8 @@
    rather than load the base" enabled.<p/>
    Option <strong>-c</strong> generates both a <a href="#perl_modules_representing_bases_of_service_implementations">service implementation</a> 
      as well as a CGI dispatcher script.<p/>
+   Option <strong>-C</strong> generates both a <a href="#perl_modules_representing_bases_of_service_implementations">service implementation</a> 
+     as well as an Asynchronous CGI dispatcher script.<p/>
    Option <strong>-A</strong> generates both a <a href="#perl_modules_representing_bases_of_service_implementations">service implementation</a> 
      as well as an asynchronous module (and it updates the dispatcher table, as well).<p/>
    Option <strong>-u</strong> updates the service cache.<p/>
@@ -949,11 +951,11 @@
 IRRI, MIPS, default, iCAPTURE, testing
 $Registries = {
    'testing' => {
-      'namespace' => 'http://mobycentral.cbr.nrc.ca:8080/MOBY/Central',
+      'namespace' => 'http://bioinfo.icapture.ubc.ca/MOBY/Central',
       'public' => 'yes',
       'name' => 'Testing BioMoby registry',
       'contact' => 'Edward Kawas (edward.kawas at gmail.com)',
-      'endpoint' => 'http://mobycentral.cbr.nrc.ca:8080/cgi-bin/MOBY05/mobycentral.pl'
+      'endpoint' => 'http://bioinfo.icapture.ubc.ca/cgi-bin/mobycentral/MOBY-Central.pl'
       },
    'IRRI' => {
       'namespace' => 'http://cropwiki.irri.org/MOBY/Central',
@@ -967,12 +969,12 @@
        'endpoint' => 'http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl'
        },
    'iCAPTURE' => {
-       'namespace' => 'http://mobycentral.icapture.ubc.ca/MOBY/Central',
+       'namespace' => 'http://moby.ucalgary.ca/MOBY/Central',
        'text' => 'A curated public registry hosted at the iCAPTURE Centre, Vancouver',
        'public' => 'yes',
        'name' => 'iCAPTURE Centre, Vancouver',
        'contact' => 'Edward Kawas (edward.kawas at gmail.com)',
-       'endpoint' => 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl'
+       'endpoint' => 'http://moby.ucalgary.ca/moby/MOBY-Central.pl'
        },
    'default' => $Registries->{'iCAPTURE'},
    'MIPS' => {



From kawas at dev.open-bio.org  Wed Apr  8 22:41:26 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:41:26 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082241.n38MfQnH009592@dev.open-bio.org>


kawas
Wed Apr  8 18:41:26 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv9557/MOBY-Server

Modified Files:
	Changes 
Log Message:
updated changes
moby-live/Perl/MOBY-Server Changes,1.24,1.25
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/08 15:39:40	1.24
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/08 22:41:26	1.25
@@ -3,6 +3,7 @@
 1.09
     - Fixed bug where data types registered into registry could contain
       illegal characters.
+    	* added some tests to Client-Central.t to test for this condition 
     
 1.08
     - Fixed META.yml in the distribution. Please refer to changes for 1.07.



From kawas at dev.open-bio.org  Wed Apr  8 22:41:39 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:41:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082241.n38MfdHA009632@dev.open-bio.org>


kawas
Wed Apr  8 18:41:39 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv9597/MOBY-Server

Modified Files:
	Makefile.PL 
Log Message:

moby-live/Perl/MOBY-Server Makefile.PL,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/06 14:16:39	1.16
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/08 22:41:39	1.17
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.08';
+	version '1.09';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';



From kawas at dev.open-bio.org  Wed Apr  8 22:42:51 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:42:51 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082242.n38MgpDN009728@dev.open-bio.org>


kawas
Wed Apr  8 18:42:51 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv9693/MOSES-MOBY/bin/scripts

Modified Files:
	moses-install.pl 
Log Message:
updated the 'Help' for this script
moby-live/Perl/MOSES-MOBY/bin/scripts moses-install.pl,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-install.pl,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-install.pl	2009/03/30 13:17:04	1.6
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-install.pl	2009/04/08 22:42:51	1.7
@@ -24,6 +24,7 @@
        services.log
        parser.log
        MobyServer.cgi
+       AsyncMobyServer.cgi
     The existing files are not overwritten - unless an option -F
     has been used.
 
@@ -66,7 +67,7 @@
 		check_module ($module);
     }
     # check for async libraries if user wants to ....
-    print STDOUT "Shall we check for the moby-async libraries\n\t(do this only if you plan on creating async moby services)? y/n [n]";
+    print STDOUT "Shall we check for the moby-async libraries\n\t(do this only if you plan on creating soap based\n\t async moby services)? y/n [n]";
     my $tmp = <STDIN>;
     $tmp =~ s/\s//g; 
     if ($tmp =~ /y/i) {



From kawas at dev.open-bio.org  Wed Apr  8 22:43:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 8 Apr 2009 18:43:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904082243.n38MhAwW009830@dev.open-bio.org>


kawas
Wed Apr  8 18:43:10 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv9787/MOSES-MOBY

Modified Files:
	META.yml Changes Makefile.PL 
Log Message:
updated version numbers and history
moby-live/Perl/MOSES-MOBY META.yml,1.6,1.7 Changes,1.11,1.12 Makefile.PL,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/07 16:29:47	1.6
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/08 22:43:10	1.7
@@ -39,5 +39,5 @@
   Want: 0.18
   WSRF::Lite: 0.8.2.5
   XML::LibXML: 1.62
-version: 0.88
+version: 0.89
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/03/30 13:18:33	1.11
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/08 22:43:10	1.12
@@ -1,11 +1,15 @@
 Revision history for Perl extension MOSES::MOBY.
 
+.89 
+	- The tag MOBY was missing in the async cgi
+	  response for 'results'.
+	- updated some documentation
+
 .88 
 	- Added support for Asynchronous POST services.
 	  moses-service-tester, moses-generate-services,
 	  and moses-install all have been updated.
 	  
-
 .87 
 	- fixed a string append bug where '+' was used
 	  instead of '.'

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/07 16:21:49	1.14
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/08 22:43:10	1.15
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.88';
+	version '0.89';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';



From kawas at dev.open-bio.org  Thu Apr  9 13:01:15 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 9 Apr 2009 09:01:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904091301.n39D1Fbl012449@dev.open-bio.org>


kawas
Thu Apr  9 09:01:15 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv12414/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
noticed that one of the 'Actions' was incorrectly labeled, so I fixed it. This should have no effect to MOSES services because we dont really validate this message (psst ... dont tell anyone)
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.9,1.10
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.9
retrieving revision 1.10
diff -u -r1.9 -r1.10
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/02 16:10:14	1.9
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/09 13:01:15	1.10
@@ -581,7 +581,7 @@
 	my ( $url, $id ) = @_;
 	return <<"END OF XML";
 <moby-wsrf>
-<wsa:Action xmlns:wsa="http://www.w3.org/2005/08/addressing">http://docs.oasis-open.org/wsrf/rpw-2/GetResourceProperty/GetResourcePropertiesRequest</wsa:Action>
+<wsa:Action xmlns:wsa="http://www.w3.org/2005/08/addressing">http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest</wsa:Action>
 <wsa:To xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd" xmlns:wsa="http://www.w3.org/2005/08/addressing" wsu:Id="To">$url</wsa:To>
 <mobyws:ServiceInvocationId xmlns:mobyws="http://biomoby.org/" xmlns:wsa="http://www.w3.org/2005/08/addressing" wsa:IsReferenceParameter="true">$id</mobyws:ServiceInvocationId>
 </moby-wsrf>



From kawas at dev.open-bio.org  Wed Apr 15 16:38:57 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:38:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151638.n3FGcvHe021303@dev.open-bio.org>


kawas
Wed Apr 15 12:38:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv21256/MOBY-Server

Modified Files:
	META.yml Changes Makefile.PL MANIFEST 
Log Message:
Added a cgi script that obtains WSDL for services in a RESTful manner. Thank you to Jos? Manuel Rodr?guez Carrasco!
moby-live/Perl/MOBY-Server META.yml,1.7,1.8 Changes,1.25,1.26 Makefile.PL,1.17,1.18 MANIFEST,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2009/04/06 14:16:39	1.7
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/META.yml	2009/04/15 16:38:57	1.8
@@ -44,4 +44,4 @@
   XML::SemanticCompare: 0
   XML::Simple: 2.18
   WSRF::Lite: 0.8.2.5
-version: 1.08
+version: 1.10

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.25
retrieving revision 1.26
diff -u -r1.25 -r1.26
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/08 22:41:26	1.25
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/15 16:38:57	1.26
@@ -1,5 +1,11 @@
 Revision history for Perl extension MOBY.
 
+1.10
+    - Added a RESTful WSDL page to the installation. Basically, you do
+      a GET on BioMobyWSDL/authURI/servicename/ and a WSDL for that service
+      is returned. 
+      ** Thanks to Jos? Manuel Rodr?guez Carrasco ** 
+
 1.09
     - Fixed bug where data types registered into registry could contain
       illegal characters.

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/08 22:41:39	1.17
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Makefile.PL	2009/04/15 16:38:57	1.18
@@ -3,7 +3,7 @@
 
 	# Define metadata
 	name 'MOBY';
-	version '1.09';
+	version '1.10';
 	license 'perl';
 	abstract
 'This distribution is for communicating with or creating your own MOBY Central registry';

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2009/04/03 16:36:35	1.11
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/MANIFEST	2009/04/15 16:38:57	1.12
@@ -91,6 +91,7 @@
 README
 share/cgi/AgentRDFValidator
 share/cgi/authority.pl
+share/cgi/BioMobyWSDL
 share/cgi/GenerateRDF.cgi
 share/cgi/Moby
 share/cgi/MOBY-Admin.pl



From kawas at dev.open-bio.org  Wed Apr 15 16:38:57 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:38:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151638.n3FGcvpo021339@dev.open-bio.org>


kawas
Wed Apr 15 12:38:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv21256/MOBY-Server/bin/scripts

Modified Files:
	moby-s-install.pl 
Log Message:
Added a cgi script that obtains WSDL for services in a RESTful manner. Thank you to Jos? Manuel Rodr?guez Carrasco!
moby-live/Perl/MOBY-Server/bin/scripts moby-s-install.pl,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2008/11/25 19:47:23	1.14
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/bin/scripts/moby-s-install.pl	2009/04/15 16:38:57	1.15
@@ -1481,6 +1481,12 @@
 	    { '#!/usr/bin/perl -w' => "#!$perl_exec", }
 	    );
 	file_from_template(
+	    "$apache_cgi/BioMobyWSDL",
+	    File::ShareDir::dist_file( 'MOBY', 'cgi/BioMobyWSDL' ),
+	    'MOBY-Central RESTful WSDL generator',
+	    { '#!/usr/bin/perl -w' => "#!$perl_exec", }
+	    );
+	file_from_template(
 	    "$apache_cgi/ServicePingerValidator",
 	    File::ShareDir::dist_file(
 		'MOBY', 'cgi/ServicePingerValidator'



From kawas at dev.open-bio.org  Wed Apr 15 16:38:57 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:38:57 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151638.n3FGcvND021318@dev.open-bio.org>


kawas
Wed Apr 15 12:38:57 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv21256/MOBY-Server/share/cgi

Added Files:
	BioMobyWSDL 
Log Message:
Added a cgi script that obtains WSDL for services in a RESTful manner. Thank you to Jos? Manuel Rodr?guez Carrasco!
moby-live/Perl/MOBY-Server/share/cgi BioMobyWSDL,NONE,1.1


From kawas at dev.open-bio.org  Wed Apr 15 16:54:25 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:54:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151654.n3FGsP4w021422@dev.open-bio.org>


kawas
Wed Apr 15 12:54:25 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv21387/MOBY-Server/share/cgi

Modified Files:
	Moby 
Log Message:
Added an example for BioMobyWSDL to the list of installed scripts.
moby-live/Perl/MOBY-Server/share/cgi Moby,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/Moby,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/Moby	2008/02/21 00:21:27	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/Moby	2009/04/15 16:54:25	1.2
@@ -277,6 +277,18 @@
 target="_blank">click here.</a><br/>
   </p>
 </blockquote>
+<p><a href="http://$location/cgi-bin/BioMobyWSDL/">BioMobyWSDL 
+</a> - RESTful app that returns WSDL for a given service. 
+</p>
+<blockquote>
+  <p>For example,</p>
+  <ol>
+    <li><a href="http://$location/cgi-bin/BioMobyWSDL/bioinfo.icapture.ubc.ca/getGoTerm">WSDL for getGoTerm, 
+    by the authority bioinfo.icapture.ubc.ca </a></li>
+  </ol>
+  <p>All that you have to do is append <strong><em>authURI/servicename</em></strong> to the path of the script. <br/>
+  The WSDL for that service, if it exists, will be returned!</p>
+</blockquote>
 <p><a href="http://$location/cgi-bin/RESOURCES/">The Resources 'Scripts' 
 </a> - Servlets that return the RDF representations of the BioMOBY 
 ontologies. </p>



From kawas at dev.open-bio.org  Wed Apr 15 16:56:01 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 12:56:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151656.n3FGu12b021462@dev.open-bio.org>


kawas
Wed Apr 15 12:56:01 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv21427/MOBY-Server/share/cgi

Modified Files:
	BioMobyWSDL 
Log Message:
fixed the $id: $ portion of the script at the top to correctly display script name and version
moby-live/Perl/MOBY-Server/share/cgi BioMobyWSDL,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL	2009/04/15 16:38:57	1.1
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL	2009/04/15 16:56:01	1.2
@@ -1,6 +1,6 @@
 #!/usr/bin/perl -W
 # _________________________________________________________________
-#$Id: getMOBYWSDL,v 1.0
+# $Id$
 # Developed by: Jose Manuel Rodriguez Carrasco -jmrodriguez at cnio.es-
 # Created: 13-April-2009
 # Updated: 14-April-2009



From kawas at dev.open-bio.org  Wed Apr 15 17:45:23 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 13:45:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151745.n3FHjN5u021811@dev.open-bio.org>


kawas
Wed Apr 15 13:45:23 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv21776/MOBY-Server/lib/MOBY

Modified Files:
	CommonSubs.pm 
Log Message:
got fed up of seeing a warning from CommonSubs, so I fixed the underlying problem
moby-live/Perl/MOBY-Server/lib/MOBY CommonSubs.pm,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm	2008/09/22 15:42:27	1.6
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/lib/MOBY/CommonSubs.pm	2009/04/15 17:45:23	1.7
@@ -1171,7 +1171,17 @@
       . "\n called from line $line";
     return '';
   }
-  return ( $xref->getAttributeNode($attr) || $xref->getAttributeNode( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr" ) );
+  # check for just the attribute by name
+  return $xref->getAttributeNode($attr)
+    if $xref->getAttributeNode($attr);
+  # check for a namespaced attribute by name
+  return $xref->getAttributeNodeNS('http://www.biomoby.org/moby', $attr)
+  	if $xref->getAttributeNodeNS('http://www.biomoby.org/moby', $attr);
+  # check for a namespaced attribute with a prefix ... this is probably redundant!
+  return $xref->getAttributeNode( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") 
+  	if $xref->lookupNamespacePrefix('http://www.biomoby.org/moby');
+  # cant find it ...
+  return '';
 }
 
 sub _moby_getAttribute {
@@ -1191,7 +1201,18 @@
     . "\n called from line $line";
     return '';
   }
-  return (   $xref->getAttribute($attr) || $xref->getAttribute( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") );
+  
+  # check for just the attribute by name
+  return $xref->getAttribute($attr)
+    if $xref->getAttribute($attr);
+  # check for a namespaced attribute by name
+  return $xref->getAttributeNS('http://www.biomoby.org/moby', $attr)
+  	if $xref->getAttributeNS('http://www.biomoby.org/moby', $attr);
+  # check for a namespaced attribute with a prefix ... this is probably redundant!
+  return $xref->getAttribute( $xref->lookupNamespacePrefix('http://www.biomoby.org/moby') . ":$attr") 
+  	if $xref->lookupNamespacePrefix('http://www.biomoby.org/moby');
+  # cant find it ...
+  return '';
 }
 
 sub _makeXrefType {



From kawas at dev.open-bio.org  Wed Apr 15 17:45:23 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 15 Apr 2009 13:45:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904151745.n3FHjNln021829@dev.open-bio.org>


kawas
Wed Apr 15 13:45:23 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server
In directory dev.open-bio.org:/tmp/cvs-serv21776/MOBY-Server

Modified Files:
	Changes 
Log Message:
got fed up of seeing a warning from CommonSubs, so I fixed the underlying problem
moby-live/Perl/MOBY-Server Changes,1.26,1.27
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/Changes,v
retrieving revision 1.26
retrieving revision 1.27
diff -u -r1.26 -r1.27
--- /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/15 16:38:57	1.26
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/Changes	2009/04/15 17:45:23	1.27
@@ -5,6 +5,9 @@
       a GET on BioMobyWSDL/authURI/servicename/ and a WSDL for that service
       is returned. 
       ** Thanks to Jos? Manuel Rodr?guez Carrasco ** 
+    - Updated _moby_getAttribute and _moby_getAttributeNode so that the
+      warning regarding unitialized value is no longer given when running
+      t/CommonSubs.t or using CommonSubs.pm.
 
 1.09
     - Fixed bug where data types registered into registry could contain



From kawas at dev.open-bio.org  Thu Apr 16 18:13:03 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Apr 2009 14:13:03 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904161813.n3GID3hI029989@dev.open-bio.org>


kawas
Thu Apr 16 14:13:03 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates
In directory dev.open-bio.org:/tmp/cvs-serv29954/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service-cgi-async.tt 
Log Message:
added a check for \r because our service message was been misinterpreted ...
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service-cgi-async.tt,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt	2009/04/02 14:53:26	1.2
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-cgi-async.tt	2009/04/16 18:13:03	1.3
@@ -117,8 +117,10 @@
 sub call_service {
 	# get the data from the 'data' parameter
 	my $data = $q->param('data') || $q->param('POSTDATA') || "";
+	# remove any \r because these cause errors in our messages with newlines
+	$data =~ s/\r//gi;
 	# call the service
-	 __PACKAGE__->[% obj.name %]($data);
+	__PACKAGE__->[% obj.name %]($data);
 	
 }
 



From kawas at dev.open-bio.org  Thu Apr 16 18:14:34 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Apr 2009 14:14:34 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904161814.n3GIEYoT030047@dev.open-bio.org>


kawas
Thu Apr 16 14:14:34 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30012/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent changes.
moby-live/Perl/MOSES-MOBY Changes,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/08 22:43:10	1.12
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/16 18:14:34	1.13
@@ -1,5 +1,10 @@
 Revision history for Perl extension MOSES::MOBY.
 
+.90
+	- bug fix: when sending data with newlines on
+	  a WinOS, \r was causing problems with the
+	  incoming message.
+
 .89 
 	- The tag MOBY was missing in the async cgi
 	  response for 'results'.



From kawas at dev.open-bio.org  Thu Apr 16 18:17:24 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Apr 2009 14:17:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904161817.n3GIHOGU030089@dev.open-bio.org>


kawas
Thu Apr 16 14:17:24 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv30054/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
message for asynchronous post was being truncated (sometimes ...). update how we post the data.
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/09 13:01:15	1.10
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/16 18:17:24	1.11
@@ -14,7 +14,7 @@
 	getopts('hdvl:e:c:C:a:');
 
 	# usage
-	if ( $opt_h or ( @ARGV == 0 and ( not $opt_c ) ) ) {
+	if ( $opt_h or ( @ARGV == 0 and ( not $opt_c or not $opt_C ) ) ) {
 		print STDOUT <<'END_OF_USAGE';
 Calling a BioMoby services (without using SOAP, just locally).
 Usage: # calling a local module representing a service, without using SOAP
@@ -291,8 +291,8 @@
 	# post to the web service
 	my $ua = LWP::UserAgent->new;
 	my $req = HTTP::Request->new( POST => $opt_C );
-	$req->content_type('application/x-www-form-urlencoded');
-	$req->content("data=$input");
+	$req->content_type('text/xml');
+	$req->content("$input");
 
 	# get the response
 	my $response = $ua->request($req);



From kawas at dev.open-bio.org  Thu Apr 16 18:18:25 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Thu, 16 Apr 2009 14:18:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904161818.n3GIIPvL030149@dev.open-bio.org>


kawas
Thu Apr 16 14:18:25 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30114/MOSES-MOBY

Modified Files:
	Changes 
Log Message:

moby-live/Perl/MOSES-MOBY Changes,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/16 18:14:34	1.13
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/04/16 18:18:25	1.14
@@ -4,6 +4,8 @@
 	- bug fix: when sending data with newlines on
 	  a WinOS, \r was causing problems with the
 	  incoming message.
+	- bug fix: moses-testing-service.pl was truncating
+	  the message sent to an async POST service.
 
 .89 
 	- The tag MOBY was missing in the async cgi



From kawas at dev.open-bio.org  Mon Apr 20 14:32:27 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 20 Apr 2009 10:32:27 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904201432.n3KEWRA4019539@dev.open-bio.org>


kawas
Mon Apr 20 10:32:26 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv19504/MOSES-MOBY

Modified Files:
	META.yml 
Log Message:
updated the version number
moby-live/Perl/MOSES-MOBY META.yml,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/08 22:43:10	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/20 14:32:26	1.8
@@ -39,5 +39,5 @@
   Want: 0.18
   WSRF::Lite: 0.8.2.5
   XML::LibXML: 1.62
-version: 0.89
+version: 0.90
 



From kawas at dev.open-bio.org  Mon Apr 20 14:32:55 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 20 Apr 2009 10:32:55 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904201432.n3KEWtLR019633@dev.open-bio.org>


kawas
Mon Apr 20 10:32:55 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv19598/MOSES-MOBY

Modified Files:
	Makefile.PL 
Log Message:
updated the version number
moby-live/Perl/MOSES-MOBY Makefile.PL,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/08 22:43:10	1.15
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/04/20 14:32:55	1.16
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.89';
+	version '0.90';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';



From kawas at dev.open-bio.org  Mon Apr 20 14:34:00 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 20 Apr 2009 10:34:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200904201434.n3KEY0UX019745@dev.open-bio.org>


kawas
Mon Apr 20 10:34:00 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi
In directory dev.open-bio.org:/tmp/cvs-serv19710/MOBY-Server/share/cgi

Modified Files:
	BioMobyWSDL 
Log Message:

moby-live/Perl/MOBY-Server/share/cgi BioMobyWSDL,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL	2009/04/15 16:56:01	1.2
+++ /home/repository/moby/moby-live/Perl/MOBY-Server/share/cgi/BioMobyWSDL	2009/04/20 14:34:00	1.3
@@ -1,5 +1,6 @@
 #!/usr/bin/perl -W
 # _________________________________________________________________
+# 
 # $Id$
 # Developed by: Jose Manuel Rodriguez Carrasco -jmrodriguez at cnio.es-
 # Created: 13-April-2009