From kawas at dev.open-bio.org  Fri Oct  2 11:15:48 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 2 Oct 2009 11:15:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910021515.n92FFmmM009604@dev.open-bio.org>


kawas
Fri Oct  2 11:15:48 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-serv9568/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service.tt 
Log Message:
make sure that we dont see undefined variables in hash warnings (thanks pieter)
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2008/11/19 14:24:14	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2009/10/02 15:15:48	1.6
@@ -239,7 +239,7 @@
 #       $response->record_error ( { code => INPUT_INCORRECT_NAMESPACE,
 #                                   msg  => 'This service requires inputs under the namespaces: {"' . join(',', keys %valid_namespaces) . '"}' } );
 #       return;
-#   } unless $valid_namespaces{$namespace};
+#   } unless defined($namespace) && $valid_namespaces{$namespace};
     [%- ELSE %]
     if (defined $[% input.name %]_collection) {
         foreach my $[% input.name %]_element (@{ $[% input.name %]_collection }) {
@@ -250,7 +250,7 @@
         #       $response->record_error ( { code => INPUT_INCORRECT_NAMESPACE,
         #                                   msg  => 'This service requires inputs under the namespaces: { "' . join(',', keys %valid_namespaces) . '"}' } );
         #       return;
-        #   } unless $valid_namespaces{$namespace};
+        #   } unless defined($namespace) && $valid_namespaces{$namespace};
         }
     }
     [%- END %]


From senger at dev.open-bio.org  Sun Oct  4 19:31:28 2009
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 4 Oct 2009 19:31:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910042331.n94NVSCh029672@dev.open-bio.org>


senger
Sun Oct  4 19:31:28 EDT 2009
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv29653/xmls

Modified Files:
	project.pom 
Log Message:
jax-ws dependencies updated
moby-live/Java/xmls project.pom,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2009/06/09 22:20:54	1.16
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2009/10/04 23:31:28	1.17
@@ -282,14 +282,39 @@
     <dependency>
       <groupId>com.sun.xml.ws</groupId>
       <artifactId>jaxws-tools</artifactId>
-      <version>2.1.3</version>
+      <version>2.1.4</version>
+      <exclusions>
+        <exclusion>
+          <groupId>javax.xml.ws</groupId>
+          <artifactId>jaxws-api</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>javax.jws</groupId>
+          <artifactId>jsr181</artifactId>
+        </exclusion>
+      </exclusions> 
     </dependency>
-
     <dependency>
-      <groupId>com.sun.xml.ws</groupId>
-      <artifactId>jaxws-rt</artifactId>
-      <version>2.1.4</version>
+      <groupId>javax.xml.ws</groupId>
+      <artifactId>jaxws-api</artifactId>
+      <version>2.1-1</version>
+      <exclusions>
+        <exclusion>
+          <groupId>javax.jws</groupId>
+          <artifactId>jsr181</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
+    <!--
+         Use geronimo-specs version of jsr181 since the BEA version of 
+         of jsr181.jar is not available at central
+         -->
+    <dependency>
+      <groupId>org.apache.geronimo.specs</groupId>
+      <artifactId>geronimo-ws-metadata_2.0_spec</artifactId>
+      <version>1.1.1</version>
+    </dependency>
+
 
     <dependency>
       <groupId>jdom</groupId>


From kawas at dev.open-bio.org  Wed Oct  7 11:40:24 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 7 Oct 2009 11:40:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910071540.n97FeOYw010557@dev.open-bio.org>


kawas
Wed Oct  7 11:40:24 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv10517/MOSES-MOBY

Modified Files:
	Changes Makefile.PL 
Log Message:
bug fix to fix warning when testing soapless service and the debug log setting.
moby-live/Perl/MOSES-MOBY Changes,1.17,1.18 Makefile.PL,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/08/27 19:44:39	1.17
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/07 15:40:24	1.18
@@ -1,5 +1,15 @@
 Revision history for Perl extension MOSES::MOBY.
 
+0.92
+    - Bug fix: Can't use string ("<moby:MOBY
+      xmlns:moby="http://ww") as a HASH ref while 
+      "strict refs" in use ... when testing CGI 
+      services.
+    - Bug fix: when namespace checking in our
+      service implementation, if no namespace
+      is passed, our code produces warnings ...
+      added check to ensure that namespace is
+      defined before checking. 
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/08/28 15:23:15	1.19
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/07 15:40:24	1.20
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.91';
+	version '0.92';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';


From kawas at dev.open-bio.org  Wed Oct  7 11:40:24 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 7 Oct 2009 11:40:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910071540.n97FeOKi010577@dev.open-bio.org>


kawas
Wed Oct  7 11:40:24 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-serv10517/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service-base.tt 
Log Message:
bug fix to fix warning when testing soapless service and the debug log setting.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service-base.tt,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt	2009/08/27 19:37:37	1.4
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt	2009/10/07 15:40:24	1.5
@@ -200,7 +200,9 @@
 	if ($LOG->is_debug) {
 	    my $soap_output = $self->finish_output ($out_package);
 	    $LOG->debug ("Output raw data (first 1000 characters): " .
-			 substr ($soap_output->{_value}->[0], 0, 1000));
+			 substr ($soap_output->{_value}->[0], 0, 1000)) if ref($soap_output) =~ m|^HASH|;
+	   $LOG->debug ("Output raw data (first 1000 characters): " .
+             substr ($soap_output, 0, 1000)) unless ref($soap_output) =~ m|^HASH|;
 	    Log::Log4perl::NDC->pop();
 	    return $soap_output;
 	} else {


From kawas at dev.open-bio.org  Fri Oct  9 11:31:01 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 11:31:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091531.n99FV1i5013333@dev.open-bio.org>


kawas
Fri Oct  9 11:31:01 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv13298/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
added a line that prints the LSAE message if $opt_v is chosen when checking the status of a submitted job.
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/16 18:17:24	1.11
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/09 15:31:00	1.12
@@ -153,6 +153,7 @@
 			$completed->{$queryID} = 1;
 		} elsif ( $status->percentage < 100 ) {
 			print "Current percentage: ", $status->percentage, "\n" if $opt_v;
+			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
 			sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
@@ -168,6 +169,7 @@
 				  || ( $status->new_state =~ m"running"i ) )
 		{
 			print "Current State: ", $status->new_state, "\n" if $opt_v;
+			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
 			sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
@@ -178,6 +180,7 @@
 			$completed->{$queryID} = 1;
 		} elsif ( $status->steps_completed < $status->total_steps ) {
 			print "Steps completed: ", $status->steps_completed, "\n" if $opt_v;
+			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
 			sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
@@ -188,6 +191,7 @@
 			$completed->{$queryID} = 1;
 		} elsif ( $status->remaining > 0 ) {
 			print "Time remaining: ", $status->remaining, "\n" if $opt_v;
+			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
 			sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";


From kawas at dev.open-bio.org  Fri Oct  9 11:39:21 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 11:39:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091539.n99FdLAs013374@dev.open-bio.org>


kawas
Fri Oct  9 11:39:21 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv13339/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent changes
moby-live/Perl/MOSES-MOBY Changes,1.18,1.19
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/07 15:40:24	1.18
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/09 15:39:21	1.19
@@ -10,6 +10,10 @@
       is passed, our code produces warnings ...
       added check to ensure that namespace is
       defined before checking. 
+    - when testing async services, added a line
+      to print out the LSAE event message if it
+      exists and if the script is running under
+      verbose settings.
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.


From kawas at dev.open-bio.org  Fri Oct  9 13:29:28 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:29:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091729.n99HTS4B013717@dev.open-bio.org>


kawas
Fri Oct  9 13:29:28 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache
In directory dev.open-bio.org:/tmp/cvs-serv13682/MOSES-MOBY/lib/MOSES/MOBY/Cache

Modified Files:
	Central.pm 
Log Message:
category had incorrect case
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Central.pm,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.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/Cache/Central.pm	2009/08/27 19:40:50	1.8
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.pm	2009/10/09 17:29:28	1.9
@@ -991,7 +991,7 @@
     $service->lsid($service_node->getAttribute('lsid') || '');
     $service->type($service_node->getChildrenByTagName('serviceType')->get_node(1)->textContent) if $service_node->getChildrenByTagName('serviceType')->size() > 0;
     $service->authoritative($service_node->getChildrenByTagName('authoritative')->get_node(1)->textContent) if $service_node->getChildrenByTagName('authoritative')->size() > 0;
-    $service->category($service_node->getChildrenByTagName('category')->get_node(1)->textContent) if $service_node->getChildrenByTagName('category')->size() > 0;
+    $service->category($service_node->getChildrenByTagName('Category')->get_node(1)->textContent) if $service_node->getChildrenByTagName('Category')->size() > 0;
     $service->description($service_node->getChildrenByTagName('Description')->get_node(1)->textContent) if $service_node->getChildrenByTagName('Description')->size() > 0;
     $service->email($service_node->getChildrenByTagName('contactEmail')->get_node(1)->textContent) if $service_node->getChildrenByTagName('contactEmail')->size() > 0;
     $service->signatureURL($service_node->getChildrenByTagName('signatureURL')->get_node(1)->textContent) if $service_node->getChildrenByTagName('signatureURL')->size() > 0;


From kawas at dev.open-bio.org  Fri Oct  9 13:32:39 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:32:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091732.n99HWdiS013799@dev.open-bio.org>


kawas
Fri Oct  9 13:32:39 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-serv13764/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service.tt 
Log Message:
added some code to modify the LSAE states
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2009/10/02 15:15:48	1.6
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2009/10/09 17:32:39	1.7
@@ -28,6 +28,10 @@
     [%- MACRO is_simple (entry) BLOCK %]
 	[%- ref (entry) == 'MOSES::MOBY::Def::PrimaryDataSimple' %]
     [%- END -%]
+    
+    [%- MACRO is_async (entry) BLOCK %]
+    [%- entry == 'cgi-async' || entry == 'moby-async' %]
+    [%- END -%]
 
     [%- MACRO set_child (child, leftpad, value) BLOCK %]
        [% FILTER indent (leftpad) -%]
@@ -202,6 +206,9 @@
 @ISA = qw( [% base.module_name %] );
 use MOSES::MOBY::Package;
 use MOSES::MOBY::ServiceException;
+[%- IF is_async(base.category) -%]
+use MOBY::Async::LSAE;
+[%- END %]
 use strict;
 
 [%# here we output use statements for our primitives %]
@@ -275,8 +282,23 @@
     [%- END %]
     [%- END %]
 
-    # do something... (sorry, can't help with that)
-
+    # do something... (sorry, can't you help with that)
+    
+    [%- IF is_async(base.category) %]
+    #simulate a long running service while providing updates
+    
+    #update the state of our service
+    $self->update_state_event($request, 'running','about to sleep for 20 seconds!');
+    
+    # sleep for 20 seconds
+    sleep(20);
+    
+    # update state again
+    $self->update_state_event($request, 'running','Woke up and going back to sleep for 20 more seconds!');
+    
+    # sleep for 20 more seconds
+    sleep(20);
+    [%- END %]
     # EDIT: PUT REAL VALUES INTO THE RESPONSE
     # fill the response
     [%- FOREACH output IN base.outputs %]
@@ -325,6 +347,272 @@
 
 }
 
+[%- IF is_async(base.category) -%]
+#-----------------------------------------------------------------
+# update_state_event
+#    This method is used to update the state of your 
+#    LSAE_STATE_CHANGED_EVENT event.
+#
+#  Parameters:  
+#    $request - $request from process_it()
+#    $state - one of (created, running, completed, terminated_by_request, terminated_by_error) 
+#    $msg   - a message to provide regarding the state of our event 
+#-----------------------------------------------------------------
+sub update_state_event {
+    my ( $self, $request, $state, $msg ) = @_;
+
+    my %valid_states = ('created'=>1,'running'=>1,'completed'=>1,'termintated_by_request'=>1,'terminated_by_error'=>1,);
+    
+    $msg = '' unless defined $msg;
+    $state = 'running' unless defined $state;
+    
+    # validate the state of the event ...
+    $state = 'running' unless $valid_states{$state};
+    
+    unless ( defined $ENV{ID} ) {
+        # hmm, local testing of service?
+        $ENV{ID} = WSRF::GSutil::CalGSH_ID();
+        WSRF::File::toFile($ENV{ID});
+    }
+
+    # our service invocation id
+    my $ID = $ENV{ID};
+
+    # our job id
+    my $jid = $request->jid;
+
+    # some variables we need to access/store our event information
+    my $property_pid    = "pid_$jid";
+    my $property_input  = "input_$jid";
+    my $property_status = "status_$jid";
+    my $property_result = "result_$jid";
+
+    # construct an LSAE object based on the old event block
+    my $old_status = LSAE::AnalysisEventBlock->new(
+                                    $WSRF::WSRP::ResourceProperties{$property_status}
+    );
+    # construct a new state changed event
+    my $status = LSAE::AnalysisEventBlock->new();
+    $status->type(LSAE_STATE_CHANGED_EVENT);
+
+    # set the previous state
+    $status->previous_state( $old_status->new_state() ) if defined ($old_status->type) and $old_status->type == LSAE_STATE_CHANGED_EVENT;
+    $status->previous_state( 'created') unless $status->previous_state;
+
+    # set the new state
+    $status->new_state($state);
+    $status->message($msg);
+
+    # set our job id for this event
+    $status->id($jid);
+
+    # create a file based resource that we will store our event information
+    my $lock = WSRF::MobyFile->new( undef, $ID );
+    $WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
+
+    # here we leave the result empty since the service is still running
+    $WSRF::WSRP::ResourceProperties{$property_result} = '';
+
+    # save the event so that our clients can access the information
+    $lock->toFile();
+    return;
+}
+#-----------------------------------------------------------------
+# update_percentage_event
+#    This method is used to update the state of your 
+#    LSAE_PERCENT_PROGRESS_EVENT event.
+#
+#  Parameters:  
+#    $request     - $request from process_it()
+#    $percentrage - an integer between 0-100 
+#    $msg         - a message to provide regarding the state of our event 
+#-----------------------------------------------------------------
+sub update_percentage_event {
+    my ( $self, $request, $percentage, $msg ) = @_;
+    
+    $msg = '' unless defined $msg;
+    $state = 1 unless defined $percentage;
+    
+    # validate the state of the event ...
+    $percentage = 1 unless $percentage >= 0 and $percentage <=100;
+    
+    unless ( defined $ENV{ID} ) {
+        # hmm, local testing of service?
+        $ENV{ID} = WSRF::GSutil::CalGSH_ID();
+        WSRF::File::toFile($ENV{ID});
+    }
+
+    # our service invocation id
+    my $ID = $ENV{ID};
+
+    # our job id
+    my $jid = $request->jid;
+
+    # some variables we need to access/store our event information
+    my $property_pid    = "pid_$jid";
+    my $property_input  = "input_$jid";
+    my $property_status = "status_$jid";
+    my $property_result = "result_$jid";
+
+    # construct an LSAE object based on the old event block
+    my $old_status = LSAE::AnalysisEventBlock->new(
+                                    $WSRF::WSRP::ResourceProperties{$property_status}
+    );
+    # construct a new state changed event
+    my $status = LSAE::AnalysisEventBlock->new();
+    $status->type(LSAE_PERCENT_PROGRESS_EVENT);
+
+    # set the new state
+    $status->percentage($percentage);
+    $status->message($msg);
+
+    # set our job id for this event
+    $status->id($jid);
+
+    # create a file based resource that we will store our event information
+    my $lock = WSRF::MobyFile->new( undef, $ID );
+    $WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
+
+    # here we leave the result empty since the service is still running
+    $WSRF::WSRP::ResourceProperties{$property_result} = '';
+
+    # save the event so that our clients can access the information
+    $lock->toFile();
+    return;
+}
+
+#-----------------------------------------------------------------
+# update_step_event
+#    This method is used to update the state of your 
+#    LSAE_STEP_PROGRESS_EVENT event.
+#
+#  Parameters:  
+#    $request         - $request from process_it()
+#    $total_steps     - integer representing total steps until completion
+#    $steps_completed - integer representing steps completed 
+#    $msg             - a message to provide regarding the state of our event 
+#-----------------------------------------------------------------
+sub update_step_event {
+    my ( $self, $request, $total_steps, $steps_completed, $msg ) = @_;
+   
+    $msg = '' unless defined $msg;
+    $total_steps = 1 unless defined $total_steps;
+    $steps_completed = 0 unless defined $steps_completed;
+    
+    # validate the state of the event ...
+    $steps_completed = $total_steps if $steps_completed > $total_steps;
+    
+    unless ( defined $ENV{ID} ) {
+        # hmm, local testing of service?
+        $ENV{ID} = WSRF::GSutil::CalGSH_ID();
+        WSRF::File::toFile($ENV{ID});
+    }
+
+    # our service invocation id
+    my $ID = $ENV{ID};
+
+    # our job id
+    my $jid = $request->jid;
+
+    # some variables we need to access/store our event information
+    my $property_pid    = "pid_$jid";
+    my $property_input  = "input_$jid";
+    my $property_status = "status_$jid";
+    my $property_result = "result_$jid";
+
+    # construct an LSAE object based on the old event block
+    my $old_status = LSAE::AnalysisEventBlock->new(
+                                    $WSRF::WSRP::ResourceProperties{$property_status}
+    );
+    # construct a new state changed event
+    my $status = LSAE::AnalysisEventBlock->new();
+    $status->type(LSAE_STEP_PROGRESS_EVENT);
+
+    # set the new state
+    $status->steps_completed($steps_completed);
+    $status->total_steps($total_steps);
+    $status->message($msg);
+
+    # set our job id for this event
+    $status->id($jid);
+
+    # create a file based resource that we will store our event information
+    my $lock = WSRF::MobyFile->new( undef, $ID );
+    $WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
+
+    # here we leave the result empty since the service is still running
+    $WSRF::WSRP::ResourceProperties{$property_result} = '';
+
+    # save the event so that our clients can access the information
+    $lock->toFile();
+    return;
+}
+
+#-----------------------------------------------------------------
+# update_time_event
+#    This method is used to update the state of your 
+#    LSAE_TIME_PROGRESS_EVENT event.
+#
+#  Parameters:  
+#    $request   - $request from process_it()
+#    $remaining - integer representing seconds until completion 
+#    $msg       - a message to provide regarding the state of our event 
+#-----------------------------------------------------------------
+sub update_time_event {
+    my ( $self, $request, $remaining, $msg ) = @_;
+    
+    $msg = '' unless defined $msg;
+    $remaining = 0 unless defined $remaining;
+    
+    # validate the state of the event ...
+    $remaining = 0 unless $remaining >= 0 ;
+    
+    unless ( defined $ENV{ID} ) {
+        # hmm, local testing of service?
+        $ENV{ID} = WSRF::GSutil::CalGSH_ID();
+        WSRF::File::toFile($ENV{ID});
+    }
+
+    # our service invocation id
+    my $ID = $ENV{ID};
+
+    # our job id
+    my $jid = $request->jid;
+
+    # some variables we need to access/store our event information
+    my $property_pid    = "pid_$jid";
+    my $property_input  = "input_$jid";
+    my $property_status = "status_$jid";
+    my $property_result = "result_$jid";
+
+    # construct an LSAE object based on the old event block
+    my $old_status = LSAE::AnalysisEventBlock->new(
+                                    $WSRF::WSRP::ResourceProperties{$property_status}
+    );
+    # construct a new state changed event
+    my $status = LSAE::AnalysisEventBlock->new();
+    $status->type(LSAE_TIME_PROGRESS_EVENT);
+
+    # set the new state
+    $status->remaining($remaining);
+    $status->message($msg);
+
+    # set our job id for this event
+    $status->id($jid);
+
+    # create a file based resource that we will store our event information
+    my $lock = WSRF::MobyFile->new( undef, $ID );
+    $WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
+
+    # here we leave the result empty since the service is still running
+    $WSRF::WSRP::ResourceProperties{$property_result} = '';
+
+    # save the event so that our clients can access the information
+    $lock->toFile();
+    return;
+}
+[%- END -%]
+
 1;
 __END__
 


From kawas at dev.open-bio.org  Fri Oct  9 13:37:49 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:37:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091737.n99HbnUf013860@dev.open-bio.org>


kawas
Fri Oct  9 13:37:49 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-serv13825/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service.tt 
Log Message:
updated the use statement IF block and fixed typo in update_percentage_event
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,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/Generators/templates/service.tt	2009/10/09 17:32:39	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2009/10/09 17:37:49	1.8
@@ -206,7 +206,7 @@
 @ISA = qw( [% base.module_name %] );
 use MOSES::MOBY::Package;
 use MOSES::MOBY::ServiceException;
-[%- IF is_async(base.category) -%]
+[% IF is_async(base.category) -%]
 use MOBY::Async::LSAE;
 [%- END %]
 use strict;
@@ -431,7 +431,7 @@
     my ( $self, $request, $percentage, $msg ) = @_;
     
     $msg = '' unless defined $msg;
-    $state = 1 unless defined $percentage;
+    $percentage = 1 unless defined $percentage;
     
     # validate the state of the event ...
     $percentage = 1 unless $percentage >= 0 and $percentage <=100;


From kawas at dev.open-bio.org  Fri Oct  9 13:46:44 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:46:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091746.n99Hki1A013903@dev.open-bio.org>


kawas
Fri Oct  9 13:46:44 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv13868/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent changes
moby-live/Perl/MOSES-MOBY Changes,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/09 15:39:21	1.19
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/09 17:46:44	1.20
@@ -14,6 +14,10 @@
       to print out the LSAE event message if it
       exists and if the script is running under
       verbose settings.
+    - Bug fix: Central->_createServiceFromXML had
+      Category as category
+    - added some code to the service.tt that aides
+      in updating a services LSAE event states. 
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.


From kawas at dev.open-bio.org  Fri Oct  9 13:50:08 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:50:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091750.n99Ho8JF013943@dev.open-bio.org>


kawas
Fri Oct  9 13:50:08 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share
In directory dev.open-bio.org:/tmp/cvs-serv13908/MOSES-MOBY/share

Modified Files:
	USER_REGISTRIES 
Log Message:

moby-live/Perl/MOSES-MOBY/share USER_REGISTRIES,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/USER_REGISTRIES,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/USER_REGISTRIES	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/USER_REGISTRIES	2009/10/09 17:50:08	1.4
@@ -1,11 +1 @@
-%USER_REGISTRIES = (
-#                    iCAPTURE => { 
-#                                  endpoint  => 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl',
-#                                  namespace => 'http://mobycentral.icapture.ubc.ca/MOBY/Central',
-#                                  name      => 'iCAPTURE Centre, Vancouver',
-#                                  contact   => 'Edward Kawas (edward.kawas at gmail.com)',
-#                                  public    => 'yes',
-#                                  text      => 'A curated public registry hosted at the iCAPTURE Centre, Vancouver',
-#                                 },
-
-                    );
+%USER_REGISTRIES = ();


From kawas at dev.open-bio.org  Tue Oct 13 11:28:36 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 11:28:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131528.n9DFSZMV004279@dev.open-bio.org>


kawas
Tue Oct 13 11:28:35 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES
In directory dev.open-bio.org:/tmp/cvs-serv4243/MOSES-MOBY/lib/MOSES

Modified Files:
	MOBY.pm 
Log Message:
added a little text to the pod name so that when users go to cpan, they know which module has the doc
moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/08 22:40:11	1.10
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/10/13 15:28:35	1.11
@@ -22,7 +22,7 @@
 
 =head1 NAME
 
-MOSES::MOBY - Perl extension for the automatic generation of BioMOBY web services
+MOSES::MOBY - Start here! Documentation for the Perl extension for the automatic generation of BioMOBY web services!
 
 =head1 SYNOPSIS
 


From kawas at dev.open-bio.org  Tue Oct 13 11:33:25 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 11:33:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131533.n9DFXOrv004319@dev.open-bio.org>


kawas
Tue Oct 13 11:33:24 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4284/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
getting ready to create cpan release. added some notes for those that read these things
moby-live/Perl/MOSES-MOBY Changes,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/09 17:46:44	1.20
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/13 15:33:24	1.21
@@ -1,6 +1,17 @@
 Revision history for Perl extension MOSES::MOBY.
 
-0.92
+0.92 Oct 13, 2009
+    *** Notes for this release ***
+        The service template has been updated.
+        The update mainly affects async service
+        implementations. The easiest thing to do
+        is to backup your async service 
+        implementations and re-generate them.
+        
+        Only do this if you had problems with 
+        erratic service behaviour in the past!
+    
+    Changes:
     - Bug fix: Can't use string ("<moby:MOBY
       xmlns:moby="http://ww") as a HASH ref while 
       "strict refs" in use ... when testing CGI 
@@ -17,7 +28,8 @@
     - Bug fix: Central->_createServiceFromXML had
       Category as category
     - added some code to the service.tt that aides
-      in updating a services LSAE event states. 
+      in updating a services LSAE event states.
+      
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.


From kawas at dev.open-bio.org  Tue Oct 13 11:38:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 11:38:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131538.n9DFcAZW004359@dev.open-bio.org>


kawas
Tue Oct 13 11:38:10 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4324/MOSES-MOBY

Modified Files:
	Makefile.PL 
Log Message:
added a no index directive for the templates/ directory so that the perldoc on cpan doesnt look messed up.
moby-live/Perl/MOSES-MOBY Makefile.PL,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/07 15:40:24	1.20
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/13 15:38:10	1.21
@@ -42,6 +42,7 @@
 
 	build_requires 'Test::More' => '0.42';
 	no_index 'directory'        => 'bin/scripts';
+	no_index 'directory'        => 'lib/MOSES/MOBY/Generators/templates';
 
 	install_script 'bin/scripts/moses-cache-tester.pl';
 	install_script 'bin/scripts/moses-config-status.pl';


From kawas at dev.open-bio.org  Tue Oct 13 11:43:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 11:43:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131543.n9DFhA57004402@dev.open-bio.org>


kawas
Tue Oct 13 11:43:10 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators
In directory dev.open-bio.org:/tmp/cvs-serv4367/MOSES-MOBY/lib/MOSES/MOBY/Generators

Modified Files:
	Utils.pm 
Log Message:
updated the perldoc (wasnt correct on cpan)
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm	2008/11/06 18:32:33	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm	2009/10/13 15:43:10	1.6
@@ -19,22 +19,16 @@
 
 MOSES::MOBY::Utils - what does not fit elsewhere
 
-=cut
-
 =head1 SYNOPSIS
 
  # find a file located somewhere in @INC
  use MOSES::MOBY::Generators::Utils;
  my $file = MOSES::MOBY::Generators::Utils->find_file ('resource.file');
- 
-=cut
 
 =head1 DESCRIPTION
 
 General purpose utilities.
 
-=cut
-
 =head1 AUTHORS
 
  Martin Senger (martin.senger [at] gmail [dot] com)
@@ -42,8 +36,6 @@
 
 =head1 SUBROUTINES
 
-=cut
-
 #-----------------------------------------------------------------
 # find_file
 #-----------------------------------------------------------------
@@ -87,4 +79,5 @@
 }
 
 1;
+
 __END__


From kawas at dev.open-bio.org  Tue Oct 13 12:08:11 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 12:08:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131608.n9DG8BUL004478@dev.open-bio.org>


kawas
Tue Oct 13 12:08:11 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4443/MOSES-MOBY/lib/MOSES/MOBY

Modified Files:
	Config.pm 
Log Message:
added perldoc for module.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Config.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm	2008/04/29 19:45:01	1.4
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm	2009/10/13 16:08:11	1.5
@@ -26,9 +26,63 @@
     $ENV_CONFIG_DIR = 'BIOMOBY_CFG_DIR';
 }
 
+=head1 NAME
+
+MOSES::MOBY::Config - A hash based configuration module based on Config::Simple
+
+=head1 SYNOPSIS
+
+ # use config allong with the MOSES config file
+ use MOSES::MOBY::Config;
+
+ # use config along with my properties.file
+ use MOSES::MOBY::Config qw /'properties.file'/;
+
+ # print the successfully read config files
+ foreach my $file (MOSES::MOBY::Config->ok_files) {
+    print "\t$file - successfully processed\n";
+ }
+
+ # print a list of files that failed to load
+ my %failed = MOSES::MOBY::Config->failed_files;
+ if (keys %failed > 0) {
+    print "Failed configuration files:\n";
+    foreach my $file (sort keys %failed) {
+    my $msg = $failed{$file}; $msg =~ s/\n$//;
+        print "\t$file => $msg\n";
+    }
+ }
+
+ # print out the config params read thus far
+ print "All configuration parameters:\n";
+ foreach my $name (sort MOSES::MOBY::Config->param()) {
+    print "\t$name => " . MOSES::MOBY::Config->param ($name);
+ }
+
+=head1 DESCRIPTION
+
+A module for reading configuration files and maintaining configuration parameters 
+
+=head1 AUTHORS
+
+ Martin Senger (martin.senger [at] gmail [dot] com)
+ Edward Kawas (edward.kawas [at] gmail [dot] com)
+
+=head1 SUBROUTINES
+
+=cut
+
 # OO access; but there are no instance attributes - everything are
 # class (shared) attributes
 
+=head2 new
+
+Instantiates a new MOSES::MOBY::Config reference. Mainly here for OO access. 
+There are no instance attributes, only class attributes
+
+=cut
+
+
 sub new {
     my ($class, @args) = @_;
 
@@ -126,6 +180,13 @@
 
 # return value of a configuration argument; or add a new argument
 
+=head2 param
+
+If called with no arguments, all of the possible config keys are returned. 
+If called with a single argument, then that argument is assumed to be a key and the value for that key is returned. 
+
+=cut
+
 sub param {
     shift;
 
@@ -146,6 +207,12 @@
 
 # remove one, more, or all configuration arguments
 
+=head2 delete
+
+removes one or more of the configuration keys and their associated values.
+
+=cut
+
 sub delete {
     shift;
 
@@ -164,6 +231,15 @@
 # this argument is passed to the Data::Dumper->Dump as the variable
 # name)
 
+=head2 dump
+
+Returns a stringified version of all configuration parameters;
+
+If passed a scalar parameter, then the dump will be given that variable name.
+This dump can be eval{}'ed.
+
+=cut
+
 sub dump {
     shift;
     my $varname = @_ ? shift : 'CONFIG';
@@ -189,6 +265,12 @@
 
 # return a list of configuration files successfully read (so far)
 
+=head2 ok_files
+
+returns a list of the configuration files successfully read thus far ...
+
+=cut
+
 sub ok_files {
     return sort keys %Success;
 }
@@ -196,11 +278,17 @@
 # return a hash of configuration files un-successfully read (so far) -
 # with corresponding error messages
 
+=head2 failed_files
+
+returns a hash of the configuration files unsuccessfully read thus far and their corresponding error messages.
+
+=cut
+
 sub failed_files {
     return %Unsuccess;
 }
 
-
+=cut
 
 1;
 __END__


From kawas at dev.open-bio.org  Tue Oct 13 12:42:20 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 12:42:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131642.n9DGgKHF004955@dev.open-bio.org>


kawas
Tue Oct 13 12:42:20 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4920/MOSES-MOBY/lib/MOSES/MOBY

Modified Files:
	Config.pm 
Log Message:

moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Config.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm	2009/10/13 16:08:11	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm	2009/10/13 16:42:20	1.6
@@ -288,7 +288,5 @@
     return %Unsuccess;
 }
 
-=cut
-
 1;
 __END__


From kawas at dev.open-bio.org  Tue Oct 13 12:46:21 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 12:46:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131646.n9DGkLAI005016@dev.open-bio.org>


kawas
Tue Oct 13 12:46:21 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators
In directory dev.open-bio.org:/tmp/cvs-serv4981/MOSES-MOBY/lib/MOSES/MOBY/Generators

Modified Files:
	Utils.pm 
Log Message:
fixed the perldoc ... doc created had errors in it.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm	2009/10/13 15:43:10	1.6
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm	2009/10/13 16:46:21	1.7
@@ -36,10 +36,6 @@
 
 =head1 SUBROUTINES
 
-#-----------------------------------------------------------------
-# find_file
-#-----------------------------------------------------------------
-
 =head2 find_file
 
 Try to locate a file whose name is created from the C<$default_start>
@@ -55,6 +51,9 @@
 
 my %full_path_of = ();
 
+#-----------------------------------------------------------------
+# find_file
+#-----------------------------------------------------------------
 sub find_file {
     my ($self, $default_start, @names) = @_;
     my $fixed_part = File::Spec->catfile (@names);


From kawas at dev.open-bio.org  Tue Oct 13 13:03:41 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 13:03:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131703.n9DH3f6V005208@dev.open-bio.org>


kawas
Tue Oct 13 13:03:41 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv5173/MOSES-MOBY

Modified Files:
	README 
Log Message:

moby-live/Perl/MOSES-MOBY README,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/README,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/README	2008/05/09 20:54:31	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/README	2009/10/13 17:03:41	1.6
@@ -1,4 +1,4 @@
-MOSES-MOBY version .85
+MOSES-MOBY version .92
 ======================
 
 OVERVIEW
@@ -16,12 +16,22 @@
 
 INSTALLATION
 
-To install this module type the following:
-
-   perl Makefile.PL
-   make
-   make test
-   make install
+	To install this module type the following:
+	
+	   perl Makefile.PL
+	   make
+	   make test
+	   make install
+
+	To install this module on WinOS:
+	
+		perl Makefile.PL
+		nmake
+		nmake test
+		nmake install
+	
+	If you have any problems installing prerequisite modules,
+	you may find it easier to use ActiveStates ppm utility.
 
 UPGRADING
 


From drepchevski at dev.open-bio.org  Fri Oct 16 08:18:47 2009
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Fri, 16 Oct 2009 08:18:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161218.n9GCIkJJ024102@dev.open-bio.org>


drepchevski
Fri Oct 16 08:18:46 EDT 2009
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv24067

Modified Files:
	inb_moby_core.html 
Log Message:
put the ontology generator applet inside
moby-live/Java/docs inb_moby_core.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/inb_moby_core.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/docs/inb_moby_core.html	2009/09/21 16:31:17	1.2
+++ /home/repository/moby/moby-live/Java/docs/inb_moby_core.html	2009/10/16 12:18:46	1.3
@@ -64,6 +64,7 @@
     }
 
     .code {
+      white-space: pre;
       vertical-align: top;
       color: #000099;
       font-size: 10pt;
@@ -131,6 +132,50 @@
     </table>
   </p>
 
+  <h2> Generating JAXB-annotated ontology classes </h2>
+
+  <p>
+    Even MobyCore may work without generated ontology classes, they facilitate a development.
+    Generated classes are nothing more than JAXB annotated beans with properties.
+
+  </p>
+  
+  <div style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px;">
+    <div style="float: left; width: 350px; margin-right: 50px">      
+      <applet width = "350" height = "350" code = "org.inb.biomoby.generator.gui.Main">
+        <param name = "jnlp_href" value = "http://inb.bsc.es/applications/java/mobygenerator/inb_generator_applet.jnlp"/>
+      </applet>
+    </div>
+
+    
+      Here is an example of generated datatype class:
+    
+       
+    <div class="code" style="margin-left: 400px; font-size: 8pt;">
+ at XmlRootElement(name="WeightedAminoAcidSequences")
+ at XmlType(name="WeightedAminoAcidSequences")
+public class WeightedAminoAcidSequences extends AminoAcidSequence implements Serializable {
+    public List&lt;? extends AminoAcidSequence&gt; getAminoAcidSequence() {
+        return getAttributes("AminoAcidSequence");
+    }
+
+    public void addAminoAcidSequence(AminoAcidSequence aminoAcidSequence) {
+        putAttribute("AminoAcidSequence", aminoAcidSequence);
+    }
+
+    public WeightedObject getWeightedObject() {
+        return getAttribute("WeightedObject");
+    }
+
+    public void setWeightedObject(WeightedObject weightedObject) {
+        putAttribute("WeightedObject", weightedObject);
+    }
+}
+    </div>
+
+    <br style="clear:both;"/>
+  </div>
+  
   <h2> Executing synchronous BioMoby services </h2>
 
   <p>
@@ -138,12 +183,10 @@
     This is done by creating a MobyMessage object:
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 MobyObject object = new MobyObject("P00807", "UniProt");
 MobySimple simple = new MobySimple(object, "id");        
 MobyData data = new MobyData(simple, "sip_1");
 MobyMessage request = new MobyMessage(data);
-</pre>
     </div>
   </p>
 
@@ -163,10 +206,8 @@
     Now we can create a MobyDispatch object and execute a service.
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 MobyDispatch dispatch = new MobyDispatch(service);
 MobyMessage response = dispatch.invoke(request);
-</pre>
     </div>
   </p>
 
@@ -181,9 +222,7 @@
     not have AminoAcidSequence class generated. In this case we would have a AnyMobyObject instead of unknown to us AminoAcidSequence.
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 MobyString string = (MobyString) any.getAttribute("SequenceString");
-</pre>
     </div>
   </p>
 
@@ -192,7 +231,6 @@
     <span class="highlight">MobySimple</span> may contain either a primitive type or a complex one, so we have to check. Here is a simple method that traverse a given element:
      
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 public void traverse(AbstractMobyObject object) throws JAXBException
 {
   System.out.println(MobyMessageContext.getMobyName(object) + " " + object.getArticleName());
@@ -206,8 +244,7 @@
        traverse(o);
      }
   }
-}
-</pre>      
+}     
     </div>
   </p>
 
@@ -219,11 +256,9 @@
     <span class="highlight">AnyMobyObject</span> can also be used to setup a datatype dynamically.
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 AnyMobyObject any = new AnyMobyObject("AminoAcidSequece");
 any.putAttribute("SequenceString", new MobyString("ATCG"));
 any.putAttribute("Length", new MobyInteger(4));
-</pre>
     </div>
   </p>
 
@@ -235,7 +270,6 @@
     Here is an example of parsing a <span class="highlight">MobyMessage</span> response:
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 MobyMessage response = dispatch.invoke(request);
 
 if (response.hasExceptions())
@@ -256,7 +290,7 @@
 
    for (MobyDataElement element : elements)
    {
-     if (element instanceof Mobysimple)
+     if (element instanceof MobySimple)
      {
        MobySimple simple = (MobySimple)element;
        AbstractMobyObject object = simple.getObject();
@@ -292,8 +326,7 @@
        throw new Exception(); // expected MobySimple
      }
    }
-}
-</pre>    
+}  
     </div>
   </p>
 
@@ -306,7 +339,6 @@
     The rest of the things are pretty the same as for synchronous invocation:
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 // AminoAcidSequence sequence = new AminoAcidSequence();
 // sequence.setSequenceString(new MobyString("ATCG")):
 // sequence.setLength(new MobyInteger(4));
@@ -326,7 +358,6 @@
 MobyDispatch dispatch = new MobyDispatch(service);
 
 MobyWSRFResource wsrf = dispatch.invokeAsync(request);
-</pre>
     </div>
   </p>
 
@@ -334,7 +365,6 @@
     The result object is an WSRF resource through which we can poll to check our execution status:
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 while(true)
 {
   AnalysisEvent lsae = wsrf.getResourcePropertyStatus("sip_1");
@@ -362,7 +392,6 @@
    // actually must be an error...
    break;
 }
-</pre>
     </div>
   </p>
 


From kawas at dev.open-bio.org  Fri Oct 16 10:13:39 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 10:13:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161413.n9GEDd0V024490@dev.open-bio.org>


kawas
Fri Oct 16 10:13:39 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv24454/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
bug fix: when polling a cgi-async service with > 1 job, only the first job is polled for and when it is complete both are assumed to be complete
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/09 15:31:00	1.12
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/16 14:13:39	1.13
@@ -341,9 +341,12 @@
 			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 );
+			my $xpath = "//*[\@*='$queryID']";
+            my $xpc   = XML::LibXML::XPathContext->new();
+            my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
+            # should only be one ...
+            die unless $nodes->size() == 1;
+			my $status = LSAE::AnalysisEventBlock->new( $nodes->get_node(1)->toString() );
 			&_check_status( $status, \%completed, $queryID, $opt_v );
 		}
 		last if scalar keys(%completed) == $#query_ids + 1;


From kawas at dev.open-bio.org  Fri Oct 16 11:51:45 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 11:51:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161551.n9GFpjdv024715@dev.open-bio.org>


kawas
Fri Oct 16 11:51:45 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv24672/MOSES-MOBY

Modified Files:
	META.yml Changes Makefile.PL 
Log Message:
updated Changes to reflect the current state of the module. Updated the makefile and META to provide a new version for MOSES (for down the road when i create a cpan update)
moby-live/Perl/MOSES-MOBY META.yml,1.8,1.9 Changes,1.21,1.22 Makefile.PL,1.21,1.22
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/20 14:32:26	1.8
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/10/16 15:51:45	1.9
@@ -39,5 +39,5 @@
   Want: 0.18
   WSRF::Lite: 0.8.2.5
   XML::LibXML: 1.62
-version: 0.90
+version: 0.93
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/13 15:33:24	1.21
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/16 15:51:45	1.22
@@ -1,5 +1,16 @@
 Revision history for Perl extension MOSES::MOBY.
 
+0.93
+
+    Changes:
+    - Bug fix: moses-testing-service.pl when 
+      polling async services, didn't actually
+      poll correctly if you had multiple query
+      IDs for a single service invocation ID.
+      The first queryID was polled and when
+      it completed, the script assumed all of
+      the invocations were completed.
+
 0.92 Oct 13, 2009
     *** Notes for this release ***
         The service template has been updated.

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/13 15:38:10	1.21
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/16 15:51:45	1.22
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.92';
+	version '0.93';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';


From kawas at dev.open-bio.org  Fri Oct 16 13:43:09 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 13:43:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161743.n9GHh9Cl025091@dev.open-bio.org>


kawas
Fri Oct 16 13:43:09 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv25056/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
moses-testing-service.pl - async cgi service portion:
        * Moved the POST request out of the foreach
          $queryID loop.
        * Added the name of the element "analysis_event"
          to $xpath.
        * Moved the sleep(20) out of the &_check_status
          sub. 
        * Added a diagnostic message for the die
          statement when we cant find our event id.
        * Moved some messages for "verbose" info in
          &_check_status, so the script always reports
          the job status whether a job has completed
          or not.
        * I also added $queryID to the verbose messaging
          so the script reports which job that status
          message corresponded to...
          
(thx to Pieter Neerincx for patience, code and suggestions)
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/16 14:13:39	1.13
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/16 17:43:09	1.14
@@ -130,9 +130,7 @@
 	  or die "$@\n";
 	eval "use MOBY::Async::WSRF; 1;"
 	  or die "$@\n";
-
 }
-
 use strict;
 
 sub _empty_input {
@@ -149,17 +147,22 @@
 sub _check_status {
 	my ( $status, $completed, $queryID, $opt_v ) = @_;
 	if ( $status->type == LSAE_PERCENT_PROGRESS_EVENT ) {
+		print "Current percentage for job $queryID: ", $status->percentage, "\n"
+		  if $opt_v;
 		if ( $status->percentage >= 100 ) {
 			$completed->{$queryID} = 1;
 		} elsif ( $status->percentage < 100 ) {
-			print "Current percentage: ", $status->percentage, "\n" if $opt_v;
-			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
-			sleep(20);
+			print "\tmsg: ",
+			  ( $status->message ? $status->message : "no message found ..." ), "\n"
+			  if $opt_v;
+
+			#sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
 		}
-
 	} elsif ( $status->type == LSAE_STATE_CHANGED_EVENT ) {
+		print "Current state for job $queryID: ", $status->new_state, "\n"
+		  if $opt_v;
 		if (    ( $status->new_state =~ m"completed"i )
 			 || ( $status->new_state =~ m"terminated_by_request"i )
 			 || ( $status->new_state =~ m"terminated_by_error"i ) )
@@ -168,36 +171,45 @@
 		} elsif (    ( $status->new_state =~ m"created"i )
 				  || ( $status->new_state =~ m"running"i ) )
 		{
-			print "Current State: ", $status->new_state, "\n" if $opt_v;
-			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
-			sleep(20);
+			print "\tmsg: ",
+			  ( $status->message ? $status->message : "no message found ..." ), "\n"
+			  if $opt_v;
+
+			#sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
 		}
-
 	} elsif ( $status->type == LSAE_STEP_PROGRESS_EVENT ) {
+		print "Steps completed for job $queryID: ", $status - > steps_completed, "\n"
+		  if $opt_v;
 		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 $opt_v;
-			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
-			sleep(20);
+			print "\tmsg: ",
+			  ( $status->message ? $status->message : "no message found ..." ), "\n"
+			  if $opt_v;
+
+			#sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
 		}
-
 	} elsif ( $status->type == LSAE_TIME_PROGRESS_EVENT ) {
+		print "Time remaining for job $queryID: ", $status->remaining, "\n"
+		  if $opt_v;
 		if ( $status->remaining == 0 ) {
 			$completed->{$queryID} = 1;
 		} elsif ( $status->remaining > 0 ) {
-			print "Time remaining: ", $status->remaining, "\n" if $opt_v;
-			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
-			sleep(20);
+			print "\tmsg: ",
+			  ( $status->message ? $status->message : "no message found ..." ), "\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";
+		warn
+"Whilst checking the status of our resource, we entered into a possible infinite loop ...\n";
 	}
 }
 
@@ -238,7 +250,6 @@
 			die $msg;
 		}
 	);
-
 	my $input = '';
 	if ( @ARGV > 0 ) {
 		my $data = shift;    # a file name
@@ -249,14 +260,11 @@
 	} else {
 		$input = _empty_input;
 	}
-
 	print $soap ->$service( SOAP::Data->type( 'string' => "$input" ) )->result;
-
 } elsif ($opt_c) {
 
 	# calling a real service, using cgi
-	my $ua = LWP::UserAgent->new;
-
+	my $ua    = LWP::UserAgent->new;
 	my $input = '';
 	if ( @ARGV > 0 ) {
 		my $data = shift;    # a file name
@@ -267,14 +275,11 @@
 	} else {
 		$input = _empty_input;
 	}
-
 	my $req = HTTP::Request->new( POST => $opt_c );
 	$req->content_type('application/x-www-form-urlencoded');
 	$req->content("data=$input");
 	print "\n" . $ua->request($req)->as_string . "\n";
-
 } elsif ($opt_C) {
-
 	my $input = '';
 	if ( @ARGV > 0 ) {
 		my $data = shift;    # a file name
@@ -289,7 +294,6 @@
 	# 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
@@ -304,7 +308,6 @@
 	# 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);
@@ -327,261 +330,267 @@
 
 	# poll
 	while (1) {
+
+#
+# Poll the service for the status of all query IDs associated with this service invocation.
+#
+		$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);
+
 		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);
-			my $xpath = "//*[\@*='$queryID']";
-            my $xpc   = XML::LibXML::XPathContext->new();
-            my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
-            # should only be one ...
-            die unless $nodes->size() == 1;
-			my $status = LSAE::AnalysisEventBlock->new( $nodes->get_node(1)->toString() );
+			#
+			# Find status of this query ID.
+			#
+			#my $xpath = "//*[local-name() = 'analysis_event'][\@id='$queryID']";
+			#my $xpath = "//analysis_event[\@id='$queryID']";
+			$xpath = "//*[local-name() = 'analysis_event'][\@*='$queryId']";
+			my $xpc = XML::LibXML::XPathContext->new();
+			my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
+
+			# should only be one ...
+			die
+"Service returned unexpected/malformed resource property XML, which should contain service status info."
+			  unless $nodes->size() == 1;
+			my $status =
+			  LSAE::AnalysisEventBlock->new( $nodes->get_node(1)->toString() );
 			&_check_status( $status, \%completed, $queryID, $opt_v );
 		}
 		last if scalar keys(%completed) == $#query_ids + 1;
+		my $interval = 20;
+		print "Checking job state again in $interval seconds.\n\n" if $opt_v;
+		sleep($interval);
 	}
+	last if scalar keys(%completed) == $#query_ids + 1;
+}
 
-	# task is finished, obtain the result
-	$searchTerm = "";
-	$searchTerm .=
+# task is finished, obtain the result
+$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
-	# call using async mode for async service ... _submit
-	$service .= "_submit";
-
-	# set up the wsrf call
-	my $soap = WSRF::Lite->proxy($opt_a)->uri($WSRF::Constants::MOBY)->on_fault(
-		sub {
-			my $soap = shift;
-			my $res  = shift;
-			my $msg =
-			  ref $res
-			  ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring
-			  : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
-			die $msg;
-		}
-	);
-
-	# get the input
-	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);
-	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 );
-
-	# Get address from the returned Endpoint Reference
-	my $address = $epr->{'EndpointReference'}->{Address};
-
-	# Get resource identifier from the returned Endpoint Reference
-	my $identifier =
-	  $epr->{'EndpointReference'}->{ReferenceParameters}->{ServiceInvocationId};
-
-	# Compose the Endpoint Reference
-	my $EPR = WSRF::WS_Address->new();
-	$EPR->Address($address);
-	$EPR->ReferenceParameters(   '<mobyws:ServiceInvocationId xmlns:mobyws="'
-							   . $WSRF::Constants::MOBY . '">'
-							   . $identifier
-							   . '</mobyws:ServiceInvocationId>' );
-	my %completed = ();
-	while (1) {
-		foreach my $queryID (@query_ids) {
-
-			# skip poll if current job completed
-			next if $completed{$queryID};
+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) {
 
-			# poll the service for given query ID
-			my $searchTerm = "";
-			$searchTerm .=
+  # calling a real service, using async soap
+  # call using async mode for async service ... _submit
+  $service .= "_submit";
+
+  # set up the wsrf call
+  my $soap = WSRF::Lite->proxy($opt_a)->uri($WSRF::Constants::MOBY)->on_fault(
+	  sub {
+		  my $soap = shift;
+		  my $res  = shift;
+		  my $msg =
+			ref $res
+			? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring
+			: "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
+		  die $msg;
+	  }
+  );
+
+  # get the input
+  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);
+  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 );
+
+  # Get address from the returned Endpoint Reference
+  my $address = $epr->{'EndpointReference'}->{Address};
+
+  # Get resource identifier from the returned Endpoint Reference
+  my $identifier =
+	$epr->{'EndpointReference'}->{ReferenceParameters}->{ServiceInvocationId};
+
+  # Compose the Endpoint Reference
+  my $EPR = WSRF::WS_Address->new();
+  $EPR->Address($address);
+  $EPR->ReferenceParameters(   '<mobyws:ServiceInvocationId xmlns:mobyws="'
+							 . $WSRF::Constants::MOBY . '">'
+							 . $identifier
+							 . '</mobyws:ServiceInvocationId>' );
+  my %completed = ();
+  while (1) {
+	  foreach my $queryID (@query_ids) {
+
+		  # skip poll if current job completed
+		  next if $completed{$queryID};
+
+		  # poll the service for given query ID
+		  my $searchTerm = "";
+		  $searchTerm .=
 "<wsrp:ResourceProperty xmlns:wsrp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
-			$searchTerm .= "mobyws:status_" . $queryID;
-			$searchTerm .= "</wsrp:ResourceProperty>";
-
-			$soap = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
-				sub {
-					sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
-				}
-			  )->wsaddress($EPR)
-			  ->GetMultipleResourceProperties(
+		  $searchTerm .= "mobyws:status_" . $queryID;
+		  $searchTerm .= "</wsrp:ResourceProperty>";
+		  $soap = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
+			  sub {
+				  sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
+			  }
+			)->wsaddress($EPR)
+			->GetMultipleResourceProperties(
 										  SOAP::Data->value($searchTerm)->type('xml') );
+		  my $parser = XML::LibXML->new();
+		  my $xml    = $soap->raw_xml;
+		  my $doc    = $parser->parse_string($xml);
+		  $soap = $doc->getDocumentElement();
+		  my $prop_name = "status_" . $queryID;
+		  my ($prop) =
+			   $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
+			|| $soap->getElementsByTagName($prop_name);
+		  my $event = $prop->getFirstChild->toString
+			unless ref $prop eq "XML::LibXML::NodeList";
+		  $event = $prop->pop()->getFirstChild->toString
+			if ref $prop eq "XML::LibXML::NodeList";
+		  my $status = LSAE::AnalysisEventBlock->new($event);
+
+		  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";
+			  }
+		  }
+	  }
+	  last if scalar keys(%completed) == $#query_ids + 1;
+  }
+  foreach my $queryID (@query_ids) {
 
-			my $parser = XML::LibXML->new();
-			my $xml    = $soap->raw_xml;
-			my $doc    = $parser->parse_string($xml);
-			$soap = $doc->getDocumentElement();
-			my $prop_name = "status_" . $queryID;
-
-			my ($prop) =
-			     $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
-			  || $soap->getElementsByTagName($prop_name);
-			my $event = $prop->getFirstChild->toString
-			  unless ref $prop eq "XML::LibXML::NodeList";
-			$event = $prop->pop()->getFirstChild->toString
-			  if ref $prop eq "XML::LibXML::NodeList";
-
-			my $status = LSAE::AnalysisEventBlock->new($event);
-			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";
-				}
-			}
-		}
-		last if scalar keys(%completed) == $#query_ids + 1;
-	}
-
-	foreach my $queryID (@query_ids) {
-
-		# get the result
-		my $searchTerm .=
+	  # get the result
+	  my $searchTerm .=
 "<wsrp:ResourceProperty xmlns:wsrp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
-		$searchTerm .= "mobyws:result_" . $queryID;
-		$searchTerm .= "</wsrp:ResourceProperty>";
-		my $ans = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
-			sub {
-				sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
-			}
-		  )->wsaddress($EPR)
-		  ->GetMultipleResourceProperties(
-										  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);
-		$soap = $doc->getDocumentElement();
-		my $prop_name = "result_" . $queryID;
-		my ($prop) = $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
-		  || $soap->getElementsByTagName($prop_name);
-		my $result = $prop->getFirstChild->toString
-		  unless ref $prop eq "XML::LibXML::NodeList";
-		$result = $prop->pop()->getFirstChild->toString
-		  if ref $prop eq "XML::LibXML::NodeList";
-		print $result;
-	}
-
-	# destroy the result
-	my $ans = WSRF::Lite->uri($WSRF::Constants::WSRL)->on_action(
-		sub {
-			sprintf '%s/ImmediateResourceTermination/%sRequest',
-			  $WSRF::Constants::WSRLW, $_[1];
-		}
-	)->wsaddress($EPR)->Destroy();
-
+	  $searchTerm .= "mobyws:result_" . $queryID;
+	  $searchTerm .= "</wsrp:ResourceProperty>";
+	  my $ans = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
+		  sub {
+			  sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
+		  }
+		)->wsaddress($EPR)
+		->GetMultipleResourceProperties( 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);
+	  $soap = $doc->getDocumentElement();
+	  my $prop_name = "result_" . $queryID;
+	  my ($prop) = $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
+		|| $soap->getElementsByTagName($prop_name);
+	  my $result = $prop->getFirstChild->toString
+		unless ref $prop eq "XML::LibXML::NodeList";
+	  $result = $prop->pop()->getFirstChild->toString
+		if ref $prop eq "XML::LibXML::NodeList";
+	  print $result;
+  }
+
+  # destroy the result
+  my $ans = WSRF::Lite->uri($WSRF::Constants::WSRL)->on_action(
+	  sub {
+		  sprintf '%s/ImmediateResourceTermination/%sRequest',
+			$WSRF::Constants::WSRLW, $_[1];
+	  }
+  )->wsaddress($EPR)->Destroy();
 } else {
 
-	# calling a local service module, without SOAP
-	my $data;
-	if ( @ARGV > 0 ) {
-		$data = shift;    # a file name
-	} else {
-		use File::Temp qw( tempfile );
-		my $fh;
-		( $fh, $data ) = tempfile( UNLINK => 1 );
-		print $fh _empty_input();
-		close $fh;
-	}
-	eval "require $module" or croak $@;
-	eval {
-		my $target = new $module;
-		print $target->$service($data), "\n";
-	} or croak $@;
+  # calling a local service module, without SOAP
+  my $data;
+  if ( @ARGV > 0 ) {
+	  $data = shift;    # a file name
+  } else {
+	  use File::Temp qw( tempfile );
+	  my $fh;
+	  ( $fh, $data ) = tempfile( UNLINK => 1 );
+	  print $fh _empty_input();
+	  close $fh;
+  }
+  eval "require $module" or croak $@;
+  eval {
+	  my $target = new $module;
+	  print $target->$service($data), "\n";
+  } or croak $@;
 }
 
 sub _moby_wsrf_header {


From kawas at dev.open-bio.org  Fri Oct 16 13:43:30 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 13:43:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161743.n9GHhUth025131@dev.open-bio.org>


kawas
Fri Oct 16 13:43:30 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv25096/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent commits
moby-live/Perl/MOSES-MOBY Changes,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/16 15:51:45	1.22
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/16 17:43:30	1.23
@@ -10,6 +10,23 @@
       The first queryID was polled and when
       it completed, the script assumed all of
       the invocations were completed.
+    - moses-testing-service.pl (thx to Pieter Neerincx)
+        * Moved the POST request out of the foreach
+          $queryID loop.
+        * Added the name of the element "analysis_event"
+          to $xpath.
+        * Moved the sleep(20) out of the &_check_status
+          sub. 
+        * Added a diagnostic message for the die
+          statement when we cant find our event id.
+        * Moved some messages for "verbose" info in
+          &_check_status, so the script always reports
+          the job status whether a job has completed
+          or not.
+        * I also added $queryID to the verbose messaging
+          so the script reports which job that status
+          message corresponded to...
+    
 
 0.92 Oct 13, 2009
     *** Notes for this release ***


From kawas at dev.open-bio.org  Fri Oct 16 13:44:23 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 13:44:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161744.n9GHiNDD025171@dev.open-bio.org>


kawas
Fri Oct 16 13:44:23 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share
In directory dev.open-bio.org:/tmp/cvs-serv25136/MOSES-MOBY/share

Modified Files:
	notes 
Log Message:
updated some of the paths in case other care to use these notes.
moby-live/Perl/MOSES-MOBY/share notes,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/notes,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/notes	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/notes	2009/10/16 17:44:23	1.4
@@ -1,9 +1,9 @@
 Perl documentation:
 ===================
 
-pod2man MOBY/Datatypes/MobyObject.pm | nroff -man | less
+pod2man lib/MOSES/MOBY/Data/Object.pm | nroff -man | less
 ---
-pods2html --index='Perl MoSeS Documentation' /home/senger/jMoby/src/Perl/ /home/senger/jMoby/src/perldoc/
+pods2html --index='Perl MoSeS Documentation' ~/moby-live/Perl/MOSES-MOBY/lib ~/moby-live/Perl/MOSES-MOBY/perldoc/
 ---
 http://search.cpan.org/~iwalz/Pod2html/lib/Pod/2/html.pm
 ----


From kawas at dev.open-bio.org  Fri Oct 23 14:02:15 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 23 Oct 2009 14:02:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910231802.n9NI2EuC003965@dev.open-bio.org>


kawas
Fri Oct 23 14:02:14 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv3929/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
missing a my in front of $xpath ... doh!
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/16 17:43:09	1.14
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/23 18:02:14	1.15
@@ -353,7 +353,7 @@
 			#
 			#my $xpath = "//*[local-name() = 'analysis_event'][\@id='$queryID']";
 			#my $xpath = "//analysis_event[\@id='$queryID']";
-			$xpath = "//*[local-name() = 'analysis_event'][\@*='$queryId']";
+			my $xpath = "//*[local-name() = 'analysis_event'][\@*='$queryId']";
 			my $xpc = XML::LibXML::XPathContext->new();
 			my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
 


From kawas at dev.open-bio.org  Fri Oct 23 14:49:31 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 23 Oct 2009 14:49:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910231849.n9NInVZw004150@dev.open-bio.org>


kawas
Fri Oct 23 14:49:31 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4111/MOSES-MOBY

Modified Files:
	Changes Makefile.PL 
Log Message:
not happy about type in testing service script, so releasing new cpan release.
moby-live/Perl/MOSES-MOBY Changes,1.23,1.24 Makefile.PL,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/16 17:43:30	1.23
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/23 18:49:31	1.24
@@ -1,5 +1,9 @@
 Revision history for Perl extension MOSES::MOBY.
 
+0.94
+    Fix to moses-testing-service.pl script. typo
+    found in script.
+    
 0.93
 
     Changes:

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/16 15:51:45	1.22
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/23 18:49:31	1.23
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.93';
+	version '0.94';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';


From drepchevski at dev.open-bio.org  Mon Oct 26 08:23:08 2009
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Mon, 26 Oct 2009 08:23:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910261223.n9QCN8TF020815@dev.open-bio.org>


drepchevski
Mon Oct 26 08:23:07 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry
In directory dev.open-bio.org:/tmp/cvs-serv20780

Modified Files:
	ObjectType.java 
Log Message:
Added an auxiliary method to get a relationship list by type
moby-live/Java/src/main/org/inb/biomoby/shared/registry ObjectType.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ObjectType.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ObjectType.java	2009/09/09 19:47:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ObjectType.java	2009/10/26 12:23:07	1.2
@@ -55,6 +55,25 @@
         getRelationships().add(relationship);
     }
     
+    /**
+     * Auxiliary method to find relationship by its type
+     * 
+     * @param relationshipType a type of relationship to be found
+     * @return found relationship object or null
+     */
+    public Relationship<ObjectType> getRelationship(Relationship.RELATIONSHIP_TYPE relationshipType)
+    {
+        for (Relationship<ObjectType> relationship : getRelationships())
+        {
+            if (relationship.getRelationshipType() == relationshipType)
+            {
+                return relationship;
+            }
+        }
+
+        return null;
+    }
+
     @XmlElement(name="relationship")
     public List<Relationship<ObjectType>> getRelationships()
     {


From kawas at dev.open-bio.org  Mon Oct 26 12:06:00 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 26 Oct 2009 12:06:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910261606.n9QG60k9030142@dev.open-bio.org>


kawas
Mon Oct 26 12:06:00 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv30106/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
xpath statement for analysis_event has been changed once again, but should stay like this for a while. This one seems to be the most correct for testing moses services.
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/23 18:02:14	1.15
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/26 16:06:00	1.16
@@ -351,9 +351,9 @@
 			#
 			# Find status of this query ID.
 			#
-			#my $xpath = "//*[local-name() = 'analysis_event'][\@id='$queryID']";
+			#my $xpath = "//*[local-name() = 'analysis_event'][\@*='$queryID']";
 			#my $xpath = "//analysis_event[\@id='$queryID']";
-			my $xpath = "//*[local-name() = 'analysis_event'][\@*='$queryId']";
+			my $xpath = "//*[local-name() = 'analysis_event'][\@id='$queryId']";
 			my $xpc = XML::LibXML::XPathContext->new();
 			my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
 


From kawas at dev.open-bio.org  Mon Oct 26 12:08:07 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 26 Oct 2009 12:08:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910261608.n9QG87Xi030525@dev.open-bio.org>


kawas
Mon Oct 26 12:08:07 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30490/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent commits
moby-live/Perl/MOSES-MOBY Changes,1.24,1.25
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/23 18:49:31	1.24
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/26 16:08:07	1.25
@@ -1,5 +1,12 @@
 Revision history for Perl extension MOSES::MOBY.
 
+
+0.95
+    * updated the xpath statement in the testing
+      service script. Change should persist until
+      the XML generated by MOSES for analysis events
+      changes.
+
 0.94
     Fix to moses-testing-service.pl script. typo
     found in script.


From kawas at dev.open-bio.org  Fri Oct  2 15:15:48 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 2 Oct 2009 11:15:48 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910021515.n92FFmmM009604@dev.open-bio.org>


kawas
Fri Oct  2 11:15:48 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-serv9568/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service.tt 
Log Message:
make sure that we dont see undefined variables in hash warnings (thanks pieter)
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2008/11/19 14:24:14	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2009/10/02 15:15:48	1.6
@@ -239,7 +239,7 @@
 #       $response->record_error ( { code => INPUT_INCORRECT_NAMESPACE,
 #                                   msg  => 'This service requires inputs under the namespaces: {"' . join(',', keys %valid_namespaces) . '"}' } );
 #       return;
-#   } unless $valid_namespaces{$namespace};
+#   } unless defined($namespace) && $valid_namespaces{$namespace};
     [%- ELSE %]
     if (defined $[% input.name %]_collection) {
         foreach my $[% input.name %]_element (@{ $[% input.name %]_collection }) {
@@ -250,7 +250,7 @@
         #       $response->record_error ( { code => INPUT_INCORRECT_NAMESPACE,
         #                                   msg  => 'This service requires inputs under the namespaces: { "' . join(',', keys %valid_namespaces) . '"}' } );
         #       return;
-        #   } unless $valid_namespaces{$namespace};
+        #   } unless defined($namespace) && $valid_namespaces{$namespace};
         }
     }
     [%- END %]



From senger at dev.open-bio.org  Sun Oct  4 23:31:28 2009
From: senger at dev.open-bio.org (Martin Senger)
Date: Sun, 4 Oct 2009 19:31:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910042331.n94NVSCh029672@dev.open-bio.org>


senger
Sun Oct  4 19:31:28 EDT 2009
Update of /home/repository/moby/moby-live/Java/xmls
In directory dev.open-bio.org:/tmp/cvs-serv29653/xmls

Modified Files:
	project.pom 
Log Message:
jax-ws dependencies updated
moby-live/Java/xmls project.pom,1.16,1.17
===================================================================
RCS file: /home/repository/moby/moby-live/Java/xmls/project.pom,v
retrieving revision 1.16
retrieving revision 1.17
diff -u -r1.16 -r1.17
--- /home/repository/moby/moby-live/Java/xmls/project.pom	2009/06/09 22:20:54	1.16
+++ /home/repository/moby/moby-live/Java/xmls/project.pom	2009/10/04 23:31:28	1.17
@@ -282,14 +282,39 @@
     <dependency>
       <groupId>com.sun.xml.ws</groupId>
       <artifactId>jaxws-tools</artifactId>
-      <version>2.1.3</version>
+      <version>2.1.4</version>
+      <exclusions>
+        <exclusion>
+          <groupId>javax.xml.ws</groupId>
+          <artifactId>jaxws-api</artifactId>
+        </exclusion>
+        <exclusion>
+          <groupId>javax.jws</groupId>
+          <artifactId>jsr181</artifactId>
+        </exclusion>
+      </exclusions> 
     </dependency>
-
     <dependency>
-      <groupId>com.sun.xml.ws</groupId>
-      <artifactId>jaxws-rt</artifactId>
-      <version>2.1.4</version>
+      <groupId>javax.xml.ws</groupId>
+      <artifactId>jaxws-api</artifactId>
+      <version>2.1-1</version>
+      <exclusions>
+        <exclusion>
+          <groupId>javax.jws</groupId>
+          <artifactId>jsr181</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
+    <!--
+         Use geronimo-specs version of jsr181 since the BEA version of 
+         of jsr181.jar is not available at central
+         -->
+    <dependency>
+      <groupId>org.apache.geronimo.specs</groupId>
+      <artifactId>geronimo-ws-metadata_2.0_spec</artifactId>
+      <version>1.1.1</version>
+    </dependency>
+
 
     <dependency>
       <groupId>jdom</groupId>



From kawas at dev.open-bio.org  Wed Oct  7 15:40:24 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 7 Oct 2009 11:40:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910071540.n97FeOYw010557@dev.open-bio.org>


kawas
Wed Oct  7 11:40:24 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv10517/MOSES-MOBY

Modified Files:
	Changes Makefile.PL 
Log Message:
bug fix to fix warning when testing soapless service and the debug log setting.
moby-live/Perl/MOSES-MOBY Changes,1.17,1.18 Makefile.PL,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.17
retrieving revision 1.18
diff -u -r1.17 -r1.18
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/08/27 19:44:39	1.17
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/07 15:40:24	1.18
@@ -1,5 +1,15 @@
 Revision history for Perl extension MOSES::MOBY.
 
+0.92
+    - Bug fix: Can't use string ("<moby:MOBY
+      xmlns:moby="http://ww") as a HASH ref while 
+      "strict refs" in use ... when testing CGI 
+      services.
+    - Bug fix: when namespace checking in our
+      service implementation, if no namespace
+      is passed, our code produces warnings ...
+      added check to ensure that namespace is
+      defined before checking. 
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/08/28 15:23:15	1.19
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/07 15:40:24	1.20
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.91';
+	version '0.92';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';



From kawas at dev.open-bio.org  Wed Oct  7 15:40:24 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Wed, 7 Oct 2009 11:40:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910071540.n97FeOKi010577@dev.open-bio.org>


kawas
Wed Oct  7 11:40:24 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-serv10517/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service-base.tt 
Log Message:
bug fix to fix warning when testing soapless service and the debug log setting.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service-base.tt,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt	2009/08/27 19:37:37	1.4
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service-base.tt	2009/10/07 15:40:24	1.5
@@ -200,7 +200,9 @@
 	if ($LOG->is_debug) {
 	    my $soap_output = $self->finish_output ($out_package);
 	    $LOG->debug ("Output raw data (first 1000 characters): " .
-			 substr ($soap_output->{_value}->[0], 0, 1000));
+			 substr ($soap_output->{_value}->[0], 0, 1000)) if ref($soap_output) =~ m|^HASH|;
+	   $LOG->debug ("Output raw data (first 1000 characters): " .
+             substr ($soap_output, 0, 1000)) unless ref($soap_output) =~ m|^HASH|;
 	    Log::Log4perl::NDC->pop();
 	    return $soap_output;
 	} else {



From kawas at dev.open-bio.org  Fri Oct  9 15:31:01 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 11:31:01 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091531.n99FV1i5013333@dev.open-bio.org>


kawas
Fri Oct  9 11:31:01 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv13298/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
added a line that prints the LSAE message if $opt_v is chosen when checking the status of a submitted job.
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.11,1.12
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -r1.11 -r1.12
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/04/16 18:17:24	1.11
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/09 15:31:00	1.12
@@ -153,6 +153,7 @@
 			$completed->{$queryID} = 1;
 		} elsif ( $status->percentage < 100 ) {
 			print "Current percentage: ", $status->percentage, "\n" if $opt_v;
+			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
 			sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
@@ -168,6 +169,7 @@
 				  || ( $status->new_state =~ m"running"i ) )
 		{
 			print "Current State: ", $status->new_state, "\n" if $opt_v;
+			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
 			sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
@@ -178,6 +180,7 @@
 			$completed->{$queryID} = 1;
 		} elsif ( $status->steps_completed < $status->total_steps ) {
 			print "Steps completed: ", $status->steps_completed, "\n" if $opt_v;
+			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
 			sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
@@ -188,6 +191,7 @@
 			$completed->{$queryID} = 1;
 		} elsif ( $status->remaining > 0 ) {
 			print "Time remaining: ", $status->remaining, "\n" if $opt_v;
+			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
 			sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";



From kawas at dev.open-bio.org  Fri Oct  9 15:39:21 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 11:39:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091539.n99FdLAs013374@dev.open-bio.org>


kawas
Fri Oct  9 11:39:21 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv13339/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent changes
moby-live/Perl/MOSES-MOBY Changes,1.18,1.19
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.18
retrieving revision 1.19
diff -u -r1.18 -r1.19
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/07 15:40:24	1.18
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/09 15:39:21	1.19
@@ -10,6 +10,10 @@
       is passed, our code produces warnings ...
       added check to ensure that namespace is
       defined before checking. 
+    - when testing async services, added a line
+      to print out the LSAE event message if it
+      exists and if the script is running under
+      verbose settings.
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.



From kawas at dev.open-bio.org  Fri Oct  9 17:29:28 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:29:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091729.n99HTS4B013717@dev.open-bio.org>


kawas
Fri Oct  9 13:29:28 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache
In directory dev.open-bio.org:/tmp/cvs-serv13682/MOSES-MOBY/lib/MOSES/MOBY/Cache

Modified Files:
	Central.pm 
Log Message:
category had incorrect case
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache Central.pm,1.8,1.9
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.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/Cache/Central.pm	2009/08/27 19:40:50	1.8
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Cache/Central.pm	2009/10/09 17:29:28	1.9
@@ -991,7 +991,7 @@
     $service->lsid($service_node->getAttribute('lsid') || '');
     $service->type($service_node->getChildrenByTagName('serviceType')->get_node(1)->textContent) if $service_node->getChildrenByTagName('serviceType')->size() > 0;
     $service->authoritative($service_node->getChildrenByTagName('authoritative')->get_node(1)->textContent) if $service_node->getChildrenByTagName('authoritative')->size() > 0;
-    $service->category($service_node->getChildrenByTagName('category')->get_node(1)->textContent) if $service_node->getChildrenByTagName('category')->size() > 0;
+    $service->category($service_node->getChildrenByTagName('Category')->get_node(1)->textContent) if $service_node->getChildrenByTagName('Category')->size() > 0;
     $service->description($service_node->getChildrenByTagName('Description')->get_node(1)->textContent) if $service_node->getChildrenByTagName('Description')->size() > 0;
     $service->email($service_node->getChildrenByTagName('contactEmail')->get_node(1)->textContent) if $service_node->getChildrenByTagName('contactEmail')->size() > 0;
     $service->signatureURL($service_node->getChildrenByTagName('signatureURL')->get_node(1)->textContent) if $service_node->getChildrenByTagName('signatureURL')->size() > 0;



From kawas at dev.open-bio.org  Fri Oct  9 17:32:39 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:32:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091732.n99HWdiS013799@dev.open-bio.org>


kawas
Fri Oct  9 13:32:39 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-serv13764/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service.tt 
Log Message:
added some code to modify the LSAE states
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2009/10/02 15:15:48	1.6
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2009/10/09 17:32:39	1.7
@@ -28,6 +28,10 @@
     [%- MACRO is_simple (entry) BLOCK %]
 	[%- ref (entry) == 'MOSES::MOBY::Def::PrimaryDataSimple' %]
     [%- END -%]
+    
+    [%- MACRO is_async (entry) BLOCK %]
+    [%- entry == 'cgi-async' || entry == 'moby-async' %]
+    [%- END -%]
 
     [%- MACRO set_child (child, leftpad, value) BLOCK %]
        [% FILTER indent (leftpad) -%]
@@ -202,6 +206,9 @@
 @ISA = qw( [% base.module_name %] );
 use MOSES::MOBY::Package;
 use MOSES::MOBY::ServiceException;
+[%- IF is_async(base.category) -%]
+use MOBY::Async::LSAE;
+[%- END %]
 use strict;
 
 [%# here we output use statements for our primitives %]
@@ -275,8 +282,23 @@
     [%- END %]
     [%- END %]
 
-    # do something... (sorry, can't help with that)
-
+    # do something... (sorry, can't you help with that)
+    
+    [%- IF is_async(base.category) %]
+    #simulate a long running service while providing updates
+    
+    #update the state of our service
+    $self->update_state_event($request, 'running','about to sleep for 20 seconds!');
+    
+    # sleep for 20 seconds
+    sleep(20);
+    
+    # update state again
+    $self->update_state_event($request, 'running','Woke up and going back to sleep for 20 more seconds!');
+    
+    # sleep for 20 more seconds
+    sleep(20);
+    [%- END %]
     # EDIT: PUT REAL VALUES INTO THE RESPONSE
     # fill the response
     [%- FOREACH output IN base.outputs %]
@@ -325,6 +347,272 @@
 
 }
 
+[%- IF is_async(base.category) -%]
+#-----------------------------------------------------------------
+# update_state_event
+#    This method is used to update the state of your 
+#    LSAE_STATE_CHANGED_EVENT event.
+#
+#  Parameters:  
+#    $request - $request from process_it()
+#    $state - one of (created, running, completed, terminated_by_request, terminated_by_error) 
+#    $msg   - a message to provide regarding the state of our event 
+#-----------------------------------------------------------------
+sub update_state_event {
+    my ( $self, $request, $state, $msg ) = @_;
+
+    my %valid_states = ('created'=>1,'running'=>1,'completed'=>1,'termintated_by_request'=>1,'terminated_by_error'=>1,);
+    
+    $msg = '' unless defined $msg;
+    $state = 'running' unless defined $state;
+    
+    # validate the state of the event ...
+    $state = 'running' unless $valid_states{$state};
+    
+    unless ( defined $ENV{ID} ) {
+        # hmm, local testing of service?
+        $ENV{ID} = WSRF::GSutil::CalGSH_ID();
+        WSRF::File::toFile($ENV{ID});
+    }
+
+    # our service invocation id
+    my $ID = $ENV{ID};
+
+    # our job id
+    my $jid = $request->jid;
+
+    # some variables we need to access/store our event information
+    my $property_pid    = "pid_$jid";
+    my $property_input  = "input_$jid";
+    my $property_status = "status_$jid";
+    my $property_result = "result_$jid";
+
+    # construct an LSAE object based on the old event block
+    my $old_status = LSAE::AnalysisEventBlock->new(
+                                    $WSRF::WSRP::ResourceProperties{$property_status}
+    );
+    # construct a new state changed event
+    my $status = LSAE::AnalysisEventBlock->new();
+    $status->type(LSAE_STATE_CHANGED_EVENT);
+
+    # set the previous state
+    $status->previous_state( $old_status->new_state() ) if defined ($old_status->type) and $old_status->type == LSAE_STATE_CHANGED_EVENT;
+    $status->previous_state( 'created') unless $status->previous_state;
+
+    # set the new state
+    $status->new_state($state);
+    $status->message($msg);
+
+    # set our job id for this event
+    $status->id($jid);
+
+    # create a file based resource that we will store our event information
+    my $lock = WSRF::MobyFile->new( undef, $ID );
+    $WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
+
+    # here we leave the result empty since the service is still running
+    $WSRF::WSRP::ResourceProperties{$property_result} = '';
+
+    # save the event so that our clients can access the information
+    $lock->toFile();
+    return;
+}
+#-----------------------------------------------------------------
+# update_percentage_event
+#    This method is used to update the state of your 
+#    LSAE_PERCENT_PROGRESS_EVENT event.
+#
+#  Parameters:  
+#    $request     - $request from process_it()
+#    $percentrage - an integer between 0-100 
+#    $msg         - a message to provide regarding the state of our event 
+#-----------------------------------------------------------------
+sub update_percentage_event {
+    my ( $self, $request, $percentage, $msg ) = @_;
+    
+    $msg = '' unless defined $msg;
+    $state = 1 unless defined $percentage;
+    
+    # validate the state of the event ...
+    $percentage = 1 unless $percentage >= 0 and $percentage <=100;
+    
+    unless ( defined $ENV{ID} ) {
+        # hmm, local testing of service?
+        $ENV{ID} = WSRF::GSutil::CalGSH_ID();
+        WSRF::File::toFile($ENV{ID});
+    }
+
+    # our service invocation id
+    my $ID = $ENV{ID};
+
+    # our job id
+    my $jid = $request->jid;
+
+    # some variables we need to access/store our event information
+    my $property_pid    = "pid_$jid";
+    my $property_input  = "input_$jid";
+    my $property_status = "status_$jid";
+    my $property_result = "result_$jid";
+
+    # construct an LSAE object based on the old event block
+    my $old_status = LSAE::AnalysisEventBlock->new(
+                                    $WSRF::WSRP::ResourceProperties{$property_status}
+    );
+    # construct a new state changed event
+    my $status = LSAE::AnalysisEventBlock->new();
+    $status->type(LSAE_PERCENT_PROGRESS_EVENT);
+
+    # set the new state
+    $status->percentage($percentage);
+    $status->message($msg);
+
+    # set our job id for this event
+    $status->id($jid);
+
+    # create a file based resource that we will store our event information
+    my $lock = WSRF::MobyFile->new( undef, $ID );
+    $WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
+
+    # here we leave the result empty since the service is still running
+    $WSRF::WSRP::ResourceProperties{$property_result} = '';
+
+    # save the event so that our clients can access the information
+    $lock->toFile();
+    return;
+}
+
+#-----------------------------------------------------------------
+# update_step_event
+#    This method is used to update the state of your 
+#    LSAE_STEP_PROGRESS_EVENT event.
+#
+#  Parameters:  
+#    $request         - $request from process_it()
+#    $total_steps     - integer representing total steps until completion
+#    $steps_completed - integer representing steps completed 
+#    $msg             - a message to provide regarding the state of our event 
+#-----------------------------------------------------------------
+sub update_step_event {
+    my ( $self, $request, $total_steps, $steps_completed, $msg ) = @_;
+   
+    $msg = '' unless defined $msg;
+    $total_steps = 1 unless defined $total_steps;
+    $steps_completed = 0 unless defined $steps_completed;
+    
+    # validate the state of the event ...
+    $steps_completed = $total_steps if $steps_completed > $total_steps;
+    
+    unless ( defined $ENV{ID} ) {
+        # hmm, local testing of service?
+        $ENV{ID} = WSRF::GSutil::CalGSH_ID();
+        WSRF::File::toFile($ENV{ID});
+    }
+
+    # our service invocation id
+    my $ID = $ENV{ID};
+
+    # our job id
+    my $jid = $request->jid;
+
+    # some variables we need to access/store our event information
+    my $property_pid    = "pid_$jid";
+    my $property_input  = "input_$jid";
+    my $property_status = "status_$jid";
+    my $property_result = "result_$jid";
+
+    # construct an LSAE object based on the old event block
+    my $old_status = LSAE::AnalysisEventBlock->new(
+                                    $WSRF::WSRP::ResourceProperties{$property_status}
+    );
+    # construct a new state changed event
+    my $status = LSAE::AnalysisEventBlock->new();
+    $status->type(LSAE_STEP_PROGRESS_EVENT);
+
+    # set the new state
+    $status->steps_completed($steps_completed);
+    $status->total_steps($total_steps);
+    $status->message($msg);
+
+    # set our job id for this event
+    $status->id($jid);
+
+    # create a file based resource that we will store our event information
+    my $lock = WSRF::MobyFile->new( undef, $ID );
+    $WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
+
+    # here we leave the result empty since the service is still running
+    $WSRF::WSRP::ResourceProperties{$property_result} = '';
+
+    # save the event so that our clients can access the information
+    $lock->toFile();
+    return;
+}
+
+#-----------------------------------------------------------------
+# update_time_event
+#    This method is used to update the state of your 
+#    LSAE_TIME_PROGRESS_EVENT event.
+#
+#  Parameters:  
+#    $request   - $request from process_it()
+#    $remaining - integer representing seconds until completion 
+#    $msg       - a message to provide regarding the state of our event 
+#-----------------------------------------------------------------
+sub update_time_event {
+    my ( $self, $request, $remaining, $msg ) = @_;
+    
+    $msg = '' unless defined $msg;
+    $remaining = 0 unless defined $remaining;
+    
+    # validate the state of the event ...
+    $remaining = 0 unless $remaining >= 0 ;
+    
+    unless ( defined $ENV{ID} ) {
+        # hmm, local testing of service?
+        $ENV{ID} = WSRF::GSutil::CalGSH_ID();
+        WSRF::File::toFile($ENV{ID});
+    }
+
+    # our service invocation id
+    my $ID = $ENV{ID};
+
+    # our job id
+    my $jid = $request->jid;
+
+    # some variables we need to access/store our event information
+    my $property_pid    = "pid_$jid";
+    my $property_input  = "input_$jid";
+    my $property_status = "status_$jid";
+    my $property_result = "result_$jid";
+
+    # construct an LSAE object based on the old event block
+    my $old_status = LSAE::AnalysisEventBlock->new(
+                                    $WSRF::WSRP::ResourceProperties{$property_status}
+    );
+    # construct a new state changed event
+    my $status = LSAE::AnalysisEventBlock->new();
+    $status->type(LSAE_TIME_PROGRESS_EVENT);
+
+    # set the new state
+    $status->remaining($remaining);
+    $status->message($msg);
+
+    # set our job id for this event
+    $status->id($jid);
+
+    # create a file based resource that we will store our event information
+    my $lock = WSRF::MobyFile->new( undef, $ID );
+    $WSRF::WSRP::ResourceProperties{$property_status} = $status->XML();
+
+    # here we leave the result empty since the service is still running
+    $WSRF::WSRP::ResourceProperties{$property_result} = '';
+
+    # save the event so that our clients can access the information
+    $lock->toFile();
+    return;
+}
+[%- END -%]
+
 1;
 __END__
 



From kawas at dev.open-bio.org  Fri Oct  9 17:37:49 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:37:49 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091737.n99HbnUf013860@dev.open-bio.org>


kawas
Fri Oct  9 13:37:49 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-serv13825/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates

Modified Files:
	service.tt 
Log Message:
updated the use statement IF block and fixed typo in update_percentage_event
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates service.tt,1.7,1.8
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt,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/Generators/templates/service.tt	2009/10/09 17:32:39	1.7
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/templates/service.tt	2009/10/09 17:37:49	1.8
@@ -206,7 +206,7 @@
 @ISA = qw( [% base.module_name %] );
 use MOSES::MOBY::Package;
 use MOSES::MOBY::ServiceException;
-[%- IF is_async(base.category) -%]
+[% IF is_async(base.category) -%]
 use MOBY::Async::LSAE;
 [%- END %]
 use strict;
@@ -431,7 +431,7 @@
     my ( $self, $request, $percentage, $msg ) = @_;
     
     $msg = '' unless defined $msg;
-    $state = 1 unless defined $percentage;
+    $percentage = 1 unless defined $percentage;
     
     # validate the state of the event ...
     $percentage = 1 unless $percentage >= 0 and $percentage <=100;



From kawas at dev.open-bio.org  Fri Oct  9 17:46:44 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:46:44 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091746.n99Hki1A013903@dev.open-bio.org>


kawas
Fri Oct  9 13:46:44 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv13868/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent changes
moby-live/Perl/MOSES-MOBY Changes,1.19,1.20
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.19
retrieving revision 1.20
diff -u -r1.19 -r1.20
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/09 15:39:21	1.19
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/09 17:46:44	1.20
@@ -14,6 +14,10 @@
       to print out the LSAE event message if it
       exists and if the script is running under
       verbose settings.
+    - Bug fix: Central->_createServiceFromXML had
+      Category as category
+    - added some code to the service.tt that aides
+      in updating a services LSAE event states. 
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.



From kawas at dev.open-bio.org  Fri Oct  9 17:50:08 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 9 Oct 2009 13:50:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910091750.n99Ho8JF013943@dev.open-bio.org>


kawas
Fri Oct  9 13:50:08 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share
In directory dev.open-bio.org:/tmp/cvs-serv13908/MOSES-MOBY/share

Modified Files:
	USER_REGISTRIES 
Log Message:

moby-live/Perl/MOSES-MOBY/share USER_REGISTRIES,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/USER_REGISTRIES,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/USER_REGISTRIES	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/USER_REGISTRIES	2009/10/09 17:50:08	1.4
@@ -1,11 +1 @@
-%USER_REGISTRIES = (
-#                    iCAPTURE => { 
-#                                  endpoint  => 'http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl',
-#                                  namespace => 'http://mobycentral.icapture.ubc.ca/MOBY/Central',
-#                                  name      => 'iCAPTURE Centre, Vancouver',
-#                                  contact   => 'Edward Kawas (edward.kawas at gmail.com)',
-#                                  public    => 'yes',
-#                                  text      => 'A curated public registry hosted at the iCAPTURE Centre, Vancouver',
-#                                 },
-
-                    );
+%USER_REGISTRIES = ();



From kawas at dev.open-bio.org  Tue Oct 13 15:28:36 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 11:28:36 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131528.n9DFSZMV004279@dev.open-bio.org>


kawas
Tue Oct 13 11:28:35 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES
In directory dev.open-bio.org:/tmp/cvs-serv4243/MOSES-MOBY/lib/MOSES

Modified Files:
	MOBY.pm 
Log Message:
added a little text to the pod name so that when users go to cpan, they know which module has the doc
moby-live/Perl/MOSES-MOBY/lib/MOSES MOBY.pm,1.10,1.11
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -r1.10 -r1.11
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/04/08 22:40:11	1.10
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY.pm	2009/10/13 15:28:35	1.11
@@ -22,7 +22,7 @@
 
 =head1 NAME
 
-MOSES::MOBY - Perl extension for the automatic generation of BioMOBY web services
+MOSES::MOBY - Start here! Documentation for the Perl extension for the automatic generation of BioMOBY web services!
 
 =head1 SYNOPSIS
 



From kawas at dev.open-bio.org  Tue Oct 13 15:33:25 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 11:33:25 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131533.n9DFXOrv004319@dev.open-bio.org>


kawas
Tue Oct 13 11:33:24 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4284/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
getting ready to create cpan release. added some notes for those that read these things
moby-live/Perl/MOSES-MOBY Changes,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/09 17:46:44	1.20
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/13 15:33:24	1.21
@@ -1,6 +1,17 @@
 Revision history for Perl extension MOSES::MOBY.
 
-0.92
+0.92 Oct 13, 2009
+    *** Notes for this release ***
+        The service template has been updated.
+        The update mainly affects async service
+        implementations. The easiest thing to do
+        is to backup your async service 
+        implementations and re-generate them.
+        
+        Only do this if you had problems with 
+        erratic service behaviour in the past!
+    
+    Changes:
     - Bug fix: Can't use string ("<moby:MOBY
       xmlns:moby="http://ww") as a HASH ref while 
       "strict refs" in use ... when testing CGI 
@@ -17,7 +28,8 @@
     - Bug fix: Central->_createServiceFromXML had
       Category as category
     - added some code to the service.tt that aides
-      in updating a services LSAE event states. 
+      in updating a services LSAE event states.
+      
 0.91
 	- Updated the Makefile.PL to handle some missing 
 	  dependencies.



From kawas at dev.open-bio.org  Tue Oct 13 15:38:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 11:38:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131538.n9DFcAZW004359@dev.open-bio.org>


kawas
Tue Oct 13 11:38:10 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4324/MOSES-MOBY

Modified Files:
	Makefile.PL 
Log Message:
added a no index directive for the templates/ directory so that the perldoc on cpan doesnt look messed up.
moby-live/Perl/MOSES-MOBY Makefile.PL,1.20,1.21
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.20
retrieving revision 1.21
diff -u -r1.20 -r1.21
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/07 15:40:24	1.20
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/13 15:38:10	1.21
@@ -42,6 +42,7 @@
 
 	build_requires 'Test::More' => '0.42';
 	no_index 'directory'        => 'bin/scripts';
+	no_index 'directory'        => 'lib/MOSES/MOBY/Generators/templates';
 
 	install_script 'bin/scripts/moses-cache-tester.pl';
 	install_script 'bin/scripts/moses-config-status.pl';



From kawas at dev.open-bio.org  Tue Oct 13 15:43:10 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 11:43:10 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131543.n9DFhA57004402@dev.open-bio.org>


kawas
Tue Oct 13 11:43:10 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators
In directory dev.open-bio.org:/tmp/cvs-serv4367/MOSES-MOBY/lib/MOSES/MOBY/Generators

Modified Files:
	Utils.pm 
Log Message:
updated the perldoc (wasnt correct on cpan)
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm	2008/11/06 18:32:33	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm	2009/10/13 15:43:10	1.6
@@ -19,22 +19,16 @@
 
 MOSES::MOBY::Utils - what does not fit elsewhere
 
-=cut
-
 =head1 SYNOPSIS
 
  # find a file located somewhere in @INC
  use MOSES::MOBY::Generators::Utils;
  my $file = MOSES::MOBY::Generators::Utils->find_file ('resource.file');
- 
-=cut
 
 =head1 DESCRIPTION
 
 General purpose utilities.
 
-=cut
-
 =head1 AUTHORS
 
  Martin Senger (martin.senger [at] gmail [dot] com)
@@ -42,8 +36,6 @@
 
 =head1 SUBROUTINES
 
-=cut
-
 #-----------------------------------------------------------------
 # find_file
 #-----------------------------------------------------------------
@@ -87,4 +79,5 @@
 }
 
 1;
+
 __END__



From kawas at dev.open-bio.org  Tue Oct 13 16:08:11 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 12:08:11 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131608.n9DG8BUL004478@dev.open-bio.org>


kawas
Tue Oct 13 12:08:11 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4443/MOSES-MOBY/lib/MOSES/MOBY

Modified Files:
	Config.pm 
Log Message:
added perldoc for module.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Config.pm,1.4,1.5
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm,v
retrieving revision 1.4
retrieving revision 1.5
diff -u -r1.4 -r1.5
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm	2008/04/29 19:45:01	1.4
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm	2009/10/13 16:08:11	1.5
@@ -26,9 +26,63 @@
     $ENV_CONFIG_DIR = 'BIOMOBY_CFG_DIR';
 }
 
+=head1 NAME
+
+MOSES::MOBY::Config - A hash based configuration module based on Config::Simple
+
+=head1 SYNOPSIS
+
+ # use config allong with the MOSES config file
+ use MOSES::MOBY::Config;
+
+ # use config along with my properties.file
+ use MOSES::MOBY::Config qw /'properties.file'/;
+
+ # print the successfully read config files
+ foreach my $file (MOSES::MOBY::Config->ok_files) {
+    print "\t$file - successfully processed\n";
+ }
+
+ # print a list of files that failed to load
+ my %failed = MOSES::MOBY::Config->failed_files;
+ if (keys %failed > 0) {
+    print "Failed configuration files:\n";
+    foreach my $file (sort keys %failed) {
+    my $msg = $failed{$file}; $msg =~ s/\n$//;
+        print "\t$file => $msg\n";
+    }
+ }
+
+ # print out the config params read thus far
+ print "All configuration parameters:\n";
+ foreach my $name (sort MOSES::MOBY::Config->param()) {
+    print "\t$name => " . MOSES::MOBY::Config->param ($name);
+ }
+
+=head1 DESCRIPTION
+
+A module for reading configuration files and maintaining configuration parameters 
+
+=head1 AUTHORS
+
+ Martin Senger (martin.senger [at] gmail [dot] com)
+ Edward Kawas (edward.kawas [at] gmail [dot] com)
+
+=head1 SUBROUTINES
+
+=cut
+
 # OO access; but there are no instance attributes - everything are
 # class (shared) attributes
 
+=head2 new
+
+Instantiates a new MOSES::MOBY::Config reference. Mainly here for OO access. 
+There are no instance attributes, only class attributes
+
+=cut
+
+
 sub new {
     my ($class, @args) = @_;
 
@@ -126,6 +180,13 @@
 
 # return value of a configuration argument; or add a new argument
 
+=head2 param
+
+If called with no arguments, all of the possible config keys are returned. 
+If called with a single argument, then that argument is assumed to be a key and the value for that key is returned. 
+
+=cut
+
 sub param {
     shift;
 
@@ -146,6 +207,12 @@
 
 # remove one, more, or all configuration arguments
 
+=head2 delete
+
+removes one or more of the configuration keys and their associated values.
+
+=cut
+
 sub delete {
     shift;
 
@@ -164,6 +231,15 @@
 # this argument is passed to the Data::Dumper->Dump as the variable
 # name)
 
+=head2 dump
+
+Returns a stringified version of all configuration parameters;
+
+If passed a scalar parameter, then the dump will be given that variable name.
+This dump can be eval{}'ed.
+
+=cut
+
 sub dump {
     shift;
     my $varname = @_ ? shift : 'CONFIG';
@@ -189,6 +265,12 @@
 
 # return a list of configuration files successfully read (so far)
 
+=head2 ok_files
+
+returns a list of the configuration files successfully read thus far ...
+
+=cut
+
 sub ok_files {
     return sort keys %Success;
 }
@@ -196,11 +278,17 @@
 # return a hash of configuration files un-successfully read (so far) -
 # with corresponding error messages
 
+=head2 failed_files
+
+returns a hash of the configuration files unsuccessfully read thus far and their corresponding error messages.
+
+=cut
+
 sub failed_files {
     return %Unsuccess;
 }
 
-
+=cut
 
 1;
 __END__



From kawas at dev.open-bio.org  Tue Oct 13 16:42:20 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 12:42:20 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131642.n9DGgKHF004955@dev.open-bio.org>


kawas
Tue Oct 13 12:42:20 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4920/MOSES-MOBY/lib/MOSES/MOBY

Modified Files:
	Config.pm 
Log Message:

moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY Config.pm,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm	2009/10/13 16:08:11	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Config.pm	2009/10/13 16:42:20	1.6
@@ -288,7 +288,5 @@
     return %Unsuccess;
 }
 
-=cut
-
 1;
 __END__



From kawas at dev.open-bio.org  Tue Oct 13 16:46:21 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 12:46:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131646.n9DGkLAI005016@dev.open-bio.org>


kawas
Tue Oct 13 12:46:21 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators
In directory dev.open-bio.org:/tmp/cvs-serv4981/MOSES-MOBY/lib/MOSES/MOBY/Generators

Modified Files:
	Utils.pm 
Log Message:
fixed the perldoc ... doc created had errors in it.
moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators Utils.pm,1.6,1.7
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm	2009/10/13 15:43:10	1.6
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/lib/MOSES/MOBY/Generators/Utils.pm	2009/10/13 16:46:21	1.7
@@ -36,10 +36,6 @@
 
 =head1 SUBROUTINES
 
-#-----------------------------------------------------------------
-# find_file
-#-----------------------------------------------------------------
-
 =head2 find_file
 
 Try to locate a file whose name is created from the C<$default_start>
@@ -55,6 +51,9 @@
 
 my %full_path_of = ();
 
+#-----------------------------------------------------------------
+# find_file
+#-----------------------------------------------------------------
 sub find_file {
     my ($self, $default_start, @names) = @_;
     my $fixed_part = File::Spec->catfile (@names);



From kawas at dev.open-bio.org  Tue Oct 13 17:03:41 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 13 Oct 2009 13:03:41 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910131703.n9DH3f6V005208@dev.open-bio.org>


kawas
Tue Oct 13 13:03:41 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv5173/MOSES-MOBY

Modified Files:
	README 
Log Message:

moby-live/Perl/MOSES-MOBY README,1.5,1.6
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/README,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -r1.5 -r1.6
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/README	2008/05/09 20:54:31	1.5
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/README	2009/10/13 17:03:41	1.6
@@ -1,4 +1,4 @@
-MOSES-MOBY version .85
+MOSES-MOBY version .92
 ======================
 
 OVERVIEW
@@ -16,12 +16,22 @@
 
 INSTALLATION
 
-To install this module type the following:
-
-   perl Makefile.PL
-   make
-   make test
-   make install
+	To install this module type the following:
+	
+	   perl Makefile.PL
+	   make
+	   make test
+	   make install
+
+	To install this module on WinOS:
+	
+		perl Makefile.PL
+		nmake
+		nmake test
+		nmake install
+	
+	If you have any problems installing prerequisite modules,
+	you may find it easier to use ActiveStates ppm utility.
 
 UPGRADING
 



From drepchevski at dev.open-bio.org  Fri Oct 16 12:18:47 2009
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Fri, 16 Oct 2009 08:18:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161218.n9GCIkJJ024102@dev.open-bio.org>


drepchevski
Fri Oct 16 08:18:46 EDT 2009
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv24067

Modified Files:
	inb_moby_core.html 
Log Message:
put the ontology generator applet inside
moby-live/Java/docs inb_moby_core.html,1.2,1.3
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/inb_moby_core.html,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/moby/moby-live/Java/docs/inb_moby_core.html	2009/09/21 16:31:17	1.2
+++ /home/repository/moby/moby-live/Java/docs/inb_moby_core.html	2009/10/16 12:18:46	1.3
@@ -64,6 +64,7 @@
     }
 
     .code {
+      white-space: pre;
       vertical-align: top;
       color: #000099;
       font-size: 10pt;
@@ -131,6 +132,50 @@
     </table>
   </p>
 
+  <h2> Generating JAXB-annotated ontology classes </h2>
+
+  <p>
+    Even MobyCore may work without generated ontology classes, they facilitate a development.
+    Generated classes are nothing more than JAXB annotated beans with properties.
+
+  </p>
+  
+  <div style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px;">
+    <div style="float: left; width: 350px; margin-right: 50px">      
+      <applet width = "350" height = "350" code = "org.inb.biomoby.generator.gui.Main">
+        <param name = "jnlp_href" value = "http://inb.bsc.es/applications/java/mobygenerator/inb_generator_applet.jnlp"/>
+      </applet>
+    </div>
+
+    
+      Here is an example of generated datatype class:
+    
+       
+    <div class="code" style="margin-left: 400px; font-size: 8pt;">
+ at XmlRootElement(name="WeightedAminoAcidSequences")
+ at XmlType(name="WeightedAminoAcidSequences")
+public class WeightedAminoAcidSequences extends AminoAcidSequence implements Serializable {
+    public List&lt;? extends AminoAcidSequence&gt; getAminoAcidSequence() {
+        return getAttributes("AminoAcidSequence");
+    }
+
+    public void addAminoAcidSequence(AminoAcidSequence aminoAcidSequence) {
+        putAttribute("AminoAcidSequence", aminoAcidSequence);
+    }
+
+    public WeightedObject getWeightedObject() {
+        return getAttribute("WeightedObject");
+    }
+
+    public void setWeightedObject(WeightedObject weightedObject) {
+        putAttribute("WeightedObject", weightedObject);
+    }
+}
+    </div>
+
+    <br style="clear:both;"/>
+  </div>
+  
   <h2> Executing synchronous BioMoby services </h2>
 
   <p>
@@ -138,12 +183,10 @@
     This is done by creating a MobyMessage object:
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 MobyObject object = new MobyObject("P00807", "UniProt");
 MobySimple simple = new MobySimple(object, "id");        
 MobyData data = new MobyData(simple, "sip_1");
 MobyMessage request = new MobyMessage(data);
-</pre>
     </div>
   </p>
 
@@ -163,10 +206,8 @@
     Now we can create a MobyDispatch object and execute a service.
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 MobyDispatch dispatch = new MobyDispatch(service);
 MobyMessage response = dispatch.invoke(request);
-</pre>
     </div>
   </p>
 
@@ -181,9 +222,7 @@
     not have AminoAcidSequence class generated. In this case we would have a AnyMobyObject instead of unknown to us AminoAcidSequence.
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 MobyString string = (MobyString) any.getAttribute("SequenceString");
-</pre>
     </div>
   </p>
 
@@ -192,7 +231,6 @@
     <span class="highlight">MobySimple</span> may contain either a primitive type or a complex one, so we have to check. Here is a simple method that traverse a given element:
      
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 public void traverse(AbstractMobyObject object) throws JAXBException
 {
   System.out.println(MobyMessageContext.getMobyName(object) + " " + object.getArticleName());
@@ -206,8 +244,7 @@
        traverse(o);
      }
   }
-}
-</pre>      
+}     
     </div>
   </p>
 
@@ -219,11 +256,9 @@
     <span class="highlight">AnyMobyObject</span> can also be used to setup a datatype dynamically.
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 AnyMobyObject any = new AnyMobyObject("AminoAcidSequece");
 any.putAttribute("SequenceString", new MobyString("ATCG"));
 any.putAttribute("Length", new MobyInteger(4));
-</pre>
     </div>
   </p>
 
@@ -235,7 +270,6 @@
     Here is an example of parsing a <span class="highlight">MobyMessage</span> response:
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 MobyMessage response = dispatch.invoke(request);
 
 if (response.hasExceptions())
@@ -256,7 +290,7 @@
 
    for (MobyDataElement element : elements)
    {
-     if (element instanceof Mobysimple)
+     if (element instanceof MobySimple)
      {
        MobySimple simple = (MobySimple)element;
        AbstractMobyObject object = simple.getObject();
@@ -292,8 +326,7 @@
        throw new Exception(); // expected MobySimple
      }
    }
-}
-</pre>    
+}  
     </div>
   </p>
 
@@ -306,7 +339,6 @@
     The rest of the things are pretty the same as for synchronous invocation:
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 // AminoAcidSequence sequence = new AminoAcidSequence();
 // sequence.setSequenceString(new MobyString("ATCG")):
 // sequence.setLength(new MobyInteger(4));
@@ -326,7 +358,6 @@
 MobyDispatch dispatch = new MobyDispatch(service);
 
 MobyWSRFResource wsrf = dispatch.invokeAsync(request);
-</pre>
     </div>
   </p>
 
@@ -334,7 +365,6 @@
     The result object is an WSRF resource through which we can poll to check our execution status:
 
     <div class="code" style="margin-left: 40px; margin-right: 40px; padding: 5px 5px 5px 5px">
-<pre>
 while(true)
 {
   AnalysisEvent lsae = wsrf.getResourcePropertyStatus("sip_1");
@@ -362,7 +392,6 @@
    // actually must be an error...
    break;
 }
-</pre>
     </div>
   </p>
 



From kawas at dev.open-bio.org  Fri Oct 16 14:13:39 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 10:13:39 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161413.n9GEDd0V024490@dev.open-bio.org>


kawas
Fri Oct 16 10:13:39 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv24454/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
bug fix: when polling a cgi-async service with > 1 job, only the first job is polled for and when it is complete both are assumed to be complete
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.12,1.13
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.12
retrieving revision 1.13
diff -u -r1.12 -r1.13
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/09 15:31:00	1.12
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/16 14:13:39	1.13
@@ -341,9 +341,12 @@
 			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 );
+			my $xpath = "//*[\@*='$queryID']";
+            my $xpc   = XML::LibXML::XPathContext->new();
+            my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
+            # should only be one ...
+            die unless $nodes->size() == 1;
+			my $status = LSAE::AnalysisEventBlock->new( $nodes->get_node(1)->toString() );
 			&_check_status( $status, \%completed, $queryID, $opt_v );
 		}
 		last if scalar keys(%completed) == $#query_ids + 1;



From kawas at dev.open-bio.org  Fri Oct 16 15:51:45 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 11:51:45 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161551.n9GFpjdv024715@dev.open-bio.org>


kawas
Fri Oct 16 11:51:45 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv24672/MOSES-MOBY

Modified Files:
	META.yml Changes Makefile.PL 
Log Message:
updated Changes to reflect the current state of the module. Updated the makefile and META to provide a new version for MOSES (for down the road when i create a cpan update)
moby-live/Perl/MOSES-MOBY META.yml,1.8,1.9 Changes,1.21,1.22 Makefile.PL,1.21,1.22
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml,v
retrieving revision 1.8
retrieving revision 1.9
diff -u -r1.8 -r1.9
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/04/20 14:32:26	1.8
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/META.yml	2009/10/16 15:51:45	1.9
@@ -39,5 +39,5 @@
   Want: 0.18
   WSRF::Lite: 0.8.2.5
   XML::LibXML: 1.62
-version: 0.90
+version: 0.93
 

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/13 15:33:24	1.21
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/16 15:51:45	1.22
@@ -1,5 +1,16 @@
 Revision history for Perl extension MOSES::MOBY.
 
+0.93
+
+    Changes:
+    - Bug fix: moses-testing-service.pl when 
+      polling async services, didn't actually
+      poll correctly if you had multiple query
+      IDs for a single service invocation ID.
+      The first queryID was polled and when
+      it completed, the script assumed all of
+      the invocations were completed.
+
 0.92 Oct 13, 2009
     *** Notes for this release ***
         The service template has been updated.

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.21
retrieving revision 1.22
diff -u -r1.21 -r1.22
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/13 15:38:10	1.21
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/16 15:51:45	1.22
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.92';
+	version '0.93';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';



From kawas at dev.open-bio.org  Fri Oct 16 17:43:09 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 13:43:09 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161743.n9GHh9Cl025091@dev.open-bio.org>


kawas
Fri Oct 16 13:43:09 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv25056/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
moses-testing-service.pl - async cgi service portion:
        * Moved the POST request out of the foreach
          $queryID loop.
        * Added the name of the element "analysis_event"
          to $xpath.
        * Moved the sleep(20) out of the &_check_status
          sub. 
        * Added a diagnostic message for the die
          statement when we cant find our event id.
        * Moved some messages for "verbose" info in
          &_check_status, so the script always reports
          the job status whether a job has completed
          or not.
        * I also added $queryID to the verbose messaging
          so the script reports which job that status
          message corresponded to...
          
(thx to Pieter Neerincx for patience, code and suggestions)
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.13,1.14
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.13
retrieving revision 1.14
diff -u -r1.13 -r1.14
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/16 14:13:39	1.13
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/16 17:43:09	1.14
@@ -130,9 +130,7 @@
 	  or die "$@\n";
 	eval "use MOBY::Async::WSRF; 1;"
 	  or die "$@\n";
-
 }
-
 use strict;
 
 sub _empty_input {
@@ -149,17 +147,22 @@
 sub _check_status {
 	my ( $status, $completed, $queryID, $opt_v ) = @_;
 	if ( $status->type == LSAE_PERCENT_PROGRESS_EVENT ) {
+		print "Current percentage for job $queryID: ", $status->percentage, "\n"
+		  if $opt_v;
 		if ( $status->percentage >= 100 ) {
 			$completed->{$queryID} = 1;
 		} elsif ( $status->percentage < 100 ) {
-			print "Current percentage: ", $status->percentage, "\n" if $opt_v;
-			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
-			sleep(20);
+			print "\tmsg: ",
+			  ( $status->message ? $status->message : "no message found ..." ), "\n"
+			  if $opt_v;
+
+			#sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
 		}
-
 	} elsif ( $status->type == LSAE_STATE_CHANGED_EVENT ) {
+		print "Current state for job $queryID: ", $status->new_state, "\n"
+		  if $opt_v;
 		if (    ( $status->new_state =~ m"completed"i )
 			 || ( $status->new_state =~ m"terminated_by_request"i )
 			 || ( $status->new_state =~ m"terminated_by_error"i ) )
@@ -168,36 +171,45 @@
 		} elsif (    ( $status->new_state =~ m"created"i )
 				  || ( $status->new_state =~ m"running"i ) )
 		{
-			print "Current State: ", $status->new_state, "\n" if $opt_v;
-			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
-			sleep(20);
+			print "\tmsg: ",
+			  ( $status->message ? $status->message : "no message found ..." ), "\n"
+			  if $opt_v;
+
+			#sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
 		}
-
 	} elsif ( $status->type == LSAE_STEP_PROGRESS_EVENT ) {
+		print "Steps completed for job $queryID: ", $status - > steps_completed, "\n"
+		  if $opt_v;
 		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 $opt_v;
-			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
-			sleep(20);
+			print "\tmsg: ",
+			  ( $status->message ? $status->message : "no message found ..." ), "\n"
+			  if $opt_v;
+
+			#sleep(20);
 		} else {
 			die "ERROR:  analysis event block not well formed.\n";
 		}
-
 	} elsif ( $status->type == LSAE_TIME_PROGRESS_EVENT ) {
+		print "Time remaining for job $queryID: ", $status->remaining, "\n"
+		  if $opt_v;
 		if ( $status->remaining == 0 ) {
 			$completed->{$queryID} = 1;
 		} elsif ( $status->remaining > 0 ) {
-			print "Time remaining: ", $status->remaining, "\n" if $opt_v;
-			print "\tmsg: ", ($status->message ? $status->message : "no message found ..."), "\n" if $opt_v;
-			sleep(20);
+			print "\tmsg: ",
+			  ( $status->message ? $status->message : "no message found ..." ), "\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";
+		warn
+"Whilst checking the status of our resource, we entered into a possible infinite loop ...\n";
 	}
 }
 
@@ -238,7 +250,6 @@
 			die $msg;
 		}
 	);
-
 	my $input = '';
 	if ( @ARGV > 0 ) {
 		my $data = shift;    # a file name
@@ -249,14 +260,11 @@
 	} else {
 		$input = _empty_input;
 	}
-
 	print $soap ->$service( SOAP::Data->type( 'string' => "$input" ) )->result;
-
 } elsif ($opt_c) {
 
 	# calling a real service, using cgi
-	my $ua = LWP::UserAgent->new;
-
+	my $ua    = LWP::UserAgent->new;
 	my $input = '';
 	if ( @ARGV > 0 ) {
 		my $data = shift;    # a file name
@@ -267,14 +275,11 @@
 	} else {
 		$input = _empty_input;
 	}
-
 	my $req = HTTP::Request->new( POST => $opt_c );
 	$req->content_type('application/x-www-form-urlencoded');
 	$req->content("data=$input");
 	print "\n" . $ua->request($req)->as_string . "\n";
-
 } elsif ($opt_C) {
-
 	my $input = '';
 	if ( @ARGV > 0 ) {
 		my $data = shift;    # a file name
@@ -289,7 +294,6 @@
 	# 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
@@ -304,7 +308,6 @@
 	# 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);
@@ -327,261 +330,267 @@
 
 	# poll
 	while (1) {
+
+#
+# Poll the service for the status of all query IDs associated with this service invocation.
+#
+		$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);
+
 		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);
-			my $xpath = "//*[\@*='$queryID']";
-            my $xpc   = XML::LibXML::XPathContext->new();
-            my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
-            # should only be one ...
-            die unless $nodes->size() == 1;
-			my $status = LSAE::AnalysisEventBlock->new( $nodes->get_node(1)->toString() );
+			#
+			# Find status of this query ID.
+			#
+			#my $xpath = "//*[local-name() = 'analysis_event'][\@id='$queryID']";
+			#my $xpath = "//analysis_event[\@id='$queryID']";
+			$xpath = "//*[local-name() = 'analysis_event'][\@*='$queryId']";
+			my $xpc = XML::LibXML::XPathContext->new();
+			my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
+
+			# should only be one ...
+			die
+"Service returned unexpected/malformed resource property XML, which should contain service status info."
+			  unless $nodes->size() == 1;
+			my $status =
+			  LSAE::AnalysisEventBlock->new( $nodes->get_node(1)->toString() );
 			&_check_status( $status, \%completed, $queryID, $opt_v );
 		}
 		last if scalar keys(%completed) == $#query_ids + 1;
+		my $interval = 20;
+		print "Checking job state again in $interval seconds.\n\n" if $opt_v;
+		sleep($interval);
 	}
+	last if scalar keys(%completed) == $#query_ids + 1;
+}
 
-	# task is finished, obtain the result
-	$searchTerm = "";
-	$searchTerm .=
+# task is finished, obtain the result
+$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
-	# call using async mode for async service ... _submit
-	$service .= "_submit";
-
-	# set up the wsrf call
-	my $soap = WSRF::Lite->proxy($opt_a)->uri($WSRF::Constants::MOBY)->on_fault(
-		sub {
-			my $soap = shift;
-			my $res  = shift;
-			my $msg =
-			  ref $res
-			  ? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring
-			  : "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
-			die $msg;
-		}
-	);
-
-	# get the input
-	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);
-	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 );
-
-	# Get address from the returned Endpoint Reference
-	my $address = $epr->{'EndpointReference'}->{Address};
-
-	# Get resource identifier from the returned Endpoint Reference
-	my $identifier =
-	  $epr->{'EndpointReference'}->{ReferenceParameters}->{ServiceInvocationId};
-
-	# Compose the Endpoint Reference
-	my $EPR = WSRF::WS_Address->new();
-	$EPR->Address($address);
-	$EPR->ReferenceParameters(   '<mobyws:ServiceInvocationId xmlns:mobyws="'
-							   . $WSRF::Constants::MOBY . '">'
-							   . $identifier
-							   . '</mobyws:ServiceInvocationId>' );
-	my %completed = ();
-	while (1) {
-		foreach my $queryID (@query_ids) {
-
-			# skip poll if current job completed
-			next if $completed{$queryID};
+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) {
 
-			# poll the service for given query ID
-			my $searchTerm = "";
-			$searchTerm .=
+  # calling a real service, using async soap
+  # call using async mode for async service ... _submit
+  $service .= "_submit";
+
+  # set up the wsrf call
+  my $soap = WSRF::Lite->proxy($opt_a)->uri($WSRF::Constants::MOBY)->on_fault(
+	  sub {
+		  my $soap = shift;
+		  my $res  = shift;
+		  my $msg =
+			ref $res
+			? "--- SOAP FAULT ---\n" . $res->faultcode . " " . $res->faultstring
+			: "--- TRANSPORT ERROR ---\n" . $soap->transport->status . "\n$res\n";
+		  die $msg;
+	  }
+  );
+
+  # get the input
+  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);
+  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 );
+
+  # Get address from the returned Endpoint Reference
+  my $address = $epr->{'EndpointReference'}->{Address};
+
+  # Get resource identifier from the returned Endpoint Reference
+  my $identifier =
+	$epr->{'EndpointReference'}->{ReferenceParameters}->{ServiceInvocationId};
+
+  # Compose the Endpoint Reference
+  my $EPR = WSRF::WS_Address->new();
+  $EPR->Address($address);
+  $EPR->ReferenceParameters(   '<mobyws:ServiceInvocationId xmlns:mobyws="'
+							 . $WSRF::Constants::MOBY . '">'
+							 . $identifier
+							 . '</mobyws:ServiceInvocationId>' );
+  my %completed = ();
+  while (1) {
+	  foreach my $queryID (@query_ids) {
+
+		  # skip poll if current job completed
+		  next if $completed{$queryID};
+
+		  # poll the service for given query ID
+		  my $searchTerm = "";
+		  $searchTerm .=
 "<wsrp:ResourceProperty xmlns:wsrp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
-			$searchTerm .= "mobyws:status_" . $queryID;
-			$searchTerm .= "</wsrp:ResourceProperty>";
-
-			$soap = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
-				sub {
-					sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
-				}
-			  )->wsaddress($EPR)
-			  ->GetMultipleResourceProperties(
+		  $searchTerm .= "mobyws:status_" . $queryID;
+		  $searchTerm .= "</wsrp:ResourceProperty>";
+		  $soap = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
+			  sub {
+				  sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
+			  }
+			)->wsaddress($EPR)
+			->GetMultipleResourceProperties(
 										  SOAP::Data->value($searchTerm)->type('xml') );
+		  my $parser = XML::LibXML->new();
+		  my $xml    = $soap->raw_xml;
+		  my $doc    = $parser->parse_string($xml);
+		  $soap = $doc->getDocumentElement();
+		  my $prop_name = "status_" . $queryID;
+		  my ($prop) =
+			   $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
+			|| $soap->getElementsByTagName($prop_name);
+		  my $event = $prop->getFirstChild->toString
+			unless ref $prop eq "XML::LibXML::NodeList";
+		  $event = $prop->pop()->getFirstChild->toString
+			if ref $prop eq "XML::LibXML::NodeList";
+		  my $status = LSAE::AnalysisEventBlock->new($event);
+
+		  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";
+			  }
+		  }
+	  }
+	  last if scalar keys(%completed) == $#query_ids + 1;
+  }
+  foreach my $queryID (@query_ids) {
 
-			my $parser = XML::LibXML->new();
-			my $xml    = $soap->raw_xml;
-			my $doc    = $parser->parse_string($xml);
-			$soap = $doc->getDocumentElement();
-			my $prop_name = "status_" . $queryID;
-
-			my ($prop) =
-			     $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
-			  || $soap->getElementsByTagName($prop_name);
-			my $event = $prop->getFirstChild->toString
-			  unless ref $prop eq "XML::LibXML::NodeList";
-			$event = $prop->pop()->getFirstChild->toString
-			  if ref $prop eq "XML::LibXML::NodeList";
-
-			my $status = LSAE::AnalysisEventBlock->new($event);
-			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";
-				}
-			}
-		}
-		last if scalar keys(%completed) == $#query_ids + 1;
-	}
-
-	foreach my $queryID (@query_ids) {
-
-		# get the result
-		my $searchTerm .=
+	  # get the result
+	  my $searchTerm .=
 "<wsrp:ResourceProperty xmlns:wsrp='$WSRF::Constants::WSRP' xmlns:mobyws='$WSRF::Constants::MOBY'>";
-		$searchTerm .= "mobyws:result_" . $queryID;
-		$searchTerm .= "</wsrp:ResourceProperty>";
-		my $ans = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
-			sub {
-				sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
-			}
-		  )->wsaddress($EPR)
-		  ->GetMultipleResourceProperties(
-										  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);
-		$soap = $doc->getDocumentElement();
-		my $prop_name = "result_" . $queryID;
-		my ($prop) = $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
-		  || $soap->getElementsByTagName($prop_name);
-		my $result = $prop->getFirstChild->toString
-		  unless ref $prop eq "XML::LibXML::NodeList";
-		$result = $prop->pop()->getFirstChild->toString
-		  if ref $prop eq "XML::LibXML::NodeList";
-		print $result;
-	}
-
-	# destroy the result
-	my $ans = WSRF::Lite->uri($WSRF::Constants::WSRL)->on_action(
-		sub {
-			sprintf '%s/ImmediateResourceTermination/%sRequest',
-			  $WSRF::Constants::WSRLW, $_[1];
-		}
-	)->wsaddress($EPR)->Destroy();
-
+	  $searchTerm .= "mobyws:result_" . $queryID;
+	  $searchTerm .= "</wsrp:ResourceProperty>";
+	  my $ans = WSRF::Lite->uri($WSRF::Constants::WSRP)->on_action(
+		  sub {
+			  sprintf '%s/%s/%sRequest', $WSRF::Constants::WSRPW, $_[1], $_[1];
+		  }
+		)->wsaddress($EPR)
+		->GetMultipleResourceProperties( 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);
+	  $soap = $doc->getDocumentElement();
+	  my $prop_name = "result_" . $queryID;
+	  my ($prop) = $soap->getElementsByTagNameNS( $WSRF::Constants::MOBY, $prop_name )
+		|| $soap->getElementsByTagName($prop_name);
+	  my $result = $prop->getFirstChild->toString
+		unless ref $prop eq "XML::LibXML::NodeList";
+	  $result = $prop->pop()->getFirstChild->toString
+		if ref $prop eq "XML::LibXML::NodeList";
+	  print $result;
+  }
+
+  # destroy the result
+  my $ans = WSRF::Lite->uri($WSRF::Constants::WSRL)->on_action(
+	  sub {
+		  sprintf '%s/ImmediateResourceTermination/%sRequest',
+			$WSRF::Constants::WSRLW, $_[1];
+	  }
+  )->wsaddress($EPR)->Destroy();
 } else {
 
-	# calling a local service module, without SOAP
-	my $data;
-	if ( @ARGV > 0 ) {
-		$data = shift;    # a file name
-	} else {
-		use File::Temp qw( tempfile );
-		my $fh;
-		( $fh, $data ) = tempfile( UNLINK => 1 );
-		print $fh _empty_input();
-		close $fh;
-	}
-	eval "require $module" or croak $@;
-	eval {
-		my $target = new $module;
-		print $target->$service($data), "\n";
-	} or croak $@;
+  # calling a local service module, without SOAP
+  my $data;
+  if ( @ARGV > 0 ) {
+	  $data = shift;    # a file name
+  } else {
+	  use File::Temp qw( tempfile );
+	  my $fh;
+	  ( $fh, $data ) = tempfile( UNLINK => 1 );
+	  print $fh _empty_input();
+	  close $fh;
+  }
+  eval "require $module" or croak $@;
+  eval {
+	  my $target = new $module;
+	  print $target->$service($data), "\n";
+  } or croak $@;
 }
 
 sub _moby_wsrf_header {



From kawas at dev.open-bio.org  Fri Oct 16 17:43:30 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 13:43:30 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161743.n9GHhUth025131@dev.open-bio.org>


kawas
Fri Oct 16 13:43:30 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv25096/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent commits
moby-live/Perl/MOSES-MOBY Changes,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/16 15:51:45	1.22
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/16 17:43:30	1.23
@@ -10,6 +10,23 @@
       The first queryID was polled and when
       it completed, the script assumed all of
       the invocations were completed.
+    - moses-testing-service.pl (thx to Pieter Neerincx)
+        * Moved the POST request out of the foreach
+          $queryID loop.
+        * Added the name of the element "analysis_event"
+          to $xpath.
+        * Moved the sleep(20) out of the &_check_status
+          sub. 
+        * Added a diagnostic message for the die
+          statement when we cant find our event id.
+        * Moved some messages for "verbose" info in
+          &_check_status, so the script always reports
+          the job status whether a job has completed
+          or not.
+        * I also added $queryID to the verbose messaging
+          so the script reports which job that status
+          message corresponded to...
+    
 
 0.92 Oct 13, 2009
     *** Notes for this release ***



From kawas at dev.open-bio.org  Fri Oct 16 17:44:23 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 16 Oct 2009 13:44:23 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910161744.n9GHiNDD025171@dev.open-bio.org>


kawas
Fri Oct 16 13:44:23 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/share
In directory dev.open-bio.org:/tmp/cvs-serv25136/MOSES-MOBY/share

Modified Files:
	notes 
Log Message:
updated some of the paths in case other care to use these notes.
moby-live/Perl/MOSES-MOBY/share notes,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/notes,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/notes	2008/02/21 00:12:55	1.3
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/share/notes	2009/10/16 17:44:23	1.4
@@ -1,9 +1,9 @@
 Perl documentation:
 ===================
 
-pod2man MOBY/Datatypes/MobyObject.pm | nroff -man | less
+pod2man lib/MOSES/MOBY/Data/Object.pm | nroff -man | less
 ---
-pods2html --index='Perl MoSeS Documentation' /home/senger/jMoby/src/Perl/ /home/senger/jMoby/src/perldoc/
+pods2html --index='Perl MoSeS Documentation' ~/moby-live/Perl/MOSES-MOBY/lib ~/moby-live/Perl/MOSES-MOBY/perldoc/
 ---
 http://search.cpan.org/~iwalz/Pod2html/lib/Pod/2/html.pm
 ----



From kawas at dev.open-bio.org  Fri Oct 23 18:02:15 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 23 Oct 2009 14:02:15 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910231802.n9NI2EuC003965@dev.open-bio.org>


kawas
Fri Oct 23 14:02:14 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv3929/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
missing a my in front of $xpath ... doh!
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.14,1.15
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.14
retrieving revision 1.15
diff -u -r1.14 -r1.15
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/16 17:43:09	1.14
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/23 18:02:14	1.15
@@ -353,7 +353,7 @@
 			#
 			#my $xpath = "//*[local-name() = 'analysis_event'][\@id='$queryID']";
 			#my $xpath = "//analysis_event[\@id='$queryID']";
-			$xpath = "//*[local-name() = 'analysis_event'][\@*='$queryId']";
+			my $xpath = "//*[local-name() = 'analysis_event'][\@*='$queryId']";
 			my $xpc = XML::LibXML::XPathContext->new();
 			my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
 



From kawas at dev.open-bio.org  Fri Oct 23 18:49:31 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Fri, 23 Oct 2009 14:49:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910231849.n9NInVZw004150@dev.open-bio.org>


kawas
Fri Oct 23 14:49:31 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv4111/MOSES-MOBY

Modified Files:
	Changes Makefile.PL 
Log Message:
not happy about type in testing service script, so releasing new cpan release.
moby-live/Perl/MOSES-MOBY Changes,1.23,1.24 Makefile.PL,1.22,1.23
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.23
retrieving revision 1.24
diff -u -r1.23 -r1.24
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/16 17:43:30	1.23
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/23 18:49:31	1.24
@@ -1,5 +1,9 @@
 Revision history for Perl extension MOSES::MOBY.
 
+0.94
+    Fix to moses-testing-service.pl script. typo
+    found in script.
+    
 0.93
 
     Changes:

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL,v
retrieving revision 1.22
retrieving revision 1.23
diff -u -r1.22 -r1.23
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/16 15:51:45	1.22
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Makefile.PL	2009/10/23 18:49:31	1.23
@@ -6,7 +6,7 @@
     
 	# Define metadata
 	name 'MOSES-MOBY';
-	version '0.93';
+	version '0.94';
 	license 'perl';
 	abstract
 'This distribution aids in the creation of BioMOBY perl based web services.';



From drepchevski at dev.open-bio.org  Mon Oct 26 12:23:08 2009
From: drepchevski at dev.open-bio.org (Dmitry Repchevski)
Date: Mon, 26 Oct 2009 08:23:08 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910261223.n9QCN8TF020815@dev.open-bio.org>


drepchevski
Mon Oct 26 08:23:07 EDT 2009
Update of /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry
In directory dev.open-bio.org:/tmp/cvs-serv20780

Modified Files:
	ObjectType.java 
Log Message:
Added an auxiliary method to get a relationship list by type
moby-live/Java/src/main/org/inb/biomoby/shared/registry ObjectType.java,1.1,1.2
===================================================================
RCS file: /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ObjectType.java,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ObjectType.java	2009/09/09 19:47:49	1.1
+++ /home/repository/moby/moby-live/Java/src/main/org/inb/biomoby/shared/registry/ObjectType.java	2009/10/26 12:23:07	1.2
@@ -55,6 +55,25 @@
         getRelationships().add(relationship);
     }
     
+    /**
+     * Auxiliary method to find relationship by its type
+     * 
+     * @param relationshipType a type of relationship to be found
+     * @return found relationship object or null
+     */
+    public Relationship<ObjectType> getRelationship(Relationship.RELATIONSHIP_TYPE relationshipType)
+    {
+        for (Relationship<ObjectType> relationship : getRelationships())
+        {
+            if (relationship.getRelationshipType() == relationshipType)
+            {
+                return relationship;
+            }
+        }
+
+        return null;
+    }
+
     @XmlElement(name="relationship")
     public List<Relationship<ObjectType>> getRelationships()
     {



From kawas at dev.open-bio.org  Mon Oct 26 16:06:00 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 26 Oct 2009 12:06:00 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910261606.n9QG60k9030142@dev.open-bio.org>


kawas
Mon Oct 26 12:06:00 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts
In directory dev.open-bio.org:/tmp/cvs-serv30106/MOSES-MOBY/bin/scripts

Modified Files:
	moses-testing-service.pl 
Log Message:
xpath statement for analysis_event has been changed once again, but should stay like this for a while. This one seems to be the most correct for testing moses services.
moby-live/Perl/MOSES-MOBY/bin/scripts moses-testing-service.pl,1.15,1.16
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl,v
retrieving revision 1.15
retrieving revision 1.16
diff -u -r1.15 -r1.16
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/23 18:02:14	1.15
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/bin/scripts/moses-testing-service.pl	2009/10/26 16:06:00	1.16
@@ -351,9 +351,9 @@
 			#
 			# Find status of this query ID.
 			#
-			#my $xpath = "//*[local-name() = 'analysis_event'][\@id='$queryID']";
+			#my $xpath = "//*[local-name() = 'analysis_event'][\@*='$queryID']";
 			#my $xpath = "//analysis_event[\@id='$queryID']";
-			my $xpath = "//*[local-name() = 'analysis_event'][\@*='$queryId']";
+			my $xpath = "//*[local-name() = 'analysis_event'][\@id='$queryId']";
 			my $xpc = XML::LibXML::XPathContext->new();
 			my $nodes = $xpc->findnodes( $xpath, $doc->documentElement );
 



From kawas at dev.open-bio.org  Mon Oct 26 16:08:07 2009
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Mon, 26 Oct 2009 12:08:07 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200910261608.n9QG87Xi030525@dev.open-bio.org>


kawas
Mon Oct 26 12:08:07 EDT 2009
Update of /home/repository/moby/moby-live/Perl/MOSES-MOBY
In directory dev.open-bio.org:/tmp/cvs-serv30490/MOSES-MOBY

Modified Files:
	Changes 
Log Message:
updated to reflect recent commits
moby-live/Perl/MOSES-MOBY Changes,1.24,1.25
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes,v
retrieving revision 1.24
retrieving revision 1.25
diff -u -r1.24 -r1.25
--- /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/23 18:49:31	1.24
+++ /home/repository/moby/moby-live/Perl/MOSES-MOBY/Changes	2009/10/26 16:08:07	1.25
@@ -1,5 +1,12 @@
 Revision history for Perl extension MOSES::MOBY.
 
+
+0.95
+    * updated the xpath statement in the testing
+      service script. Change should persist until
+      the XML generated by MOSES for analysis events
+      changes.
+
 0.94
     Fix to moses-testing-service.pl script. typo
     found in script.