From kawas at dev.open-bio.org  Tue Sep  4 13:40:35 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 4 Sep 2007 13:40:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709041740.l84HeZ7M013610@dev.open-bio.org>


kawas
Tue Sep  4 13:40:34 EDT 2007
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv13575

Modified Files:
	Makefile.PL 
Log Message:
removing the requirement that the module LS must be installed for Makefile to be created
moby-live/Perl Makefile.PL,1.28,1.29
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2007/08/28 23:54:46	1.28
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/04 17:40:34	1.29
@@ -27,7 +27,6 @@
 
 END_OF_TEXT
 
-exit(0);
 }
 
 sub MY::postamble {


From kawas at dev.open-bio.org  Tue Sep  4 18:28:14 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 4 Sep 2007 18:28:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709042228.l84MSETs013914@dev.open-bio.org>


kawas
Tue Sep  4 18:28:14 EDT 2007
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv13879

Modified Files:
	Makefile.PL 
Log Message:

moby-live/Perl Makefile.PL,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/04 17:40:34	1.29
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/04 22:28:14	1.30
@@ -1,427 +1,427 @@
-use ExtUtils::MakeMaker;
-use FindBin '$Bin';
-use strict;
-my $VERSION = '0.87';
-
-# need a way of relaying the information that LS cannot be found on CPAN
-eval "require LS";
-if ($@) {
-	print STDOUT <<'END_OF_TEXT';
-	
-############## IMPORTANT ##############
-Module 'LS' is not installed. This module is used
-**only** if you are wanting to host a LSID Authority!
-
-Unfortunately, this module is not available on CPAN 
-and must be manually installed. Some of the 
-dependencies are beta and as such, may not be stable.
-
-You can try searching Google using the keywords:
-
-	'perl LS lsid' 
-
-or, try downloading it from the following link:
-	
-	'http://sourceforge.net/project/showfiles.php?group_id=130827'
-
-
-END_OF_TEXT
-
-}
-
-sub MY::postamble {
-  # Now build documentation.
-  use Pod::Find qw(pod_find simplify_name);
-  use Cwd;
-  my $cur_dir = getcwd();
-  # Find the files that contain POD, starting from the top-level build directory, and do it silently.
-  my %pods = pod_find({ -verbose => 0}, 
-		      File::Spec->catfile($cur_dir, "MOBY") );
-  my @PM = sort keys %pods;
-  my @MOD_NAMES = map {$pods{$_}} @PM;
-  # Make home for all docs
-  # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
-  # It's more robust to put it directly into the Makefile, 
-  # so that it can be rebuilt with a simple "make" if needed.
-  # But that would require figuring out how to walk a tree from the shell,
-  # and I don't have time for that. Maybe some other day.
-  my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
-  mkdir File::Spec->catfile($cur_dir, "docs") 
-    unless -e File::Spec->catfile($cur_dir, "docs");
-  mkdir $HTML_ROOT unless -e $HTML_ROOT;
-  # Create a new directory tree for the documentation, that mirrors the source tree.
-  use File::Find;
-  my @make_dirs_list;
-  sub wanted { # Define nested subroutine, to inherit variable scope
-    my $src_dir = $File::Find::dir;
-    (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
-#    print STDERR "EXamining $doc_dir\n";
-    if ( !($doc_dir =~ /CVS$/) ) {
-      push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
-	unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
-      if (!(-e $doc_dir)) {
-	my $made_dir = mkdir $doc_dir;
-	if (!$made_dir) { 
-	  print STDERR "Couldn't create directory '$doc_dir' because '$!'"; 
-	}
-      }
-    }
-  }
-  find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
-  # Finally, start writing the rules.
-  # Let's make a big rule to build all the docs at once, call it 'html'
-  # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
-  my @HTML = map {  # Edit beginning and end of PM files, to make HTML filenames
-    my $x = $_; # Don't want to change the original...
-    $x =~ s/\.p[lm]$/\.html/; 
-    $x =~ s/^$cur_dir/$HTML_ROOT/; 
-    $x} @PM;
-  my $postamble = "# Rules to keep developer docs up-to-date.\n";
-  $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) 
-    . "\n\nhtml: \$(POD_TO_HTML)\n";
-#  $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
-#    . "\n\nhtml:\n"; # \$(HTML_DIRS)
-#  $postamble .= "\$(HTML_DIRS):\n\tfor file in " 
-#    . join(" \\\n", @make_dirs_list) .
-#    "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
-
-  # Now, finally, we build rules for the makefile.
-  # The TAB ('\t') characters are essential,  otherwise 'make' will silently ignore the rules.
-  # Don't be tempted to remove them.
-  for (my $i = 0;  $i < @PM; $i++) {
-    $postamble .= <<RULE;
-$HTML[$i]:$PM[$i]
-	\$(NOECHO) \$(ECHO) Generating HTML for MOBY::$MOD_NAMES[$i]
-	\$(NOECHO) pod2html --htmlroot=$HTML_ROOT --outfile=$HTML[$i] $PM[$i]
-RULE
-  }
-#  print "HTML_ROOT: $HTML_ROOT\n";
-  # Auto-generate an index page, with links to the individual POD-generated pages.
-  # Make sure it works on the local filesystem.
-  # Trim HTML files down to relative paths.
-  make_index_page(\@PM ,
-		  [ map { my $x= $_; $x =~ s/^$cur_dir\///; $x} @HTML ], 
-		  \@MOD_NAMES);
-  return $postamble;
-}
-
-
-sub make_index_page {
-  # Generate an index to the auto-generated HTML docs.
-  my ($pms, $html, $mod_names) = @_;
-  open INDEX, ">index.html" or die "Couldn't open index.html ($!)";
-  print INDEX <<HEAD;
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-  <meta http-equiv="content-type"
- content="text/html; charset=ISO-8859-1">
-  <title>MOBY-S Perl Module Documentation</title>
-</head>
-<body>
-<div style="text-align: center;">
-<h1>MOBY-S Perl Modules Documentation</h1>
-</div>
-For an overview of how to do various things in Perl, see the <a href='http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial'>
-Perl Tutorial</a><p>
-The documents below (including this one) are generated by pod2html from the various perl
-modules and give specific interface information for each of the Perl modules described in the tutorial.
-
-<ul>
-HEAD
-  for (my $i = 0; $i < @{$pms}; $i++) {
-    print INDEX "<li><a href=\"$html->[$i]\">MOBY::$mod_names->[$i]</a></li>\n";
-  }
-print INDEX <<FOOT;
-</ul>
-</body>
-</html>
-FOOT
-}
-
-
-# Override built-in target, by adding the 'html' dependency
-# Now HTML gets updated every time you type "make"
-sub MY::top_targets {
-  my $self = shift;
-  my $string = $self->MM::top_targets;
-  my $add = 'html';
-  $string =~ s/\s+(pure_all)/ $add $1/;
-  return $string;
-}
-
-#sub MY::install {
-#  my $self = shift;
-#  my $string = $self->MM::install;
-#  my $add = 'html';
-#  $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
-#  print "INSTALL: $string\n";
-#  return $string;
-#}
-
-WriteMakefile(
-	      NAME	      => 'MOBY-S',
-	      VERSION	      => $VERSION, 
-	      # VERSION_FROM    => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
-	      PMLIBDIRS       => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
-	      # Version numbers specified for prerequiisites are simply "desired" versions,
-	      # not minimum, or anything else.
-	      PREREQ_PM     => {
-				'SOAP::Lite'       => 0.69,
-				'SOAP::MIME'       => 0.55,
-				'XML::LibXML'      => 1.58,
-				'XML::XPath'       => 1.12,
-				'Text::Shellwords' => 1.00,
-				'HTML::Entities'   => 0.01,
-				'Test::More'       => 0.60,
-				# Database stuff required only for local registry, but notify user if missing anyway.
-				'DBI'              => 0.01,
-				'DBD::mysql'       => 0.01,
-				'WSRF::Lite'		=> '',
-                'Test::Simple' => 0.44,
-                'XML::DOM'     => '',
-                'DateTime::Format::Epoch'  => '',
-                'DateTime::Format::W3CDTF' => '',
-                'HTTP::Daemon' => '',
-                'HTTP::Daemon::SSL' => '',
-                'MIME::Base64' => '',
-                'Digest::SHA1' => '',
-                'Crypt::OpenSSL::X509' => '',
-                'Crypt::OpenSSL::RSA' => '',
-                'XML::CanonicalizeXML' => 0.02,
-                'Sys::Hostname::Long' => '',
-			   	'RDF::Core' => '.51',
-				# Sharable only used for isAlive script
-	   			'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
-		  	    #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
-			    #'LS' => 1.1.4,
-					 
-	    }, # e.g., Module::Name => 1.1
-	    #PM_FILTER     => "", 
-	    ($] >= 5.005 ?    ## Add these new keywords supported since 5.005
-	    (ABSTRACT      => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
-		AUTHOR        => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
-);
-
-#
-# Insert additional MOBY specific Makefile targets
-#
-# 
-#sub MY::postamble {
-#	return <<"MAKE_FRAG";
-#Central:
-#	echo 'Make (local) MOBY Central stub'
-#
-#Server:
-#	echo 'Make (local) MOBY Server stub'
-#
-#WWWClient:
-#	echo 'Setting up MOBY WWW Client'
-#	cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
-#	chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
-# 
-#MAKE_FRAG
-#}
-
-use ExtUtils::MakeMaker;
-use FindBin '$Bin';
-use strict;
-my $VERSION = '0.87';
-
-
-sub MY::postamble {
-  # Now build documentation.
-  use Pod::Find qw(pod_find simplify_name);
-  use Cwd;
-  my $cur_dir = getcwd();
-  # Find the files that contain POD, starting from the top-level build directory, and do it silently.
-  my %pods = pod_find({ -verbose => 0}, 
-		      File::Spec->catfile($cur_dir, "MOBY") );
-  my @PM = sort keys %pods;
-  my @MOD_NAMES = map {$pods{$_}} @PM;
-  # Make home for all docs
-  # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
-  # It's more robust to put it directly into the Makefile, 
-  # so that it can be rebuilt with a simple "make" if needed.
-  # But that would require figuring out how to walk a tree from the shell,
-  # and I don't have time for that. Maybe some other day.
-  my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
-  mkdir File::Spec->catfile($cur_dir, "docs") 
-    unless -e File::Spec->catfile($cur_dir, "docs");
-  mkdir $HTML_ROOT unless -e $HTML_ROOT;
-  # Create a new directory tree for the documentation, that mirrors the source tree.
-  use File::Find;
-  my @make_dirs_list;
-  sub wanted { # Define nested subroutine, to inherit variable scope
-    my $src_dir = $File::Find::dir;
-    (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
-#    print STDERR "EXamining $doc_dir\n";
-    if ( !($doc_dir =~ /CVS$/) ) {
-      push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
-	unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
-      if (!(-e $doc_dir)) {
-	my $made_dir = mkdir $doc_dir;
-	if (!$made_dir) { 
-	  print STDERR "Couldn't create directory '$doc_dir' because '$!'"; 
-	}
-      }
-    }
-  }
-  find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
-  # Finally, start writing the rules.
-  # Let's make a big rule to build all the docs at once, call it 'html'
-  # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
-  my @HTML = map {  # Edit beginning and end of PM files, to make HTML filenames
-    my $x = $_; # Don't want to change the original...
-    $x =~ s/\.p[lm]$/\.html/; 
-    $x =~ s/^$cur_dir/$HTML_ROOT/; 
-    $x} @PM;
-  my $postamble = "# Rules to keep developer docs up-to-date.\n";
-  $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) 
-    . "\n\nhtml: \$(POD_TO_HTML)\n";
-#  $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
-#    . "\n\nhtml:\n"; # \$(HTML_DIRS)
-#  $postamble .= "\$(HTML_DIRS):\n\tfor file in " 
-#    . join(" \\\n", @make_dirs_list) .
-#    "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
-
-  # Now, finally, we build rules for the makefile.
-  # The TAB ('\t') characters are essential,  otherwise 'make' will silently ignore the rules.
-  # Don't be tempted to remove them.
-  for (my $i = 0;  $i < @PM; $i++) {
-    $postamble .= <<RULE;
-$HTML[$i]:$PM[$i]
-	\$(NOECHO) \$(ECHO) Generating HTML for MOBY::$MOD_NAMES[$i]
-	\$(NOECHO) pod2html --htmlroot=$HTML_ROOT --outfile=$HTML[$i] $PM[$i]
-RULE
-  }
-#  print "HTML_ROOT: $HTML_ROOT\n";
-  # Auto-generate an index page, with links to the individual POD-generated pages.
-  # Make sure it works on the local filesystem.
-  # Trim HTML files down to relative paths.
-  make_index_page(\@PM ,
-		  [ map { my $x= $_; $x =~ s/^$cur_dir\///; $x} @HTML ], 
-		  \@MOD_NAMES);
-  return $postamble;
-}
-
-
-sub make_index_page {
-  # Generate an index to the auto-generated HTML docs.
-  my ($pms, $html, $mod_names) = @_;
-  open INDEX, ">index.html" or die "Couldn't open index.html ($!)";
-  print INDEX <<HEAD;
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-  <meta http-equiv="content-type"
- content="text/html; charset=ISO-8859-1">
-  <title>MOBY-S Perl Module Documentation</title>
-</head>
-<body>
-<div style="text-align: center;">
-<h1>MOBY-S Perl Modules Documentation</h1>
-</div>
-For an overview of how to do various things in Perl, see the <a href='http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial'>
-Perl Tutorial</a><p>
-The documents below (including this one) are generated by pod2html from the various perl
-modules and give specific interface information for each of the Perl modules described in the tutorial.
-
-<ul>
-HEAD
-  for (my $i = 0; $i < @{$pms}; $i++) {
-    print INDEX "<li><a href=\"$html->[$i]\">MOBY::$mod_names->[$i]</a></li>\n";
-  }
-print INDEX <<FOOT;
-</ul>
-</body>
-</html>
-FOOT
-}
-
-
-# Override built-in target, by adding the 'html' dependency
-# Now HTML gets updated every time you type "make"
-sub MY::top_targets {
-  my $self = shift;
-  my $string = $self->MM::top_targets;
-  my $add = 'html';
-  $string =~ s/\s+(pure_all)/ $add $1/;
-  return $string;
-}
-
-#sub MY::install {
-#  my $self = shift;
-#  my $string = $self->MM::install;
-#  my $add = 'html';
-#  $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
-#  print "INSTALL: $string\n";
-#  return $string;
-#}
-
-WriteMakefile(
-	      NAME	      => 'MOBY-S',
-	      VERSION	      => $VERSION, 
-	      # VERSION_FROM    => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
-	      PMLIBDIRS       => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
-	      # Version numbers specified for prerequiisites are simply "desired" versions,
-	      # not minimum, or anything else.
-	      PREREQ_PM     => {
-				'SOAP::Lite'       => 0.69,
-				'SOAP::MIME'       => 0.55,
-				'XML::LibXML'      => 1.58,
-				'XML::XPath'       => 1.12,
-				'Text::Shellwords' => 1.00,
-				'HTML::Entities'   => 0.01,
-				'Test::More'       => 0.60,
-				# Database stuff required only for local registry, but notify user if missing anyway.
-				'DBI'              => 0.01,
-				'DBD::mysql'       => 0.01,
-				# 'WSRF::Lite'		=> '0.8.2.1', but it is not declared in the proper way there
-				'WSRF::Lite'		=> '',
-                 'Test::Simple' => 0.44,
-                 'XML::DOM'     => '',
-                 'DateTime::Format::Epoch'  => '',
-                 'DateTime::Format::W3CDTF' => '',
-                 'HTTP::Daemon' => '',
-                 'HTTP::Daemon::SSL' => '',
-                 'MIME::Base64' => '',
-                 'Digest::SHA1' => '',
-                 'Crypt::OpenSSL::X509' => '',
-                 'Crypt::OpenSSL::RSA' => '',
-                 'XML::CanonicalizeXML' => 0.02,
-                 'Sys::Hostname::Long' => '',
-		  		 'RDF::Core' => '.51',
-				 #Sharable only used for isAlive script
-	   			 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
-		  	     #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
-			     #'LS' => 1.1.4,
-	      }, # e.g., Module::Name => 1.1
-	      #PM_FILTER     => "", 
-	      ($] >= 5.005 ?    ## Add these new keywords supported since 5.005
-	       (ABSTRACT      => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
-		AUTHOR        => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
-);
-
-#
-# Insert additional MOBY specific Makefile targets
-#
-# 
-#sub MY::postamble {
-#	return <<"MAKE_FRAG";
-#Central:
-#	echo 'Make (local) MOBY Central stub'
-#
-#Server:
-#	echo 'Make (local) MOBY Server stub'
-#
-#WWWClient:
-#	echo 'Setting up MOBY WWW Client'
-#	cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
-#	chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
-# 
-#MAKE_FRAG
-#}
-
+use ExtUtils::MakeMaker;
+use FindBin '$Bin';
+use strict;
+my $VERSION = '0.87';
+
+# need a way of relaying the information that LS cannot be found on CPAN
+eval "require LS";
+if ($@) {
+	print STDOUT <<'END_OF_TEXT';
+	
+############## IMPORTANT ##############
+Module 'LS' is not installed. This module is used
+**only** if you are wanting to host a LSID Authority!
+
+Unfortunately, this module is not available on CPAN 
+and must be manually installed. Some of the 
+dependencies are beta and as such, may not be stable.
+
+You can try searching Google using the keywords:
+
+	'perl LS lsid' 
+
+or, try downloading it from the following link:
+	
+	'http://sourceforge.net/project/showfiles.php?group_id=130827'
+
+
+END_OF_TEXT
+
+}
+
+sub MY::postamble {
+  # Now build documentation.
+  use Pod::Find qw(pod_find simplify_name);
+  use Cwd;
+  my $cur_dir = getcwd();
+  # Find the files that contain POD, starting from the top-level build directory, and do it silently.
+  my %pods = pod_find({ -verbose => 0}, 
+		      File::Spec->catfile($cur_dir, "MOBY") );
+  my @PM = sort keys %pods;
+  my @MOD_NAMES = map {$pods{$_}} @PM;
+  # Make home for all docs
+  # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
+  # It's more robust to put it directly into the Makefile, 
+  # so that it can be rebuilt with a simple "make" if needed.
+  # But that would require figuring out how to walk a tree from the shell,
+  # and I don't have time for that. Maybe some other day.
+  my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
+  mkdir File::Spec->catfile($cur_dir, "docs") 
+    unless -e File::Spec->catfile($cur_dir, "docs");
+  mkdir $HTML_ROOT unless -e $HTML_ROOT;
+  # Create a new directory tree for the documentation, that mirrors the source tree.
+  use File::Find;
+  my @make_dirs_list;
+  sub wanted { # Define nested subroutine, to inherit variable scope
+    my $src_dir = $File::Find::dir;
+    (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
+#    print STDERR "EXamining $doc_dir\n";
+    if ( !($doc_dir =~ /CVS$/) ) {
+      push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
+	unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
+      if (!(-e $doc_dir)) {
+	my $made_dir = mkdir $doc_dir;
+	if (!$made_dir) { 
+	  print STDERR "Couldn't create directory '$doc_dir' because '$!'"; 
+	}
+      }
+    }
+  }
+  find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
+  # Finally, start writing the rules.
+  # Let's make a big rule to build all the docs at once, call it 'html'
+  # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
+  my @HTML = map {  # Edit beginning and end of PM files, to make HTML filenames
+    my $x = $_; # Don't want to change the original...
+    $x =~ s/\.p[lm]$/\.html/; 
+    $x =~ s/^$cur_dir/$HTML_ROOT/; 
+    $x} @PM;
+  my $postamble = "# Rules to keep developer docs up-to-date.\n";
+  $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) 
+    . "\n\nhtml: \$(POD_TO_HTML)\n";
+#  $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
+#    . "\n\nhtml:\n"; # \$(HTML_DIRS)
+#  $postamble .= "\$(HTML_DIRS):\n\tfor file in " 
+#    . join(" \\\n", @make_dirs_list) .
+#    "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
+
+  # Now, finally, we build rules for the makefile.
+  # The TAB ('\t') characters are essential,  otherwise 'make' will silently ignore the rules.
+  # Don't be tempted to remove them.
+  for (my $i = 0;  $i < @PM; $i++) {
+    $postamble .= <<RULE;
+$HTML[$i]:$PM[$i]
+	\$(NOECHO) \$(ECHO) Generating HTML for MOBY::$MOD_NAMES[$i]
+	\$(NOECHO) pod2html --htmlroot=$HTML_ROOT --outfile=$HTML[$i] $PM[$i]
+RULE
+  }
+#  print "HTML_ROOT: $HTML_ROOT\n";
+  # Auto-generate an index page, with links to the individual POD-generated pages.
+  # Make sure it works on the local filesystem.
+  # Trim HTML files down to relative paths.
+  make_index_page(\@PM ,
+		  [ map { my $x= $_; $x =~ s/^$cur_dir\///; $x} @HTML ], 
+		  \@MOD_NAMES);
+  return $postamble;
+}
+
+
+sub make_index_page {
+  # Generate an index to the auto-generated HTML docs.
+  my ($pms, $html, $mod_names) = @_;
+  open INDEX, ">index.html" or die "Couldn't open index.html ($!)";
+  print INDEX <<HEAD;
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>MOBY-S Perl Module Documentation</title>
+</head>
+<body>
+<div style="text-align: center;">
+<h1>MOBY-S Perl Modules Documentation</h1>
+</div>
+For an overview of how to do various things in Perl, see the <a href='http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial'>
+Perl Tutorial</a><p>
+The documents below (including this one) are generated by pod2html from the various perl
+modules and give specific interface information for each of the Perl modules described in the tutorial.
+
+<ul>
+HEAD
+  for (my $i = 0; $i < @{$pms}; $i++) {
+    print INDEX "<li><a href=\"$html->[$i]\">MOBY::$mod_names->[$i]</a></li>\n";
+  }
+print INDEX <<FOOT;
+</ul>
+</body>
+</html>
+FOOT
+}
+
+
+# Override built-in target, by adding the 'html' dependency
+# Now HTML gets updated every time you type "make"
+sub MY::top_targets {
+  my $self = shift;
+  my $string = $self->MM::top_targets;
+  my $add = 'html';
+  $string =~ s/\s+(pure_all)/ $add $1/;
+  return $string;
+}
+
+#sub MY::install {
+#  my $self = shift;
+#  my $string = $self->MM::install;
+#  my $add = 'html';
+#  $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
+#  print "INSTALL: $string\n";
+#  return $string;
+#}
+
+WriteMakefile(
+	      NAME	      => 'MOBY-S',
+	      VERSION	      => $VERSION, 
+	      # VERSION_FROM    => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
+	      PMLIBDIRS       => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
+	      # Version numbers specified for prerequiisites are simply "desired" versions,
+	      # not minimum, or anything else.
+	      PREREQ_PM     => {
+				'SOAP::Lite'       => 0.69,
+				'SOAP::MIME'       => 0.55,
+				'XML::LibXML'      => 1.58,
+				'XML::XPath'       => 1.12,
+				'Text::Shellwords' => 1.00,
+				'HTML::Entities'   => 0.01,
+				'Test::More'       => 0.60,
+				# Database stuff required only for local registry, but notify user if missing anyway.
+				'DBI'              => 0.01,
+				'DBD::mysql'       => 0.01,
+				'WSRF::Lite'		=> '',
+                'Test::Simple' => 0.44,
+                'XML::DOM'     => '',
+                'DateTime::Format::Epoch'  => '',
+                'DateTime::Format::W3CDTF' => '',
+                'HTTP::Daemon' => '',
+                'HTTP::Daemon::SSL' => '',
+                'MIME::Base64' => '',
+                'Digest::SHA1' => '',
+                'Crypt::OpenSSL::X509' => '',
+                'Crypt::OpenSSL::RSA' => '',
+                'XML::CanonicalizeXML' => 0.02,
+                'Sys::Hostname::Long' => '',
+			   	'RDF::Core' => '.51',
+				# Sharable only used for isAlive script
+	   			#'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
+		  	    #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
+			    #'LS' => 1.1.4,
+					 
+	    }, # e.g., Module::Name => 1.1
+	    #PM_FILTER     => "", 
+	    ($] >= 5.005 ?    ## Add these new keywords supported since 5.005
+	    (ABSTRACT      => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
+		AUTHOR        => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
+);
+
+#
+# Insert additional MOBY specific Makefile targets
+#
+# 
+#sub MY::postamble {
+#	return <<"MAKE_FRAG";
+#Central:
+#	echo 'Make (local) MOBY Central stub'
+#
+#Server:
+#	echo 'Make (local) MOBY Server stub'
+#
+#WWWClient:
+#	echo 'Setting up MOBY WWW Client'
+#	cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
+#	chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
+# 
+#MAKE_FRAG
+#}
+
+use ExtUtils::MakeMaker;
+use FindBin '$Bin';
+use strict;
+my $VERSION = '0.87';
+
+
+sub MY::postamble {
+  # Now build documentation.
+  use Pod::Find qw(pod_find simplify_name);
+  use Cwd;
+  my $cur_dir = getcwd();
+  # Find the files that contain POD, starting from the top-level build directory, and do it silently.
+  my %pods = pod_find({ -verbose => 0}, 
+		      File::Spec->catfile($cur_dir, "MOBY") );
+  my @PM = sort keys %pods;
+  my @MOD_NAMES = map {$pods{$_}} @PM;
+  # Make home for all docs
+  # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
+  # It's more robust to put it directly into the Makefile, 
+  # so that it can be rebuilt with a simple "make" if needed.
+  # But that would require figuring out how to walk a tree from the shell,
+  # and I don't have time for that. Maybe some other day.
+  my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
+  mkdir File::Spec->catfile($cur_dir, "docs") 
+    unless -e File::Spec->catfile($cur_dir, "docs");
+  mkdir $HTML_ROOT unless -e $HTML_ROOT;
+  # Create a new directory tree for the documentation, that mirrors the source tree.
+  use File::Find;
+  my @make_dirs_list;
+  sub wanted { # Define nested subroutine, to inherit variable scope
+    my $src_dir = $File::Find::dir;
+    (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
+#    print STDERR "EXamining $doc_dir\n";
+    if ( !($doc_dir =~ /CVS$/) ) {
+      push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
+	unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
+      if (!(-e $doc_dir)) {
+	my $made_dir = mkdir $doc_dir;
+	if (!$made_dir) { 
+	  print STDERR "Couldn't create directory '$doc_dir' because '$!'"; 
+	}
+      }
+    }
+  }
+  find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
+  # Finally, start writing the rules.
+  # Let's make a big rule to build all the docs at once, call it 'html'
+  # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
+  my @HTML = map {  # Edit beginning and end of PM files, to make HTML filenames
+    my $x = $_; # Don't want to change the original...
+    $x =~ s/\.p[lm]$/\.html/; 
+    $x =~ s/^$cur_dir/$HTML_ROOT/; 
+    $x} @PM;
+  my $postamble = "# Rules to keep developer docs up-to-date.\n";
+  $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) 
+    . "\n\nhtml: \$(POD_TO_HTML)\n";
+#  $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
+#    . "\n\nhtml:\n"; # \$(HTML_DIRS)
+#  $postamble .= "\$(HTML_DIRS):\n\tfor file in " 
+#    . join(" \\\n", @make_dirs_list) .
+#    "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
+
+  # Now, finally, we build rules for the makefile.
+  # The TAB ('\t') characters are essential,  otherwise 'make' will silently ignore the rules.
+  # Don't be tempted to remove them.
+  for (my $i = 0;  $i < @PM; $i++) {
+    $postamble .= <<RULE;
+$HTML[$i]:$PM[$i]
+	\$(NOECHO) \$(ECHO) Generating HTML for MOBY::$MOD_NAMES[$i]
+	\$(NOECHO) pod2html --htmlroot=$HTML_ROOT --outfile=$HTML[$i] $PM[$i]
+RULE
+  }
+#  print "HTML_ROOT: $HTML_ROOT\n";
+  # Auto-generate an index page, with links to the individual POD-generated pages.
+  # Make sure it works on the local filesystem.
+  # Trim HTML files down to relative paths.
+  make_index_page(\@PM ,
+		  [ map { my $x= $_; $x =~ s/^$cur_dir\///; $x} @HTML ], 
+		  \@MOD_NAMES);
+  return $postamble;
+}
+
+
+sub make_index_page {
+  # Generate an index to the auto-generated HTML docs.
+  my ($pms, $html, $mod_names) = @_;
+  open INDEX, ">index.html" or die "Couldn't open index.html ($!)";
+  print INDEX <<HEAD;
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>MOBY-S Perl Module Documentation</title>
+</head>
+<body>
+<div style="text-align: center;">
+<h1>MOBY-S Perl Modules Documentation</h1>
+</div>
+For an overview of how to do various things in Perl, see the <a href='http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial'>
+Perl Tutorial</a><p>
+The documents below (including this one) are generated by pod2html from the various perl
+modules and give specific interface information for each of the Perl modules described in the tutorial.
+
+<ul>
+HEAD
+  for (my $i = 0; $i < @{$pms}; $i++) {
+    print INDEX "<li><a href=\"$html->[$i]\">MOBY::$mod_names->[$i]</a></li>\n";
+  }
+print INDEX <<FOOT;
+</ul>
+</body>
+</html>
+FOOT
+}
+
+
+# Override built-in target, by adding the 'html' dependency
+# Now HTML gets updated every time you type "make"
+sub MY::top_targets {
+  my $self = shift;
+  my $string = $self->MM::top_targets;
+  my $add = 'html';
+  $string =~ s/\s+(pure_all)/ $add $1/;
+  return $string;
+}
+
+#sub MY::install {
+#  my $self = shift;
+#  my $string = $self->MM::install;
+#  my $add = 'html';
+#  $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
+#  print "INSTALL: $string\n";
+#  return $string;
+#}
+
+WriteMakefile(
+	      NAME	      => 'MOBY-S',
+	      VERSION	      => $VERSION, 
+	      # VERSION_FROM    => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
+	      PMLIBDIRS       => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
+	      # Version numbers specified for prerequiisites are simply "desired" versions,
+	      # not minimum, or anything else.
+	      PREREQ_PM     => {
+				'SOAP::Lite'       => 0.69,
+				'SOAP::MIME'       => 0.55,
+				'XML::LibXML'      => 1.58,
+				'XML::XPath'       => 1.12,
+				'Text::Shellwords' => 1.00,
+				'HTML::Entities'   => 0.01,
+				'Test::More'       => 0.60,
+				# Database stuff required only for local registry, but notify user if missing anyway.
+				'DBI'              => 0.01,
+				'DBD::mysql'       => 0.01,
+				# 'WSRF::Lite'		=> '0.8.2.1', but it is not declared in the proper way there
+				'WSRF::Lite'		=> '',
+                 'Test::Simple' => 0.44,
+                 'XML::DOM'     => '',
+                 'DateTime::Format::Epoch'  => '',
+                 'DateTime::Format::W3CDTF' => '',
+                 'HTTP::Daemon' => '',
+                 'HTTP::Daemon::SSL' => '',
+                 'MIME::Base64' => '',
+                 'Digest::SHA1' => '',
+                 'Crypt::OpenSSL::X509' => '',
+                 'Crypt::OpenSSL::RSA' => '',
+                 'XML::CanonicalizeXML' => 0.02,
+                 'Sys::Hostname::Long' => '',
+		  		 'RDF::Core' => '.51',
+				 #Sharable only used for isAlive script
+	   			 #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
+		  	     #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
+			     #'LS' => 1.1.4,
+	      }, # e.g., Module::Name => 1.1
+	      #PM_FILTER     => "", 
+	      ($] >= 5.005 ?    ## Add these new keywords supported since 5.005
+	       (ABSTRACT      => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
+		AUTHOR        => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
+);
+
+#
+# Insert additional MOBY specific Makefile targets
+#
+# 
+#sub MY::postamble {
+#	return <<"MAKE_FRAG";
+#Central:
+#	echo 'Make (local) MOBY Central stub'
+#
+#Server:
+#	echo 'Make (local) MOBY Server stub'
+#
+#WWWClient:
+#	echo 'Setting up MOBY WWW Client'
+#	cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
+#	chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
+# 
+#MAKE_FRAG
+#}
+


From kawas at dev.open-bio.org  Tue Sep 11 12:48:28 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 11 Sep 2007 12:48:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709111648.l8BGmSoB006345@dev.open-bio.org>


kawas
Tue Sep 11 12:48:27 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv6310/Java/docs

Modified Files:
	ConfigureRDFAgent.html 
Log Message:

moby-live/Java/docs ConfigureRDFAgent.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2006/10/05 15:32:47	1.3
+++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2007/09/11 16:48:27	1.4
@@ -29,14 +29,15 @@
   using 'mail', a UNIX/Linux/*nix email client. Moreover, The agent can choose to 
   ignore those services that do not contain signature urls or to remove 
   them.</p>
-</p>
+<p></p>
 <h4>This document is broken down into the following sections: </h4>
 <ul>
   <li><a href="#getting_started">Getting Started</a></li>
   <li><a href="#configuring_the_agent">Configuring the Agent</a></li>
   <li><a href="#setting_up_a_cron_job">Setting up a Cron Job</a></li>
-  <li><a href="moby_admin_dispatcher">MOBY-Admin Dispatcher</a></li>
+  <li><a href="#moby_admin_dispatcher">MOBY-Admin Dispatcher</a></li>
   <li><a href="#uses_for_the_agent">Uses for the Agent</a></li>
+  <li><a href="#faq">FAQ</a></li>
 </ul>
 <p>&nbsp;</p>
 <h3><a name="getting_started"></a>Getting Started</h3>
@@ -86,7 +87,7 @@
       <br>
     These variable must be set for the agent to work properly with these scripts.<br>
     <br>
-    <span class="note">Also, note that it is important to place the variable <strong>JAVA_HOME</strong> in the environment of the web server you are using so that Mobycentral can access it!</span> <br>
+    <span class="note">Also, note that it is <strong>important</strong> to place the variable <strong>JAVA_HOME</strong> in the environment of the web server you are using so that Mobycentral can access it!</span> <br>
       <br>
     </li>
     <li class="dcount"> Add the path to the RDFagent to the <b class="step">[mobycentral]</b> section of your mobycentral.config file:
@@ -411,7 +412,7 @@
 </blockquote>
 <p>This file must be called '.htaccess'.<br>
   <br>
-  Assuming that the MOBY-Admin.pl file is located in the cgi-bin directory of apache, you will have to add the following line to http.conf where the cgi-bin directory is defined:</p>
+  Assuming that the MOBY-Admin.pl file is located in the cgi-bin directory of apache, you will have to add the following line to httpd.conf where the cgi-bin directory is defined:</p>
 <p> <b class="step">AllowOverride AuthConfig</b></p>
 <p> <em>i.e. </em><br>
 </p>
@@ -440,11 +441,11 @@
     file at <em><strong>/path/that/exists/</strong></em></p>
   <p><em><strong>username</strong></em> would be the newly created login name</p>
 </blockquote>
-<p>You will be prompted for a password.<br>
+<p>You will be prompted for a password.<br/>
 <p class="note"> This login name and password will have to be entered into the agents 
   configuration file. </p>
 </p>
-</p>
+<strong>Don't forget to restart apache each and every time that you modify the httpd.conf file!</strong>
 <h3><a name="uses_for_the_agent"></a>Uses for the Agent</h3>
 <p>The following are some uses for the agent:</p>
 <ol>
@@ -472,6 +473,20 @@
 </ol>
 <p><br>
   If you have any other uses for the agent, please let me know.</p>
+  
+<h3><a name="faq"></a>FAQ</h3>
+<p>Below are the frequently asked questions. If you have a question not on this list, please let me know!</p>
+<ol>
+  <li class="dcount"> I have installed everything according to this document, but when I run the agent, I get an error stating:<br/>
+    <br/>
+    <pre class=script>
+    "An empty value was found where a yes or no was expected in the config file ..."</pre>
+    <p>What did I do wrong?</p>
+    <p><strong>A.</strong><br/>First, please ensure that all of the values are filled out properly. If that wasn't the problem, then try adding the following line to the bottom of the config file:</p>
+    <pre class=script>    agent.output.flatfile = yes </pre>
+    <p>Once you have added that value to the config file, try testing the agent again.</p>
+  </li>
+</ol>
 <hr>
 <div align=right class="address">
   <address>
@@ -480,6 +495,7 @@
   <!-- hhmts start -->
   Last modified: Tue May 17 15:49:04 2005
   <!-- hhmts end -->
+  <p>$Date$</p>
 </div>
 </body>
 </html>


From mwilkinson at dev.open-bio.org  Fri Sep 14 10:55:31 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 10:55:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141455.l8EEtVkt022090@dev.open-bio.org>


mwilkinson
Fri Sep 14 10:55:31 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory dev.open-bio.org:/tmp/cvs-serv22049/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
modifying SQL layer to get more ontology information out of various calls.  Starting with the Service ontology
moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.83,1.84
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.83
retrieving revision 1.84
diff -u -r1.83 -r1.84
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/02/07 15:19:00	1.83
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 14:55:31	1.84
@@ -836,8 +836,49 @@
           service_type,
           description,
           authority,
-          contact_email
-          from service $condition";
+          contact_email,
+	  from
+	  service 
+          $condition";
+	my $result;
+	if ($type){
+	    $result = do_query($dbh, $statement, ($type));
+	} else {
+	    $result = do_query($dbh, $statement);
+	}
+ 	return $result;		
+}
+
+sub new_query_service{
+	my ($self, %args) = @_;
+	my $type = $args{type};
+	my $condition = "";
+	if ($type =~ /^urn\:lsid/){
+	    $condition = "where s1.service_lsid = ?";
+	} elsif ($type) {
+	    $condition = "where s1.service_type = ?";
+	} else {
+	    $condition = "";
+	}
+	
+	my $dbh = _getDBHandle("mobyservice");
+
+	my $statement = "select
+	  s1.service_id, 
+          s1.service_lsid,
+          s1.service_type,
+          s1.description,
+          s1.authority,
+          s1.contact_email,
+	  s2.service_type,
+	  s2.service_lsid 
+          from
+	  service as s1
+	  left join service_term2term as t
+	    on s1.service_id= t.service1_id
+	left join service as s2
+	on s2.service_id=t.service2_id
+        $condition";
 	my $result;
 	if ($type){
 	    $result = do_query($dbh, $statement, ($type));
@@ -847,6 +888,8 @@
  	return $result;		
 }
 
+
+
 # pass in ....
 sub insert_service{
 	my ($self, %args) = @_;	


From mwilkinson at dev.open-bio.org  Fri Sep 14 10:55:31 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 10:55:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141455.l8EEtV89022072@dev.open-bio.org>


mwilkinson
Fri Sep 14 10:55:30 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22049/MOBY

Modified Files:
	Central.pm OntologyServer.pm 
Log Message:
modifying SQL layer to get more ontology information out of various calls.  Starting with the Service ontology
moby-live/Perl/MOBY Central.pm,1.286,1.287 OntologyServer.pm,1.102,1.103
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.286
retrieving revision 1.287
diff -u -r1.286 -r1.287
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/08/28 22:43:16	1.286
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 14:55:30	1.287
@@ -2712,7 +2712,7 @@
 	my %types = %{ $OS->retrieveAllServiceTypes() };
 	my $types = "<serviceTypes>\n";
 	while ( my ( $serv, $descr ) = each %types ) { #UNCOMMENT
-		my ($desc, $lsid, $contact, $auth) = @$descr;
+		my ($desc, $lsid, $contact, $auth, $isa_type, $isa_lsid) = @$descr;
 		if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
 			$desc = $1;
 		}

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.102
retrieving revision 1.103
diff -u -r1.102 -r1.103
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/01/30 14:49:20	1.102
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/09/14 14:55:30	1.103
@@ -1002,11 +1002,11 @@
 	my ($self) = @_;
 	$CONFIG ||= MOBY::Config->new;    # exported by Config.pm
 	my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobyservice' );
-	my $types = $adaptor->query_service();
+	my $types = $adaptor->new_query_service();
 
 	my %response;
 	foreach (@$types) {
-		$response{ $_->{service_type} } = [$_->{description}, $_->{service_lsid}, $_->{contact_email}, $_->{authority}]; #UNCOMMENT
+		$response{ $_->{'s1.service_type'} } = [$_->{'s1.description'}, $_->{'s1.service_lsid'}, $_->{'s1.contact_email'}, $_->{'s1.authority'}, $_->{'s2.service_type'}, $_->{'s2.service_lsid'}]; #UNCOMMENT
 	}
 	return \%response;
 }


From mwilkinson at dev.open-bio.org  Fri Sep 14 12:04:21 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:04:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141604.l8EG4L9d022468@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:04:20 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory dev.open-bio.org:/tmp/cvs-serv22449/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
doh.  Extra comma removed from sql query
moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.84,1.85
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.84
retrieving revision 1.85
diff -u -r1.84 -r1.85
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 14:55:31	1.84
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 16:04:20	1.85
@@ -836,7 +836,7 @@
           service_type,
           description,
           authority,
-          contact_email,
+          contact_email
 	  from
 	  service 
           $condition";


From mwilkinson at dev.open-bio.org  Fri Sep 14 12:26:50 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:26:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141626.l8EGQog9022559@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:26:50 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory dev.open-bio.org:/tmp/cvs-serv22520/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
proper naming of columns
moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.85,1.86
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.85
retrieving revision 1.86
diff -u -r1.85 -r1.86
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 16:04:20	1.85
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 16:26:50	1.86
@@ -818,7 +818,7 @@
 # pass service_type, as term or LSID
 sub query_service{
 	my ($self, %args) = @_;
-	my $type = $args{type};
+	my $type = $args{type}||"";
 	my $condition = "";
 	if ($type =~ /^urn\:lsid/){
 	    $condition = "where service_lsid = ?";
@@ -851,7 +851,7 @@
 
 sub new_query_service{
 	my ($self, %args) = @_;
-	my $type = $args{type};
+	my $type = $args{type}||"";
 	my $condition = "";
 	if ($type =~ /^urn\:lsid/){
 	    $condition = "where s1.service_lsid = ?";
@@ -864,14 +864,14 @@
 	my $dbh = _getDBHandle("mobyservice");
 
 	my $statement = "select
-	  s1.service_id, 
-          s1.service_lsid,
-          s1.service_type,
-          s1.description,
-          s1.authority,
-          s1.contact_email,
-	  s2.service_type,
-	  s2.service_lsid 
+	  s1.service_id as service_id, 
+          s1.service_lsid as service_lsid,
+          s1.service_type as service_type,
+          s1.description as description,
+          s1.authority as authority,
+          s1.contact_email as contact_email,
+	  s2.service_type as parent_type,
+	  s2.service_lsid as parent_lsid  
           from
 	  service as s1
 	  left join service_term2term as t


From mwilkinson at dev.open-bio.org  Fri Sep 14 12:26:50 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:26:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141626.l8EGQojL022539@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:26:50 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22520/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
proper naming of columns
moby-live/Perl/MOBY OntologyServer.pm,1.103,1.104
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.103
retrieving revision 1.104
diff -u -r1.103 -r1.104
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/09/14 14:55:30	1.103
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/09/14 16:26:50	1.104
@@ -1006,7 +1006,7 @@
 
 	my %response;
 	foreach (@$types) {
-		$response{ $_->{'s1.service_type'} } = [$_->{'s1.description'}, $_->{'s1.service_lsid'}, $_->{'s1.contact_email'}, $_->{'s1.authority'}, $_->{'s2.service_type'}, $_->{'s2.service_lsid'}]; #UNCOMMENT
+		$response{ $_->{'service_type'} } = [$_->{'description'}, $_->{'service_lsid'}, $_->{'contact_email'}, $_->{'authority'}, $_->{'parent_type'}, $_->{'parent_lsid'}]; #UNCOMMENT
 	}
 	return \%response;
 }


From mwilkinson at dev.open-bio.org  Fri Sep 14 12:53:04 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:53:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141653.l8EGr4SJ022693@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:53:04 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22674/MOBY

Modified Files:
	Central.pm 
Log Message:
get info out of XML in client central
moby-live/Perl/MOBY Central.pm,1.287,1.288
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.287
retrieving revision 1.288
diff -u -r1.287 -r1.288
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 14:55:30	1.287
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 16:53:04	1.288
@@ -2695,10 +2695,11 @@
  Args      :	none
  XML       :
 	<serviceTypes>
-	   <serviceType name="serviceName" lsid="urn:lsid...">
+	   <serviceType name="serviceTypeName" lsid="urn:lsid...">
 		  <Description><![CDATA[free text description here]]></Description>
 		  <contactEmail>your at email.here</contactEmail>
 		  <authURI>authority.uri.here</authURI>
+		  <ISA lsid="urn:lsid...">parentTypeName</ISA>  <!-- empty for root! -->
 	   </serviceType>
 		...
 		...
@@ -2716,7 +2717,14 @@
 		if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
 			$desc = $1;
 		}
-		$types .="<serviceType name='$serv' lsid='$lsid'>\n<Description><![CDATA[$desc]]></Description>\n<contactEmail>$contact</contactEmail>\n<authURI>$auth</authURI>\n</serviceType>\n"; #UNCOMMENT
+		$isa_type ||="";
+		$isa_lsid ||="";
+		$types .="<serviceType name='$serv' lsid='$lsid'>
+		<Description><![CDATA[$desc]]></Description>
+		<contactEmail>$contact</contactEmail>
+		<authURI>$auth</authURI>
+		<ISA lsid='$isa_lsid'>$isa_type</ISA>
+		</serviceType>\n"; #UNCOMMENT
 	}
 	$types .= "</serviceTypes>\n";
 	return $types;


From mwilkinson at dev.open-bio.org  Fri Sep 14 12:53:04 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:53:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141653.l8EGr40M022713@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:53:04 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv22674/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
get info out of XML in client central
moby-live/Perl/MOBY/Client Central.pm,1.149,1.150
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.149
retrieving revision 1.150
diff -u -r1.149 -r1.150
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/07/31 12:29:15	1.149
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 16:53:04	1.150
@@ -1338,7 +1338,7 @@
 		} else {
 		    $lsid = $type;
 		}
-		my ($desc, $auth, $email);
+		my ($desc, $auth, $email, $ISA, $ISA_LSID) = ("","","","","");
 		for
 		  my $elem ( $types->get_node($x)->getElementsByTagName('Description') )
 		{
@@ -1363,8 +1363,18 @@
 				$email = $1;
 			}
 		}
+				for
+		  my $elem ( $types->get_node($x)->getElementsByTagName('ISA') )
+		{
+			$ISA = $elem->firstChild->toString;
+			if ( $email =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
+				$email = $1;
+			}
+			$ISA_LSID = $elem->getAttributeNode('lsid')->getValue;
+		}
+
 		$desc =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;  # somehow these CDATA elements are nested sometimes???
-		$servicetypes{$as_lsid?$lsid:$type} = {Description => $desc, authURI => $auth, contactEmail => $email};
+		$servicetypes{$as_lsid?$lsid:$type} = {Description => $desc, authURI => $auth, contactEmail => $email, ISA => $ISA, ISA_LSID => $ISA_LSID};
 	}
 	return \%servicetypes;
 }


From mwilkinson at dev.open-bio.org  Fri Sep 14 13:02:24 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 13:02:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141702.l8EH2Oe4022790@dev.open-bio.org>


mwilkinson
Fri Sep 14 13:02:24 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv22771/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
get info out of XML in client central
moby-live/Perl/MOBY/Client Central.pm,1.150,1.151
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.150
retrieving revision 1.151
diff -u -r1.150 -r1.151
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 16:53:04	1.150
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 17:02:24	1.151
@@ -1363,10 +1363,11 @@
 				$email = $1;
 			}
 		}
-				for
+		for
 		  my $elem ( $types->get_node($x)->getElementsByTagName('ISA') )
 		{
-			$ISA = $elem->firstChild->toString;
+			$ISA = $elem->firstChild;
+			$ISA = $ISA?$ISA->toString:"";
 			if ( $email =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
 				$email = $1;
 			}


From mwilkinson at dev.open-bio.org  Fri Sep 14 13:23:47 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 13:23:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141723.l8EHNlEx022863@dev.open-bio.org>


mwilkinson
Fri Sep 14 13:23:47 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22844/MOBY

Modified Files:
	Central.pm 
Log Message:
update docs
moby-live/Perl/MOBY Central.pm,1.288,1.289
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.288
retrieving revision 1.289
diff -u -r1.288 -r1.289
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 16:53:04	1.288
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 17:23:47	1.289
@@ -2699,7 +2699,7 @@
 		  <Description><![CDATA[free text description here]]></Description>
 		  <contactEmail>your at email.here</contactEmail>
 		  <authURI>authority.uri.here</authURI>
-		  <ISA lsid="urn:lsid...">parentTypeName</ISA>  <!-- empty for root! -->
+		  <ISA lsid="urn:lsid...">parentTypeName</ISA>  <!-- both empty for root Service! -->
 	   </serviceType>
 		...
 		...


From mwilkinson at dev.open-bio.org  Fri Sep 14 13:23:47 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 13:23:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141723.l8EHNl9f022883@dev.open-bio.org>


mwilkinson
Fri Sep 14 13:23:47 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv22844/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
update docs
moby-live/Perl/MOBY/Client Central.pm,1.151,1.152
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.151
retrieving revision 1.152
diff -u -r1.151 -r1.152
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 17:02:24	1.151
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 17:23:47	1.152
@@ -1307,7 +1307,9 @@
  Function  :	get all details of all service types
  Returns   :	hashref of $types{$type} = {Description => "definition",
                                             authURI  => "authority.uri.here",
-					    contactEmail => "email at addy.here"}
+					    contactEmail => "email at addy.here",
+					    ISA => "parentType", # possibly empty string ""
+					    ISA_LSID => "urn:lsid...parentLSID"} # possibly empty string ""
  Args      :	registry => $reg_name:  name of registry you wish to retrieve from (optional)
                 as_lsid  => $boolean:  return the $type as its corresponding LSID (defualt off)
 


From mwilkinson at dev.open-bio.org  Fri Sep 14 13:33:12 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 13:33:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141733.l8EHXCn0022937@dev.open-bio.org>


mwilkinson
Fri Sep 14 13:33:12 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22918/MOBY

Modified Files:
	Central.pm 
Log Message:
update docs
moby-live/Perl/MOBY Central.pm,1.289,1.290
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.289
retrieving revision 1.290
diff -u -r1.289 -r1.290
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 17:23:47	1.289
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 17:33:12	1.290
@@ -2703,7 +2703,7 @@
 	   </serviceType>
 		...
 		...
-	</serviceNames>
+	</serviceTypes>
 
 =cut
 


From jmrc at dev.open-bio.org  Mon Sep 24 14:53:37 2007
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 24 Sep 2007 18:53:37 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709241853.l8OIrWMa019938@dev.open-bio.org>


jmrc
Mon Sep 24 14:53:32 EDT 2007
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv19902/Perl

Modified Files:
	Makefile.PL 
Log Message:
*	Latest WSRF::Lite package has a proper VERSION declaration,
	so we can restrict the version of the package to the one
	which is known to work.
*	WSRF::Lite is not in CPAN, so we have added a warning about
	where it can be fetched/found (beware older versions!).
*	Asynchronous WSDL template has now UTF-8 encoding. Previously,
	it had no encoding...
*	New WSRF::Lite (version 0.8.2.2) allows removing some hacks
	from MOBY::Async::WSRF.

moby-live/Perl Makefile.PL,1.30,1.31
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/04 22:28:14	1.30
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/24 18:53:32	1.31
@@ -29,6 +29,31 @@
 
 }
 
+eval "require WSRF::Lite";
+if ($@) {
+	print STDOUT <<'EOF_WSRF';
+	
+############## IMPORTANT ##############
+Module 'WSRF::Lite' is not installed.
+This module is used **only** if you are thinking on
+developing BioMOBY Asynchronous service.
+
+Unfortunately, this module is not available on CPAN 
+and must be manually installed. Some of the 
+dependencies are beta and as such, may not be stable.
+
+Try downloading it from the following link:
+
+http://www.rcs.manchester.ac.uk/research/projects/wsrflite
+
+or you can try searching Google using the keywords:
+
+	'perl WSRF::Lite' 
+
+(beware outdated sites!)
+EOF_WSRF
+}
+
 sub MY::postamble {
   # Now build documentation.
   use Pod::Find qw(pod_find simplify_name);
@@ -178,7 +203,7 @@
 				# Database stuff required only for local registry, but notify user if missing anyway.
 				'DBI'              => 0.01,
 				'DBD::mysql'       => 0.01,
-				'WSRF::Lite'		=> '',
+				'WSRF::Lite'       => 0.8.2.2,
                 'Test::Simple' => 0.44,
                 'XML::DOM'     => '',
                 'DateTime::Format::Epoch'  => '',


From jmrc at dev.open-bio.org  Mon Sep 24 14:53:40 2007
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 24 Sep 2007 18:53:40 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709241853.l8OIrWCh019958@dev.open-bio.org>


jmrc
Mon Sep 24 14:53:32 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv19902/Perl/MOBY

Modified Files:
	Central.pm 
Log Message:
*	Latest WSRF::Lite package has a proper VERSION declaration,
	so we can restrict the version of the package to the one
	which is known to work.
*	WSRF::Lite is not in CPAN, so we have added a warning about
	where it can be fetched/found (beware older versions!).
*	Asynchronous WSDL template has now UTF-8 encoding. Previously,
	it had no encoding...
*	New WSRF::Lite (version 0.8.2.2) allows removing some hacks
	from MOBY::Async::WSRF.

moby-live/Perl/MOBY Central.pm,1.290,1.291
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.290
retrieving revision 1.291
diff -u -r1.290 -r1.291
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 17:33:12	1.290
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/24 18:53:32	1.291
@@ -4123,7 +4123,7 @@
 # for MOBY Asynchronous services.  This WSDL is not correct YET!
 
 $WSDL_ASYNC_TEMPLATE = <<END;
-<?xml version="1.0"?>
+<?xml version="1.0" encoding="UTF-8"?>
 <wsdl:definitions name="MOBY_Central_Generated_WSDL" targetNamespace="http://biomoby.org/Central.wsdl"
    xmlns:tns="http://biomoby.org/Central.wsdl"
    xmlns:xsd1="http://biomoby.org/CentralXSDs.xsd"


From jmrc at dev.open-bio.org  Mon Sep 24 14:53:43 2007
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 24 Sep 2007 18:53:43 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709241853.l8OIrXSm019980@dev.open-bio.org>


jmrc
Mon Sep 24 14:53:32 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Async
In directory dev.open-bio.org:/tmp/cvs-serv19902/Perl/MOBY/Async

Modified Files:
	WSRF.pm 
Log Message:
*	Latest WSRF::Lite package has a proper VERSION declaration,
	so we can restrict the version of the package to the one
	which is known to work.
*	WSRF::Lite is not in CPAN, so we have added a warning about
	where it can be fetched/found (beware older versions!).
*	Asynchronous WSDL template has now UTF-8 encoding. Previously,
	it had no encoding...
*	New WSRF::Lite (version 0.8.2.2) allows removing some hacks
	from MOBY::Async::WSRF.

moby-live/Perl/MOBY/Async WSRF.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Async/WSRF.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/Async/WSRF.pm	2007/07/18 10:47:24	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/Async/WSRF.pm	2007/09/24 18:53:32	1.4
@@ -27,7 +27,7 @@
 
 package MOBY::Async::WSRF;
 use strict;
-use WSRF::Lite;
+use WSRF::Lite 0.8.2.2;
 
 $WSRF::WSRP::Private{queryIDs} = [];
 $WSRF::WSRP::MobyPrivatePrefixes    = ['pid', 'input'];
@@ -36,12 +36,12 @@
 $WSRF::Constants::Data  = '/tmp/moby_';
 $WSRF::Constants::MOBY  = 'http://biomoby.org/';
 $WSRF::Constants::MOBY_MESSAGE_NS  = 'http://www.biomoby.org/moby';
-$WSRF::Constants::WSA   = 'http://www.w3.org/2005/08/addressing';
-$WSRF::Constants::WSRP  = 'http://docs.oasis-open.org/wsrf/rp-2';
-$WSRF::Constants::WSRL  = 'http://docs.oasis-open.org/wsrf/rl-2';
-$WSRF::Constants::WSSG  = 'http://docs.oasis-open.org/wsrf/sg-2';
-$WSRF::Constants::WSBF  = 'http://docs.oasis-open.org/wsrf/bf-2';
-$WSRF::Constants::WSA_ANON = 'http://www.w3.org/2005/08/addressing/anonymous';
+#$WSRF::Constants::WSA   = 'http://www.w3.org/2005/08/addressing';
+#$WSRF::Constants::WSRP  = 'http://docs.oasis-open.org/wsrf/rp-2';
+#$WSRF::Constants::WSRL  = 'http://docs.oasis-open.org/wsrf/rl-2';
+#$WSRF::Constants::WSSG  = 'http://docs.oasis-open.org/wsrf/sg-2';
+#$WSRF::Constants::WSBF  = 'http://docs.oasis-open.org/wsrf/bf-2';
+#$WSRF::Constants::WSA_ANON = 'http://www.w3.org/2005/08/addressing/anonymous';
 
 #===============================================================================
 # WSRF::Serializer


From kawas at dev.open-bio.org  Tue Sep  4 17:40:35 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 4 Sep 2007 13:40:35 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709041740.l84HeZ7M013610@dev.open-bio.org>


kawas
Tue Sep  4 13:40:34 EDT 2007
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv13575

Modified Files:
	Makefile.PL 
Log Message:
removing the requirement that the module LS must be installed for Makefile to be created
moby-live/Perl Makefile.PL,1.28,1.29
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.28
retrieving revision 1.29
diff -u -r1.28 -r1.29
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2007/08/28 23:54:46	1.28
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/04 17:40:34	1.29
@@ -27,7 +27,6 @@
 
 END_OF_TEXT
 
-exit(0);
 }
 
 sub MY::postamble {



From kawas at dev.open-bio.org  Tue Sep  4 22:28:14 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 4 Sep 2007 18:28:14 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709042228.l84MSETs013914@dev.open-bio.org>


kawas
Tue Sep  4 18:28:14 EDT 2007
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv13879

Modified Files:
	Makefile.PL 
Log Message:

moby-live/Perl Makefile.PL,1.29,1.30
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.29
retrieving revision 1.30
diff -u -r1.29 -r1.30
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/04 17:40:34	1.29
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/04 22:28:14	1.30
@@ -1,427 +1,427 @@
-use ExtUtils::MakeMaker;
-use FindBin '$Bin';
-use strict;
-my $VERSION = '0.87';
-
-# need a way of relaying the information that LS cannot be found on CPAN
-eval "require LS";
-if ($@) {
-	print STDOUT <<'END_OF_TEXT';
-	
-############## IMPORTANT ##############
-Module 'LS' is not installed. This module is used
-**only** if you are wanting to host a LSID Authority!
-
-Unfortunately, this module is not available on CPAN 
-and must be manually installed. Some of the 
-dependencies are beta and as such, may not be stable.
-
-You can try searching Google using the keywords:
-
-	'perl LS lsid' 
-
-or, try downloading it from the following link:
-	
-	'http://sourceforge.net/project/showfiles.php?group_id=130827'
-
-
-END_OF_TEXT
-
-}
-
-sub MY::postamble {
-  # Now build documentation.
-  use Pod::Find qw(pod_find simplify_name);
-  use Cwd;
-  my $cur_dir = getcwd();
-  # Find the files that contain POD, starting from the top-level build directory, and do it silently.
-  my %pods = pod_find({ -verbose => 0}, 
-		      File::Spec->catfile($cur_dir, "MOBY") );
-  my @PM = sort keys %pods;
-  my @MOD_NAMES = map {$pods{$_}} @PM;
-  # Make home for all docs
-  # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
-  # It's more robust to put it directly into the Makefile, 
-  # so that it can be rebuilt with a simple "make" if needed.
-  # But that would require figuring out how to walk a tree from the shell,
-  # and I don't have time for that. Maybe some other day.
-  my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
-  mkdir File::Spec->catfile($cur_dir, "docs") 
-    unless -e File::Spec->catfile($cur_dir, "docs");
-  mkdir $HTML_ROOT unless -e $HTML_ROOT;
-  # Create a new directory tree for the documentation, that mirrors the source tree.
-  use File::Find;
-  my @make_dirs_list;
-  sub wanted { # Define nested subroutine, to inherit variable scope
-    my $src_dir = $File::Find::dir;
-    (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
-#    print STDERR "EXamining $doc_dir\n";
-    if ( !($doc_dir =~ /CVS$/) ) {
-      push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
-	unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
-      if (!(-e $doc_dir)) {
-	my $made_dir = mkdir $doc_dir;
-	if (!$made_dir) { 
-	  print STDERR "Couldn't create directory '$doc_dir' because '$!'"; 
-	}
-      }
-    }
-  }
-  find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
-  # Finally, start writing the rules.
-  # Let's make a big rule to build all the docs at once, call it 'html'
-  # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
-  my @HTML = map {  # Edit beginning and end of PM files, to make HTML filenames
-    my $x = $_; # Don't want to change the original...
-    $x =~ s/\.p[lm]$/\.html/; 
-    $x =~ s/^$cur_dir/$HTML_ROOT/; 
-    $x} @PM;
-  my $postamble = "# Rules to keep developer docs up-to-date.\n";
-  $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) 
-    . "\n\nhtml: \$(POD_TO_HTML)\n";
-#  $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
-#    . "\n\nhtml:\n"; # \$(HTML_DIRS)
-#  $postamble .= "\$(HTML_DIRS):\n\tfor file in " 
-#    . join(" \\\n", @make_dirs_list) .
-#    "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
-
-  # Now, finally, we build rules for the makefile.
-  # The TAB ('\t') characters are essential,  otherwise 'make' will silently ignore the rules.
-  # Don't be tempted to remove them.
-  for (my $i = 0;  $i < @PM; $i++) {
-    $postamble .= <<RULE;
-$HTML[$i]:$PM[$i]
-	\$(NOECHO) \$(ECHO) Generating HTML for MOBY::$MOD_NAMES[$i]
-	\$(NOECHO) pod2html --htmlroot=$HTML_ROOT --outfile=$HTML[$i] $PM[$i]
-RULE
-  }
-#  print "HTML_ROOT: $HTML_ROOT\n";
-  # Auto-generate an index page, with links to the individual POD-generated pages.
-  # Make sure it works on the local filesystem.
-  # Trim HTML files down to relative paths.
-  make_index_page(\@PM ,
-		  [ map { my $x= $_; $x =~ s/^$cur_dir\///; $x} @HTML ], 
-		  \@MOD_NAMES);
-  return $postamble;
-}
-
-
-sub make_index_page {
-  # Generate an index to the auto-generated HTML docs.
-  my ($pms, $html, $mod_names) = @_;
-  open INDEX, ">index.html" or die "Couldn't open index.html ($!)";
-  print INDEX <<HEAD;
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-  <meta http-equiv="content-type"
- content="text/html; charset=ISO-8859-1">
-  <title>MOBY-S Perl Module Documentation</title>
-</head>
-<body>
-<div style="text-align: center;">
-<h1>MOBY-S Perl Modules Documentation</h1>
-</div>
-For an overview of how to do various things in Perl, see the <a href='http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial'>
-Perl Tutorial</a><p>
-The documents below (including this one) are generated by pod2html from the various perl
-modules and give specific interface information for each of the Perl modules described in the tutorial.
-
-<ul>
-HEAD
-  for (my $i = 0; $i < @{$pms}; $i++) {
-    print INDEX "<li><a href=\"$html->[$i]\">MOBY::$mod_names->[$i]</a></li>\n";
-  }
-print INDEX <<FOOT;
-</ul>
-</body>
-</html>
-FOOT
-}
-
-
-# Override built-in target, by adding the 'html' dependency
-# Now HTML gets updated every time you type "make"
-sub MY::top_targets {
-  my $self = shift;
-  my $string = $self->MM::top_targets;
-  my $add = 'html';
-  $string =~ s/\s+(pure_all)/ $add $1/;
-  return $string;
-}
-
-#sub MY::install {
-#  my $self = shift;
-#  my $string = $self->MM::install;
-#  my $add = 'html';
-#  $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
-#  print "INSTALL: $string\n";
-#  return $string;
-#}
-
-WriteMakefile(
-	      NAME	      => 'MOBY-S',
-	      VERSION	      => $VERSION, 
-	      # VERSION_FROM    => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
-	      PMLIBDIRS       => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
-	      # Version numbers specified for prerequiisites are simply "desired" versions,
-	      # not minimum, or anything else.
-	      PREREQ_PM     => {
-				'SOAP::Lite'       => 0.69,
-				'SOAP::MIME'       => 0.55,
-				'XML::LibXML'      => 1.58,
-				'XML::XPath'       => 1.12,
-				'Text::Shellwords' => 1.00,
-				'HTML::Entities'   => 0.01,
-				'Test::More'       => 0.60,
-				# Database stuff required only for local registry, but notify user if missing anyway.
-				'DBI'              => 0.01,
-				'DBD::mysql'       => 0.01,
-				'WSRF::Lite'		=> '',
-                'Test::Simple' => 0.44,
-                'XML::DOM'     => '',
-                'DateTime::Format::Epoch'  => '',
-                'DateTime::Format::W3CDTF' => '',
-                'HTTP::Daemon' => '',
-                'HTTP::Daemon::SSL' => '',
-                'MIME::Base64' => '',
-                'Digest::SHA1' => '',
-                'Crypt::OpenSSL::X509' => '',
-                'Crypt::OpenSSL::RSA' => '',
-                'XML::CanonicalizeXML' => 0.02,
-                'Sys::Hostname::Long' => '',
-			   	'RDF::Core' => '.51',
-				# Sharable only used for isAlive script
-	   			'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
-		  	    #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
-			    #'LS' => 1.1.4,
-					 
-	    }, # e.g., Module::Name => 1.1
-	    #PM_FILTER     => "", 
-	    ($] >= 5.005 ?    ## Add these new keywords supported since 5.005
-	    (ABSTRACT      => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
-		AUTHOR        => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
-);
-
-#
-# Insert additional MOBY specific Makefile targets
-#
-# 
-#sub MY::postamble {
-#	return <<"MAKE_FRAG";
-#Central:
-#	echo 'Make (local) MOBY Central stub'
-#
-#Server:
-#	echo 'Make (local) MOBY Server stub'
-#
-#WWWClient:
-#	echo 'Setting up MOBY WWW Client'
-#	cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
-#	chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
-# 
-#MAKE_FRAG
-#}
-
-use ExtUtils::MakeMaker;
-use FindBin '$Bin';
-use strict;
-my $VERSION = '0.87';
-
-
-sub MY::postamble {
-  # Now build documentation.
-  use Pod::Find qw(pod_find simplify_name);
-  use Cwd;
-  my $cur_dir = getcwd();
-  # Find the files that contain POD, starting from the top-level build directory, and do it silently.
-  my %pods = pod_find({ -verbose => 0}, 
-		      File::Spec->catfile($cur_dir, "MOBY") );
-  my @PM = sort keys %pods;
-  my @MOD_NAMES = map {$pods{$_}} @PM;
-  # Make home for all docs
-  # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
-  # It's more robust to put it directly into the Makefile, 
-  # so that it can be rebuilt with a simple "make" if needed.
-  # But that would require figuring out how to walk a tree from the shell,
-  # and I don't have time for that. Maybe some other day.
-  my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
-  mkdir File::Spec->catfile($cur_dir, "docs") 
-    unless -e File::Spec->catfile($cur_dir, "docs");
-  mkdir $HTML_ROOT unless -e $HTML_ROOT;
-  # Create a new directory tree for the documentation, that mirrors the source tree.
-  use File::Find;
-  my @make_dirs_list;
-  sub wanted { # Define nested subroutine, to inherit variable scope
-    my $src_dir = $File::Find::dir;
-    (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
-#    print STDERR "EXamining $doc_dir\n";
-    if ( !($doc_dir =~ /CVS$/) ) {
-      push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
-	unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
-      if (!(-e $doc_dir)) {
-	my $made_dir = mkdir $doc_dir;
-	if (!$made_dir) { 
-	  print STDERR "Couldn't create directory '$doc_dir' because '$!'"; 
-	}
-      }
-    }
-  }
-  find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
-  # Finally, start writing the rules.
-  # Let's make a big rule to build all the docs at once, call it 'html'
-  # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
-  my @HTML = map {  # Edit beginning and end of PM files, to make HTML filenames
-    my $x = $_; # Don't want to change the original...
-    $x =~ s/\.p[lm]$/\.html/; 
-    $x =~ s/^$cur_dir/$HTML_ROOT/; 
-    $x} @PM;
-  my $postamble = "# Rules to keep developer docs up-to-date.\n";
-  $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) 
-    . "\n\nhtml: \$(POD_TO_HTML)\n";
-#  $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
-#    . "\n\nhtml:\n"; # \$(HTML_DIRS)
-#  $postamble .= "\$(HTML_DIRS):\n\tfor file in " 
-#    . join(" \\\n", @make_dirs_list) .
-#    "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
-
-  # Now, finally, we build rules for the makefile.
-  # The TAB ('\t') characters are essential,  otherwise 'make' will silently ignore the rules.
-  # Don't be tempted to remove them.
-  for (my $i = 0;  $i < @PM; $i++) {
-    $postamble .= <<RULE;
-$HTML[$i]:$PM[$i]
-	\$(NOECHO) \$(ECHO) Generating HTML for MOBY::$MOD_NAMES[$i]
-	\$(NOECHO) pod2html --htmlroot=$HTML_ROOT --outfile=$HTML[$i] $PM[$i]
-RULE
-  }
-#  print "HTML_ROOT: $HTML_ROOT\n";
-  # Auto-generate an index page, with links to the individual POD-generated pages.
-  # Make sure it works on the local filesystem.
-  # Trim HTML files down to relative paths.
-  make_index_page(\@PM ,
-		  [ map { my $x= $_; $x =~ s/^$cur_dir\///; $x} @HTML ], 
-		  \@MOD_NAMES);
-  return $postamble;
-}
-
-
-sub make_index_page {
-  # Generate an index to the auto-generated HTML docs.
-  my ($pms, $html, $mod_names) = @_;
-  open INDEX, ">index.html" or die "Couldn't open index.html ($!)";
-  print INDEX <<HEAD;
-
-<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
-<html>
-<head>
-  <meta http-equiv="content-type"
- content="text/html; charset=ISO-8859-1">
-  <title>MOBY-S Perl Module Documentation</title>
-</head>
-<body>
-<div style="text-align: center;">
-<h1>MOBY-S Perl Modules Documentation</h1>
-</div>
-For an overview of how to do various things in Perl, see the <a href='http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial'>
-Perl Tutorial</a><p>
-The documents below (including this one) are generated by pod2html from the various perl
-modules and give specific interface information for each of the Perl modules described in the tutorial.
-
-<ul>
-HEAD
-  for (my $i = 0; $i < @{$pms}; $i++) {
-    print INDEX "<li><a href=\"$html->[$i]\">MOBY::$mod_names->[$i]</a></li>\n";
-  }
-print INDEX <<FOOT;
-</ul>
-</body>
-</html>
-FOOT
-}
-
-
-# Override built-in target, by adding the 'html' dependency
-# Now HTML gets updated every time you type "make"
-sub MY::top_targets {
-  my $self = shift;
-  my $string = $self->MM::top_targets;
-  my $add = 'html';
-  $string =~ s/\s+(pure_all)/ $add $1/;
-  return $string;
-}
-
-#sub MY::install {
-#  my $self = shift;
-#  my $string = $self->MM::install;
-#  my $add = 'html';
-#  $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
-#  print "INSTALL: $string\n";
-#  return $string;
-#}
-
-WriteMakefile(
-	      NAME	      => 'MOBY-S',
-	      VERSION	      => $VERSION, 
-	      # VERSION_FROM    => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
-	      PMLIBDIRS       => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
-	      # Version numbers specified for prerequiisites are simply "desired" versions,
-	      # not minimum, or anything else.
-	      PREREQ_PM     => {
-				'SOAP::Lite'       => 0.69,
-				'SOAP::MIME'       => 0.55,
-				'XML::LibXML'      => 1.58,
-				'XML::XPath'       => 1.12,
-				'Text::Shellwords' => 1.00,
-				'HTML::Entities'   => 0.01,
-				'Test::More'       => 0.60,
-				# Database stuff required only for local registry, but notify user if missing anyway.
-				'DBI'              => 0.01,
-				'DBD::mysql'       => 0.01,
-				# 'WSRF::Lite'		=> '0.8.2.1', but it is not declared in the proper way there
-				'WSRF::Lite'		=> '',
-                 'Test::Simple' => 0.44,
-                 'XML::DOM'     => '',
-                 'DateTime::Format::Epoch'  => '',
-                 'DateTime::Format::W3CDTF' => '',
-                 'HTTP::Daemon' => '',
-                 'HTTP::Daemon::SSL' => '',
-                 'MIME::Base64' => '',
-                 'Digest::SHA1' => '',
-                 'Crypt::OpenSSL::X509' => '',
-                 'Crypt::OpenSSL::RSA' => '',
-                 'XML::CanonicalizeXML' => 0.02,
-                 'Sys::Hostname::Long' => '',
-		  		 'RDF::Core' => '.51',
-				 #Sharable only used for isAlive script
-	   			 'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
-		  	     #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
-			     #'LS' => 1.1.4,
-	      }, # e.g., Module::Name => 1.1
-	      #PM_FILTER     => "", 
-	      ($] >= 5.005 ?    ## Add these new keywords supported since 5.005
-	       (ABSTRACT      => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
-		AUTHOR        => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
-);
-
-#
-# Insert additional MOBY specific Makefile targets
-#
-# 
-#sub MY::postamble {
-#	return <<"MAKE_FRAG";
-#Central:
-#	echo 'Make (local) MOBY Central stub'
-#
-#Server:
-#	echo 'Make (local) MOBY Server stub'
-#
-#WWWClient:
-#	echo 'Setting up MOBY WWW Client'
-#	cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
-#	chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
-# 
-#MAKE_FRAG
-#}
-
+use ExtUtils::MakeMaker;
+use FindBin '$Bin';
+use strict;
+my $VERSION = '0.87';
+
+# need a way of relaying the information that LS cannot be found on CPAN
+eval "require LS";
+if ($@) {
+	print STDOUT <<'END_OF_TEXT';
+	
+############## IMPORTANT ##############
+Module 'LS' is not installed. This module is used
+**only** if you are wanting to host a LSID Authority!
+
+Unfortunately, this module is not available on CPAN 
+and must be manually installed. Some of the 
+dependencies are beta and as such, may not be stable.
+
+You can try searching Google using the keywords:
+
+	'perl LS lsid' 
+
+or, try downloading it from the following link:
+	
+	'http://sourceforge.net/project/showfiles.php?group_id=130827'
+
+
+END_OF_TEXT
+
+}
+
+sub MY::postamble {
+  # Now build documentation.
+  use Pod::Find qw(pod_find simplify_name);
+  use Cwd;
+  my $cur_dir = getcwd();
+  # Find the files that contain POD, starting from the top-level build directory, and do it silently.
+  my %pods = pod_find({ -verbose => 0}, 
+		      File::Spec->catfile($cur_dir, "MOBY") );
+  my @PM = sort keys %pods;
+  my @MOD_NAMES = map {$pods{$_}} @PM;
+  # Make home for all docs
+  # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
+  # It's more robust to put it directly into the Makefile, 
+  # so that it can be rebuilt with a simple "make" if needed.
+  # But that would require figuring out how to walk a tree from the shell,
+  # and I don't have time for that. Maybe some other day.
+  my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
+  mkdir File::Spec->catfile($cur_dir, "docs") 
+    unless -e File::Spec->catfile($cur_dir, "docs");
+  mkdir $HTML_ROOT unless -e $HTML_ROOT;
+  # Create a new directory tree for the documentation, that mirrors the source tree.
+  use File::Find;
+  my @make_dirs_list;
+  sub wanted { # Define nested subroutine, to inherit variable scope
+    my $src_dir = $File::Find::dir;
+    (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
+#    print STDERR "EXamining $doc_dir\n";
+    if ( !($doc_dir =~ /CVS$/) ) {
+      push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
+	unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
+      if (!(-e $doc_dir)) {
+	my $made_dir = mkdir $doc_dir;
+	if (!$made_dir) { 
+	  print STDERR "Couldn't create directory '$doc_dir' because '$!'"; 
+	}
+      }
+    }
+  }
+  find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
+  # Finally, start writing the rules.
+  # Let's make a big rule to build all the docs at once, call it 'html'
+  # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
+  my @HTML = map {  # Edit beginning and end of PM files, to make HTML filenames
+    my $x = $_; # Don't want to change the original...
+    $x =~ s/\.p[lm]$/\.html/; 
+    $x =~ s/^$cur_dir/$HTML_ROOT/; 
+    $x} @PM;
+  my $postamble = "# Rules to keep developer docs up-to-date.\n";
+  $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) 
+    . "\n\nhtml: \$(POD_TO_HTML)\n";
+#  $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
+#    . "\n\nhtml:\n"; # \$(HTML_DIRS)
+#  $postamble .= "\$(HTML_DIRS):\n\tfor file in " 
+#    . join(" \\\n", @make_dirs_list) .
+#    "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
+
+  # Now, finally, we build rules for the makefile.
+  # The TAB ('\t') characters are essential,  otherwise 'make' will silently ignore the rules.
+  # Don't be tempted to remove them.
+  for (my $i = 0;  $i < @PM; $i++) {
+    $postamble .= <<RULE;
+$HTML[$i]:$PM[$i]
+	\$(NOECHO) \$(ECHO) Generating HTML for MOBY::$MOD_NAMES[$i]
+	\$(NOECHO) pod2html --htmlroot=$HTML_ROOT --outfile=$HTML[$i] $PM[$i]
+RULE
+  }
+#  print "HTML_ROOT: $HTML_ROOT\n";
+  # Auto-generate an index page, with links to the individual POD-generated pages.
+  # Make sure it works on the local filesystem.
+  # Trim HTML files down to relative paths.
+  make_index_page(\@PM ,
+		  [ map { my $x= $_; $x =~ s/^$cur_dir\///; $x} @HTML ], 
+		  \@MOD_NAMES);
+  return $postamble;
+}
+
+
+sub make_index_page {
+  # Generate an index to the auto-generated HTML docs.
+  my ($pms, $html, $mod_names) = @_;
+  open INDEX, ">index.html" or die "Couldn't open index.html ($!)";
+  print INDEX <<HEAD;
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>MOBY-S Perl Module Documentation</title>
+</head>
+<body>
+<div style="text-align: center;">
+<h1>MOBY-S Perl Modules Documentation</h1>
+</div>
+For an overview of how to do various things in Perl, see the <a href='http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial'>
+Perl Tutorial</a><p>
+The documents below (including this one) are generated by pod2html from the various perl
+modules and give specific interface information for each of the Perl modules described in the tutorial.
+
+<ul>
+HEAD
+  for (my $i = 0; $i < @{$pms}; $i++) {
+    print INDEX "<li><a href=\"$html->[$i]\">MOBY::$mod_names->[$i]</a></li>\n";
+  }
+print INDEX <<FOOT;
+</ul>
+</body>
+</html>
+FOOT
+}
+
+
+# Override built-in target, by adding the 'html' dependency
+# Now HTML gets updated every time you type "make"
+sub MY::top_targets {
+  my $self = shift;
+  my $string = $self->MM::top_targets;
+  my $add = 'html';
+  $string =~ s/\s+(pure_all)/ $add $1/;
+  return $string;
+}
+
+#sub MY::install {
+#  my $self = shift;
+#  my $string = $self->MM::install;
+#  my $add = 'html';
+#  $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
+#  print "INSTALL: $string\n";
+#  return $string;
+#}
+
+WriteMakefile(
+	      NAME	      => 'MOBY-S',
+	      VERSION	      => $VERSION, 
+	      # VERSION_FROM    => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
+	      PMLIBDIRS       => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
+	      # Version numbers specified for prerequiisites are simply "desired" versions,
+	      # not minimum, or anything else.
+	      PREREQ_PM     => {
+				'SOAP::Lite'       => 0.69,
+				'SOAP::MIME'       => 0.55,
+				'XML::LibXML'      => 1.58,
+				'XML::XPath'       => 1.12,
+				'Text::Shellwords' => 1.00,
+				'HTML::Entities'   => 0.01,
+				'Test::More'       => 0.60,
+				# Database stuff required only for local registry, but notify user if missing anyway.
+				'DBI'              => 0.01,
+				'DBD::mysql'       => 0.01,
+				'WSRF::Lite'		=> '',
+                'Test::Simple' => 0.44,
+                'XML::DOM'     => '',
+                'DateTime::Format::Epoch'  => '',
+                'DateTime::Format::W3CDTF' => '',
+                'HTTP::Daemon' => '',
+                'HTTP::Daemon::SSL' => '',
+                'MIME::Base64' => '',
+                'Digest::SHA1' => '',
+                'Crypt::OpenSSL::X509' => '',
+                'Crypt::OpenSSL::RSA' => '',
+                'XML::CanonicalizeXML' => 0.02,
+                'Sys::Hostname::Long' => '',
+			   	'RDF::Core' => '.51',
+				# Sharable only used for isAlive script
+	   			#'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
+		  	    #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
+			    #'LS' => 1.1.4,
+					 
+	    }, # e.g., Module::Name => 1.1
+	    #PM_FILTER     => "", 
+	    ($] >= 5.005 ?    ## Add these new keywords supported since 5.005
+	    (ABSTRACT      => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
+		AUTHOR        => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
+);
+
+#
+# Insert additional MOBY specific Makefile targets
+#
+# 
+#sub MY::postamble {
+#	return <<"MAKE_FRAG";
+#Central:
+#	echo 'Make (local) MOBY Central stub'
+#
+#Server:
+#	echo 'Make (local) MOBY Server stub'
+#
+#WWWClient:
+#	echo 'Setting up MOBY WWW Client'
+#	cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
+#	chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
+# 
+#MAKE_FRAG
+#}
+
+use ExtUtils::MakeMaker;
+use FindBin '$Bin';
+use strict;
+my $VERSION = '0.87';
+
+
+sub MY::postamble {
+  # Now build documentation.
+  use Pod::Find qw(pod_find simplify_name);
+  use Cwd;
+  my $cur_dir = getcwd();
+  # Find the files that contain POD, starting from the top-level build directory, and do it silently.
+  my %pods = pod_find({ -verbose => 0}, 
+		      File::Spec->catfile($cur_dir, "MOBY") );
+  my @PM = sort keys %pods;
+  my @MOD_NAMES = map {$pods{$_}} @PM;
+  # Make home for all docs
+  # If we build the home from here, it will only be built when the user runs "perl Makefile.PL"
+  # It's more robust to put it directly into the Makefile, 
+  # so that it can be rebuilt with a simple "make" if needed.
+  # But that would require figuring out how to walk a tree from the shell,
+  # and I don't have time for that. Maybe some other day.
+  my $HTML_ROOT = File::Spec->catfile($cur_dir, qw(docs html));
+  mkdir File::Spec->catfile($cur_dir, "docs") 
+    unless -e File::Spec->catfile($cur_dir, "docs");
+  mkdir $HTML_ROOT unless -e $HTML_ROOT;
+  # Create a new directory tree for the documentation, that mirrors the source tree.
+  use File::Find;
+  my @make_dirs_list;
+  sub wanted { # Define nested subroutine, to inherit variable scope
+    my $src_dir = $File::Find::dir;
+    (my $doc_dir = $src_dir) =~ s/$cur_dir/$HTML_ROOT/;
+#    print STDERR "EXamining $doc_dir\n";
+    if ( !($doc_dir =~ /CVS$/) ) {
+      push @make_dirs_list, $doc_dir # Always put into list, whether exists or not, since it goes into a rule
+	unless (grep /^$doc_dir$/, @make_dirs_list); # unless seen already
+      if (!(-e $doc_dir)) {
+	my $made_dir = mkdir $doc_dir;
+	if (!$made_dir) { 
+	  print STDERR "Couldn't create directory '$doc_dir' because '$!'"; 
+	}
+      }
+    }
+  }
+  find(\&wanted, File::Spec->catfile($cur_dir, "MOBY"));
+  # Finally, start writing the rules.
+  # Let's make a big rule to build all the docs at once, call it 'html'
+  # Then other little rules to keep each PM-file's docs up to date, without having to build everything.
+  my @HTML = map {  # Edit beginning and end of PM files, to make HTML filenames
+    my $x = $_; # Don't want to change the original...
+    $x =~ s/\.p[lm]$/\.html/; 
+    $x =~ s/^$cur_dir/$HTML_ROOT/; 
+    $x} @PM;
+  my $postamble = "# Rules to keep developer docs up-to-date.\n";
+  $postamble .= "POD_TO_HTML = " . join(" \\\n", @HTML) 
+    . "\n\nhtml: \$(POD_TO_HTML)\n";
+#  $postamble .= "\n\nHTML_DIRS = " . join(" \\\n", @make_dirs_list) . "\n";
+#    . "\n\nhtml:\n"; # \$(HTML_DIRS)
+#  $postamble .= "\$(HTML_DIRS):\n\tfor file in " 
+#    . join(" \\\n", @make_dirs_list) .
+#    "\\\n; do \\\n if [! -d \$\$file ] ; then mkdir \$\$file ; fi\\\n done\n\n";
+
+  # Now, finally, we build rules for the makefile.
+  # The TAB ('\t') characters are essential,  otherwise 'make' will silently ignore the rules.
+  # Don't be tempted to remove them.
+  for (my $i = 0;  $i < @PM; $i++) {
+    $postamble .= <<RULE;
+$HTML[$i]:$PM[$i]
+	\$(NOECHO) \$(ECHO) Generating HTML for MOBY::$MOD_NAMES[$i]
+	\$(NOECHO) pod2html --htmlroot=$HTML_ROOT --outfile=$HTML[$i] $PM[$i]
+RULE
+  }
+#  print "HTML_ROOT: $HTML_ROOT\n";
+  # Auto-generate an index page, with links to the individual POD-generated pages.
+  # Make sure it works on the local filesystem.
+  # Trim HTML files down to relative paths.
+  make_index_page(\@PM ,
+		  [ map { my $x= $_; $x =~ s/^$cur_dir\///; $x} @HTML ], 
+		  \@MOD_NAMES);
+  return $postamble;
+}
+
+
+sub make_index_page {
+  # Generate an index to the auto-generated HTML docs.
+  my ($pms, $html, $mod_names) = @_;
+  open INDEX, ">index.html" or die "Couldn't open index.html ($!)";
+  print INDEX <<HEAD;
+
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+  <meta http-equiv="content-type"
+ content="text/html; charset=ISO-8859-1">
+  <title>MOBY-S Perl Module Documentation</title>
+</head>
+<body>
+<div style="text-align: center;">
+<h1>MOBY-S Perl Modules Documentation</h1>
+</div>
+For an overview of how to do various things in Perl, see the <a href='http://biomoby.open-bio.org/index.php/for-developers/perl_tutorial'>
+Perl Tutorial</a><p>
+The documents below (including this one) are generated by pod2html from the various perl
+modules and give specific interface information for each of the Perl modules described in the tutorial.
+
+<ul>
+HEAD
+  for (my $i = 0; $i < @{$pms}; $i++) {
+    print INDEX "<li><a href=\"$html->[$i]\">MOBY::$mod_names->[$i]</a></li>\n";
+  }
+print INDEX <<FOOT;
+</ul>
+</body>
+</html>
+FOOT
+}
+
+
+# Override built-in target, by adding the 'html' dependency
+# Now HTML gets updated every time you type "make"
+sub MY::top_targets {
+  my $self = shift;
+  my $string = $self->MM::top_targets;
+  my $add = 'html';
+  $string =~ s/\s+(pure_all)/ $add $1/;
+  return $string;
+}
+
+#sub MY::install {
+#  my $self = shift;
+#  my $string = $self->MM::install;
+#  my $add = 'html';
+#  $string =~ s/(pure_install\s+)(.*)/$1 $add $2/;
+#  print "INSTALL: $string\n";
+#  return $string;
+#}
+
+WriteMakefile(
+	      NAME	      => 'MOBY-S',
+	      VERSION	      => $VERSION, 
+	      # VERSION_FROM    => Would be nicer not to have to specify the version number here, but to take it directly from the codebase....
+	      PMLIBDIRS       => ['MOBY'], #Get code from "MOBY", not "lib/MOBY"
+	      # Version numbers specified for prerequiisites are simply "desired" versions,
+	      # not minimum, or anything else.
+	      PREREQ_PM     => {
+				'SOAP::Lite'       => 0.69,
+				'SOAP::MIME'       => 0.55,
+				'XML::LibXML'      => 1.58,
+				'XML::XPath'       => 1.12,
+				'Text::Shellwords' => 1.00,
+				'HTML::Entities'   => 0.01,
+				'Test::More'       => 0.60,
+				# Database stuff required only for local registry, but notify user if missing anyway.
+				'DBI'              => 0.01,
+				'DBD::mysql'       => 0.01,
+				# 'WSRF::Lite'		=> '0.8.2.1', but it is not declared in the proper way there
+				'WSRF::Lite'		=> '',
+                 'Test::Simple' => 0.44,
+                 'XML::DOM'     => '',
+                 'DateTime::Format::Epoch'  => '',
+                 'DateTime::Format::W3CDTF' => '',
+                 'HTTP::Daemon' => '',
+                 'HTTP::Daemon::SSL' => '',
+                 'MIME::Base64' => '',
+                 'Digest::SHA1' => '',
+                 'Crypt::OpenSSL::X509' => '',
+                 'Crypt::OpenSSL::RSA' => '',
+                 'XML::CanonicalizeXML' => 0.02,
+                 'Sys::Hostname::Long' => '',
+		  		 'RDF::Core' => '.51',
+				 #Sharable only used for isAlive script
+	   			 #'IPC::Shareable' => '0.6', #presence of this lib makes windows a no no ...
+		  	     #obtain from http://sourceforge.net/project/showfiles.php?group_id=130827
+			     #'LS' => 1.1.4,
+	      }, # e.g., Module::Name => 1.1
+	      #PM_FILTER     => "", 
+	      ($] >= 5.005 ?    ## Add these new keywords supported since 5.005
+	       (ABSTRACT      => 'Perl binding for MOBY-S, a web-services toolkit for exchanging bioinformatic data',
+		AUTHOR        => 'Mark Wilkinson [markw at illuminae.com] and the BioMOBY Core Developers') : ()),
+);
+
+#
+# Insert additional MOBY specific Makefile targets
+#
+# 
+#sub MY::postamble {
+#	return <<"MAKE_FRAG";
+#Central:
+#	echo 'Make (local) MOBY Central stub'
+#
+#Server:
+#	echo 'Make (local) MOBY Server stub'
+#
+#WWWClient:
+#	echo 'Setting up MOBY WWW Client'
+#	cp scripts/MOBY-Client.cgi \$(MOBY_CGI_BIN_PATH)
+#	chown \$(MOBY_WWW_USER):\$(MOBY_WWW_GROUP) \$(MOBY_CGI_BIN_PATH)/MOBY-Client.cgi
+# 
+#MAKE_FRAG
+#}
+



From kawas at dev.open-bio.org  Tue Sep 11 16:48:28 2007
From: kawas at dev.open-bio.org (Eddie Kawas)
Date: Tue, 11 Sep 2007 12:48:28 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709111648.l8BGmSoB006345@dev.open-bio.org>


kawas
Tue Sep 11 12:48:27 EDT 2007
Update of /home/repository/moby/moby-live/Java/docs
In directory dev.open-bio.org:/tmp/cvs-serv6310/Java/docs

Modified Files:
	ConfigureRDFAgent.html 
Log Message:

moby-live/Java/docs ConfigureRDFAgent.html,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2006/10/05 15:32:47	1.3
+++ /home/repository/moby/moby-live/Java/docs/ConfigureRDFAgent.html	2007/09/11 16:48:27	1.4
@@ -29,14 +29,15 @@
   using 'mail', a UNIX/Linux/*nix email client. Moreover, The agent can choose to 
   ignore those services that do not contain signature urls or to remove 
   them.</p>
-</p>
+<p></p>
 <h4>This document is broken down into the following sections: </h4>
 <ul>
   <li><a href="#getting_started">Getting Started</a></li>
   <li><a href="#configuring_the_agent">Configuring the Agent</a></li>
   <li><a href="#setting_up_a_cron_job">Setting up a Cron Job</a></li>
-  <li><a href="moby_admin_dispatcher">MOBY-Admin Dispatcher</a></li>
+  <li><a href="#moby_admin_dispatcher">MOBY-Admin Dispatcher</a></li>
   <li><a href="#uses_for_the_agent">Uses for the Agent</a></li>
+  <li><a href="#faq">FAQ</a></li>
 </ul>
 <p>&nbsp;</p>
 <h3><a name="getting_started"></a>Getting Started</h3>
@@ -86,7 +87,7 @@
       <br>
     These variable must be set for the agent to work properly with these scripts.<br>
     <br>
-    <span class="note">Also, note that it is important to place the variable <strong>JAVA_HOME</strong> in the environment of the web server you are using so that Mobycentral can access it!</span> <br>
+    <span class="note">Also, note that it is <strong>important</strong> to place the variable <strong>JAVA_HOME</strong> in the environment of the web server you are using so that Mobycentral can access it!</span> <br>
       <br>
     </li>
     <li class="dcount"> Add the path to the RDFagent to the <b class="step">[mobycentral]</b> section of your mobycentral.config file:
@@ -411,7 +412,7 @@
 </blockquote>
 <p>This file must be called '.htaccess'.<br>
   <br>
-  Assuming that the MOBY-Admin.pl file is located in the cgi-bin directory of apache, you will have to add the following line to http.conf where the cgi-bin directory is defined:</p>
+  Assuming that the MOBY-Admin.pl file is located in the cgi-bin directory of apache, you will have to add the following line to httpd.conf where the cgi-bin directory is defined:</p>
 <p> <b class="step">AllowOverride AuthConfig</b></p>
 <p> <em>i.e. </em><br>
 </p>
@@ -440,11 +441,11 @@
     file at <em><strong>/path/that/exists/</strong></em></p>
   <p><em><strong>username</strong></em> would be the newly created login name</p>
 </blockquote>
-<p>You will be prompted for a password.<br>
+<p>You will be prompted for a password.<br/>
 <p class="note"> This login name and password will have to be entered into the agents 
   configuration file. </p>
 </p>
-</p>
+<strong>Don't forget to restart apache each and every time that you modify the httpd.conf file!</strong>
 <h3><a name="uses_for_the_agent"></a>Uses for the Agent</h3>
 <p>The following are some uses for the agent:</p>
 <ol>
@@ -472,6 +473,20 @@
 </ol>
 <p><br>
   If you have any other uses for the agent, please let me know.</p>
+  
+<h3><a name="faq"></a>FAQ</h3>
+<p>Below are the frequently asked questions. If you have a question not on this list, please let me know!</p>
+<ol>
+  <li class="dcount"> I have installed everything according to this document, but when I run the agent, I get an error stating:<br/>
+    <br/>
+    <pre class=script>
+    "An empty value was found where a yes or no was expected in the config file ..."</pre>
+    <p>What did I do wrong?</p>
+    <p><strong>A.</strong><br/>First, please ensure that all of the values are filled out properly. If that wasn't the problem, then try adding the following line to the bottom of the config file:</p>
+    <pre class=script>    agent.output.flatfile = yes </pre>
+    <p>Once you have added that value to the config file, try testing the agent again.</p>
+  </li>
+</ol>
 <hr>
 <div align=right class="address">
   <address>
@@ -480,6 +495,7 @@
   <!-- hhmts start -->
   Last modified: Tue May 17 15:49:04 2005
   <!-- hhmts end -->
+  <p>$Date$</p>
 </div>
 </body>
 </html>



From mwilkinson at dev.open-bio.org  Fri Sep 14 14:55:31 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 10:55:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141455.l8EEtVkt022090@dev.open-bio.org>


mwilkinson
Fri Sep 14 10:55:31 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory dev.open-bio.org:/tmp/cvs-serv22049/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
modifying SQL layer to get more ontology information out of various calls.  Starting with the Service ontology
moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.83,1.84
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.83
retrieving revision 1.84
diff -u -r1.83 -r1.84
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/02/07 15:19:00	1.83
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 14:55:31	1.84
@@ -836,8 +836,49 @@
           service_type,
           description,
           authority,
-          contact_email
-          from service $condition";
+          contact_email,
+	  from
+	  service 
+          $condition";
+	my $result;
+	if ($type){
+	    $result = do_query($dbh, $statement, ($type));
+	} else {
+	    $result = do_query($dbh, $statement);
+	}
+ 	return $result;		
+}
+
+sub new_query_service{
+	my ($self, %args) = @_;
+	my $type = $args{type};
+	my $condition = "";
+	if ($type =~ /^urn\:lsid/){
+	    $condition = "where s1.service_lsid = ?";
+	} elsif ($type) {
+	    $condition = "where s1.service_type = ?";
+	} else {
+	    $condition = "";
+	}
+	
+	my $dbh = _getDBHandle("mobyservice");
+
+	my $statement = "select
+	  s1.service_id, 
+          s1.service_lsid,
+          s1.service_type,
+          s1.description,
+          s1.authority,
+          s1.contact_email,
+	  s2.service_type,
+	  s2.service_lsid 
+          from
+	  service as s1
+	  left join service_term2term as t
+	    on s1.service_id= t.service1_id
+	left join service as s2
+	on s2.service_id=t.service2_id
+        $condition";
 	my $result;
 	if ($type){
 	    $result = do_query($dbh, $statement, ($type));
@@ -847,6 +888,8 @@
  	return $result;		
 }
 
+
+
 # pass in ....
 sub insert_service{
 	my ($self, %args) = @_;	



From mwilkinson at dev.open-bio.org  Fri Sep 14 14:55:31 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 10:55:31 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141455.l8EEtV89022072@dev.open-bio.org>


mwilkinson
Fri Sep 14 10:55:30 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22049/MOBY

Modified Files:
	Central.pm OntologyServer.pm 
Log Message:
modifying SQL layer to get more ontology information out of various calls.  Starting with the Service ontology
moby-live/Perl/MOBY Central.pm,1.286,1.287 OntologyServer.pm,1.102,1.103
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.286
retrieving revision 1.287
diff -u -r1.286 -r1.287
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/08/28 22:43:16	1.286
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 14:55:30	1.287
@@ -2712,7 +2712,7 @@
 	my %types = %{ $OS->retrieveAllServiceTypes() };
 	my $types = "<serviceTypes>\n";
 	while ( my ( $serv, $descr ) = each %types ) { #UNCOMMENT
-		my ($desc, $lsid, $contact, $auth) = @$descr;
+		my ($desc, $lsid, $contact, $auth, $isa_type, $isa_lsid) = @$descr;
 		if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
 			$desc = $1;
 		}

===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.102
retrieving revision 1.103
diff -u -r1.102 -r1.103
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/01/30 14:49:20	1.102
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/09/14 14:55:30	1.103
@@ -1002,11 +1002,11 @@
 	my ($self) = @_;
 	$CONFIG ||= MOBY::Config->new;    # exported by Config.pm
 	my $adaptor = $CONFIG->getDataAdaptor( datasource => 'mobyservice' );
-	my $types = $adaptor->query_service();
+	my $types = $adaptor->new_query_service();
 
 	my %response;
 	foreach (@$types) {
-		$response{ $_->{service_type} } = [$_->{description}, $_->{service_lsid}, $_->{contact_email}, $_->{authority}]; #UNCOMMENT
+		$response{ $_->{'s1.service_type'} } = [$_->{'s1.description'}, $_->{'s1.service_lsid'}, $_->{'s1.contact_email'}, $_->{'s1.authority'}, $_->{'s2.service_type'}, $_->{'s2.service_lsid'}]; #UNCOMMENT
 	}
 	return \%response;
 }



From mwilkinson at dev.open-bio.org  Fri Sep 14 16:04:21 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:04:21 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141604.l8EG4L9d022468@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:04:20 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory dev.open-bio.org:/tmp/cvs-serv22449/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
doh.  Extra comma removed from sql query
moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.84,1.85
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.84
retrieving revision 1.85
diff -u -r1.84 -r1.85
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 14:55:31	1.84
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 16:04:20	1.85
@@ -836,7 +836,7 @@
           service_type,
           description,
           authority,
-          contact_email,
+          contact_email
 	  from
 	  service 
           $condition";



From mwilkinson at dev.open-bio.org  Fri Sep 14 16:26:50 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:26:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141626.l8EGQog9022559@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:26:50 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi
In directory dev.open-bio.org:/tmp/cvs-serv22520/MOBY/Adaptor/moby/queryapi

Modified Files:
	mysql.pm 
Log Message:
proper naming of columns
moby-live/Perl/MOBY/Adaptor/moby/queryapi mysql.pm,1.85,1.86
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm,v
retrieving revision 1.85
retrieving revision 1.86
diff -u -r1.85 -r1.86
--- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 16:04:20	1.85
+++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/queryapi/mysql.pm	2007/09/14 16:26:50	1.86
@@ -818,7 +818,7 @@
 # pass service_type, as term or LSID
 sub query_service{
 	my ($self, %args) = @_;
-	my $type = $args{type};
+	my $type = $args{type}||"";
 	my $condition = "";
 	if ($type =~ /^urn\:lsid/){
 	    $condition = "where service_lsid = ?";
@@ -851,7 +851,7 @@
 
 sub new_query_service{
 	my ($self, %args) = @_;
-	my $type = $args{type};
+	my $type = $args{type}||"";
 	my $condition = "";
 	if ($type =~ /^urn\:lsid/){
 	    $condition = "where s1.service_lsid = ?";
@@ -864,14 +864,14 @@
 	my $dbh = _getDBHandle("mobyservice");
 
 	my $statement = "select
-	  s1.service_id, 
-          s1.service_lsid,
-          s1.service_type,
-          s1.description,
-          s1.authority,
-          s1.contact_email,
-	  s2.service_type,
-	  s2.service_lsid 
+	  s1.service_id as service_id, 
+          s1.service_lsid as service_lsid,
+          s1.service_type as service_type,
+          s1.description as description,
+          s1.authority as authority,
+          s1.contact_email as contact_email,
+	  s2.service_type as parent_type,
+	  s2.service_lsid as parent_lsid  
           from
 	  service as s1
 	  left join service_term2term as t



From mwilkinson at dev.open-bio.org  Fri Sep 14 16:26:50 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:26:50 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141626.l8EGQojL022539@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:26:50 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22520/MOBY

Modified Files:
	OntologyServer.pm 
Log Message:
proper naming of columns
moby-live/Perl/MOBY OntologyServer.pm,1.103,1.104
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm,v
retrieving revision 1.103
retrieving revision 1.104
diff -u -r1.103 -r1.104
--- /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/09/14 14:55:30	1.103
+++ /home/repository/moby/moby-live/Perl/MOBY/OntologyServer.pm	2007/09/14 16:26:50	1.104
@@ -1006,7 +1006,7 @@
 
 	my %response;
 	foreach (@$types) {
-		$response{ $_->{'s1.service_type'} } = [$_->{'s1.description'}, $_->{'s1.service_lsid'}, $_->{'s1.contact_email'}, $_->{'s1.authority'}, $_->{'s2.service_type'}, $_->{'s2.service_lsid'}]; #UNCOMMENT
+		$response{ $_->{'service_type'} } = [$_->{'description'}, $_->{'service_lsid'}, $_->{'contact_email'}, $_->{'authority'}, $_->{'parent_type'}, $_->{'parent_lsid'}]; #UNCOMMENT
 	}
 	return \%response;
 }



From mwilkinson at dev.open-bio.org  Fri Sep 14 16:53:04 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:53:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141653.l8EGr4SJ022693@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:53:04 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22674/MOBY

Modified Files:
	Central.pm 
Log Message:
get info out of XML in client central
moby-live/Perl/MOBY Central.pm,1.287,1.288
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.287
retrieving revision 1.288
diff -u -r1.287 -r1.288
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 14:55:30	1.287
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 16:53:04	1.288
@@ -2695,10 +2695,11 @@
  Args      :	none
  XML       :
 	<serviceTypes>
-	   <serviceType name="serviceName" lsid="urn:lsid...">
+	   <serviceType name="serviceTypeName" lsid="urn:lsid...">
 		  <Description><![CDATA[free text description here]]></Description>
 		  <contactEmail>your at email.here</contactEmail>
 		  <authURI>authority.uri.here</authURI>
+		  <ISA lsid="urn:lsid...">parentTypeName</ISA>  <!-- empty for root! -->
 	   </serviceType>
 		...
 		...
@@ -2716,7 +2717,14 @@
 		if ( $desc =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
 			$desc = $1;
 		}
-		$types .="<serviceType name='$serv' lsid='$lsid'>\n<Description><![CDATA[$desc]]></Description>\n<contactEmail>$contact</contactEmail>\n<authURI>$auth</authURI>\n</serviceType>\n"; #UNCOMMENT
+		$isa_type ||="";
+		$isa_lsid ||="";
+		$types .="<serviceType name='$serv' lsid='$lsid'>
+		<Description><![CDATA[$desc]]></Description>
+		<contactEmail>$contact</contactEmail>
+		<authURI>$auth</authURI>
+		<ISA lsid='$isa_lsid'>$isa_type</ISA>
+		</serviceType>\n"; #UNCOMMENT
 	}
 	$types .= "</serviceTypes>\n";
 	return $types;



From mwilkinson at dev.open-bio.org  Fri Sep 14 16:53:04 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 12:53:04 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141653.l8EGr40M022713@dev.open-bio.org>


mwilkinson
Fri Sep 14 12:53:04 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv22674/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
get info out of XML in client central
moby-live/Perl/MOBY/Client Central.pm,1.149,1.150
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.149
retrieving revision 1.150
diff -u -r1.149 -r1.150
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/07/31 12:29:15	1.149
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 16:53:04	1.150
@@ -1338,7 +1338,7 @@
 		} else {
 		    $lsid = $type;
 		}
-		my ($desc, $auth, $email);
+		my ($desc, $auth, $email, $ISA, $ISA_LSID) = ("","","","","");
 		for
 		  my $elem ( $types->get_node($x)->getElementsByTagName('Description') )
 		{
@@ -1363,8 +1363,18 @@
 				$email = $1;
 			}
 		}
+				for
+		  my $elem ( $types->get_node($x)->getElementsByTagName('ISA') )
+		{
+			$ISA = $elem->firstChild->toString;
+			if ( $email =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
+				$email = $1;
+			}
+			$ISA_LSID = $elem->getAttributeNode('lsid')->getValue;
+		}
+
 		$desc =~ s/<!\[CDATA\[((?>[^\]]+))\]\]>/$1/gs;  # somehow these CDATA elements are nested sometimes???
-		$servicetypes{$as_lsid?$lsid:$type} = {Description => $desc, authURI => $auth, contactEmail => $email};
+		$servicetypes{$as_lsid?$lsid:$type} = {Description => $desc, authURI => $auth, contactEmail => $email, ISA => $ISA, ISA_LSID => $ISA_LSID};
 	}
 	return \%servicetypes;
 }



From mwilkinson at dev.open-bio.org  Fri Sep 14 17:02:24 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 13:02:24 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141702.l8EH2Oe4022790@dev.open-bio.org>


mwilkinson
Fri Sep 14 13:02:24 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv22771/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
get info out of XML in client central
moby-live/Perl/MOBY/Client Central.pm,1.150,1.151
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.150
retrieving revision 1.151
diff -u -r1.150 -r1.151
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 16:53:04	1.150
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 17:02:24	1.151
@@ -1363,10 +1363,11 @@
 				$email = $1;
 			}
 		}
-				for
+		for
 		  my $elem ( $types->get_node($x)->getElementsByTagName('ISA') )
 		{
-			$ISA = $elem->firstChild->toString;
+			$ISA = $elem->firstChild;
+			$ISA = $ISA?$ISA->toString:"";
 			if ( $email =~ /<!\[CDATA\[((?>[^\]]+))\]\]>/ ) {
 				$email = $1;
 			}



From mwilkinson at dev.open-bio.org  Fri Sep 14 17:23:47 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 13:23:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141723.l8EHNlEx022863@dev.open-bio.org>


mwilkinson
Fri Sep 14 13:23:47 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22844/MOBY

Modified Files:
	Central.pm 
Log Message:
update docs
moby-live/Perl/MOBY Central.pm,1.288,1.289
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.288
retrieving revision 1.289
diff -u -r1.288 -r1.289
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 16:53:04	1.288
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 17:23:47	1.289
@@ -2699,7 +2699,7 @@
 		  <Description><![CDATA[free text description here]]></Description>
 		  <contactEmail>your at email.here</contactEmail>
 		  <authURI>authority.uri.here</authURI>
-		  <ISA lsid="urn:lsid...">parentTypeName</ISA>  <!-- empty for root! -->
+		  <ISA lsid="urn:lsid...">parentTypeName</ISA>  <!-- both empty for root Service! -->
 	   </serviceType>
 		...
 		...



From mwilkinson at dev.open-bio.org  Fri Sep 14 17:23:47 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 13:23:47 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141723.l8EHNl9f022883@dev.open-bio.org>


mwilkinson
Fri Sep 14 13:23:47 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Client
In directory dev.open-bio.org:/tmp/cvs-serv22844/MOBY/Client

Modified Files:
	Central.pm 
Log Message:
update docs
moby-live/Perl/MOBY/Client Central.pm,1.151,1.152
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm,v
retrieving revision 1.151
retrieving revision 1.152
diff -u -r1.151 -r1.152
--- /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 17:02:24	1.151
+++ /home/repository/moby/moby-live/Perl/MOBY/Client/Central.pm	2007/09/14 17:23:47	1.152
@@ -1307,7 +1307,9 @@
  Function  :	get all details of all service types
  Returns   :	hashref of $types{$type} = {Description => "definition",
                                             authURI  => "authority.uri.here",
-					    contactEmail => "email at addy.here"}
+					    contactEmail => "email at addy.here",
+					    ISA => "parentType", # possibly empty string ""
+					    ISA_LSID => "urn:lsid...parentLSID"} # possibly empty string ""
  Args      :	registry => $reg_name:  name of registry you wish to retrieve from (optional)
                 as_lsid  => $boolean:  return the $type as its corresponding LSID (defualt off)
 



From mwilkinson at dev.open-bio.org  Fri Sep 14 17:33:12 2007
From: mwilkinson at dev.open-bio.org (Mark Wilkinson)
Date: Fri, 14 Sep 2007 13:33:12 -0400
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709141733.l8EHXCn0022937@dev.open-bio.org>


mwilkinson
Fri Sep 14 13:33:12 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv22918/MOBY

Modified Files:
	Central.pm 
Log Message:
update docs
moby-live/Perl/MOBY Central.pm,1.289,1.290
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.289
retrieving revision 1.290
diff -u -r1.289 -r1.290
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 17:23:47	1.289
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 17:33:12	1.290
@@ -2703,7 +2703,7 @@
 	   </serviceType>
 		...
 		...
-	</serviceNames>
+	</serviceTypes>
 
 =cut
 



From jmrc at dev.open-bio.org  Mon Sep 24 18:53:37 2007
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 24 Sep 2007 18:53:37 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709241853.l8OIrWMa019938@dev.open-bio.org>


jmrc
Mon Sep 24 14:53:32 EDT 2007
Update of /home/repository/moby/moby-live/Perl
In directory dev.open-bio.org:/tmp/cvs-serv19902/Perl

Modified Files:
	Makefile.PL 
Log Message:
*	Latest WSRF::Lite package has a proper VERSION declaration,
	so we can restrict the version of the package to the one
	which is known to work.
*	WSRF::Lite is not in CPAN, so we have added a warning about
	where it can be fetched/found (beware older versions!).
*	Asynchronous WSDL template has now UTF-8 encoding. Previously,
	it had no encoding...
*	New WSRF::Lite (version 0.8.2.2) allows removing some hacks
	from MOBY::Async::WSRF.

moby-live/Perl Makefile.PL,1.30,1.31
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v
retrieving revision 1.30
retrieving revision 1.31
diff -u -r1.30 -r1.31
--- /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/04 22:28:14	1.30
+++ /home/repository/moby/moby-live/Perl/Makefile.PL	2007/09/24 18:53:32	1.31
@@ -29,6 +29,31 @@
 
 }
 
+eval "require WSRF::Lite";
+if ($@) {
+	print STDOUT <<'EOF_WSRF';
+	
+############## IMPORTANT ##############
+Module 'WSRF::Lite' is not installed.
+This module is used **only** if you are thinking on
+developing BioMOBY Asynchronous service.
+
+Unfortunately, this module is not available on CPAN 
+and must be manually installed. Some of the 
+dependencies are beta and as such, may not be stable.
+
+Try downloading it from the following link:
+
+http://www.rcs.manchester.ac.uk/research/projects/wsrflite
+
+or you can try searching Google using the keywords:
+
+	'perl WSRF::Lite' 
+
+(beware outdated sites!)
+EOF_WSRF
+}
+
 sub MY::postamble {
   # Now build documentation.
   use Pod::Find qw(pod_find simplify_name);
@@ -178,7 +203,7 @@
 				# Database stuff required only for local registry, but notify user if missing anyway.
 				'DBI'              => 0.01,
 				'DBD::mysql'       => 0.01,
-				'WSRF::Lite'		=> '',
+				'WSRF::Lite'       => 0.8.2.2,
                 'Test::Simple' => 0.44,
                 'XML::DOM'     => '',
                 'DateTime::Format::Epoch'  => '',



From jmrc at dev.open-bio.org  Mon Sep 24 18:53:40 2007
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 24 Sep 2007 18:53:40 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709241853.l8OIrWCh019958@dev.open-bio.org>


jmrc
Mon Sep 24 14:53:32 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY
In directory dev.open-bio.org:/tmp/cvs-serv19902/Perl/MOBY

Modified Files:
	Central.pm 
Log Message:
*	Latest WSRF::Lite package has a proper VERSION declaration,
	so we can restrict the version of the package to the one
	which is known to work.
*	WSRF::Lite is not in CPAN, so we have added a warning about
	where it can be fetched/found (beware older versions!).
*	Asynchronous WSDL template has now UTF-8 encoding. Previously,
	it had no encoding...
*	New WSRF::Lite (version 0.8.2.2) allows removing some hacks
	from MOBY::Async::WSRF.

moby-live/Perl/MOBY Central.pm,1.290,1.291
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Central.pm,v
retrieving revision 1.290
retrieving revision 1.291
diff -u -r1.290 -r1.291
--- /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/14 17:33:12	1.290
+++ /home/repository/moby/moby-live/Perl/MOBY/Central.pm	2007/09/24 18:53:32	1.291
@@ -4123,7 +4123,7 @@
 # for MOBY Asynchronous services.  This WSDL is not correct YET!
 
 $WSDL_ASYNC_TEMPLATE = <<END;
-<?xml version="1.0"?>
+<?xml version="1.0" encoding="UTF-8"?>
 <wsdl:definitions name="MOBY_Central_Generated_WSDL" targetNamespace="http://biomoby.org/Central.wsdl"
    xmlns:tns="http://biomoby.org/Central.wsdl"
    xmlns:xsd1="http://biomoby.org/CentralXSDs.xsd"



From jmrc at dev.open-bio.org  Mon Sep 24 18:53:43 2007
From: jmrc at dev.open-bio.org (José Manuel Rodríguez Carrasco)
Date: Mon, 24 Sep 2007 18:53:43 -0000
Subject: [MOBY-guts] biomoby commit
Message-ID: <200709241853.l8OIrXSm019980@dev.open-bio.org>


jmrc
Mon Sep 24 14:53:32 EDT 2007
Update of /home/repository/moby/moby-live/Perl/MOBY/Async
In directory dev.open-bio.org:/tmp/cvs-serv19902/Perl/MOBY/Async

Modified Files:
	WSRF.pm 
Log Message:
*	Latest WSRF::Lite package has a proper VERSION declaration,
	so we can restrict the version of the package to the one
	which is known to work.
*	WSRF::Lite is not in CPAN, so we have added a warning about
	where it can be fetched/found (beware older versions!).
*	Asynchronous WSDL template has now UTF-8 encoding. Previously,
	it had no encoding...
*	New WSRF::Lite (version 0.8.2.2) allows removing some hacks
	from MOBY::Async::WSRF.

moby-live/Perl/MOBY/Async WSRF.pm,1.3,1.4
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/MOBY/Async/WSRF.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -u -r1.3 -r1.4
--- /home/repository/moby/moby-live/Perl/MOBY/Async/WSRF.pm	2007/07/18 10:47:24	1.3
+++ /home/repository/moby/moby-live/Perl/MOBY/Async/WSRF.pm	2007/09/24 18:53:32	1.4
@@ -27,7 +27,7 @@
 
 package MOBY::Async::WSRF;
 use strict;
-use WSRF::Lite;
+use WSRF::Lite 0.8.2.2;
 
 $WSRF::WSRP::Private{queryIDs} = [];
 $WSRF::WSRP::MobyPrivatePrefixes    = ['pid', 'input'];
@@ -36,12 +36,12 @@
 $WSRF::Constants::Data  = '/tmp/moby_';
 $WSRF::Constants::MOBY  = 'http://biomoby.org/';
 $WSRF::Constants::MOBY_MESSAGE_NS  = 'http://www.biomoby.org/moby';
-$WSRF::Constants::WSA   = 'http://www.w3.org/2005/08/addressing';
-$WSRF::Constants::WSRP  = 'http://docs.oasis-open.org/wsrf/rp-2';
-$WSRF::Constants::WSRL  = 'http://docs.oasis-open.org/wsrf/rl-2';
-$WSRF::Constants::WSSG  = 'http://docs.oasis-open.org/wsrf/sg-2';
-$WSRF::Constants::WSBF  = 'http://docs.oasis-open.org/wsrf/bf-2';
-$WSRF::Constants::WSA_ANON = 'http://www.w3.org/2005/08/addressing/anonymous';
+#$WSRF::Constants::WSA   = 'http://www.w3.org/2005/08/addressing';
+#$WSRF::Constants::WSRP  = 'http://docs.oasis-open.org/wsrf/rp-2';
+#$WSRF::Constants::WSRL  = 'http://docs.oasis-open.org/wsrf/rl-2';
+#$WSRF::Constants::WSSG  = 'http://docs.oasis-open.org/wsrf/sg-2';
+#$WSRF::Constants::WSBF  = 'http://docs.oasis-open.org/wsrf/bf-2';
+#$WSRF::Constants::WSA_ANON = 'http://www.w3.org/2005/08/addressing/anonymous';
 
 #===============================================================================
 # WSRF::Serializer