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++) {
- $postamble .= <index.html" or die "Couldn't open index.html ($!)";
- print INDEX <
-
-
-
- MOBY-S Perl Module Documentation
-
-
-
-
MOBY-S Perl Modules Documentation
-
-For an overview of how to do various things in Perl, see the
-Perl Tutorial
-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.
-
-
-HEAD
- for (my $i = 0; $i < @{$pms}; $i++) {
- print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
- }
-print INDEX <
-
-
-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++) {
- $postamble .= <index.html" or die "Couldn't open index.html ($!)";
- print INDEX <
-
-
-
- MOBY-S Perl Module Documentation
-
-
-
-
MOBY-S Perl Modules Documentation
-
-For an overview of how to do various things in Perl, see the
-Perl Tutorial
-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.
-
-
-HEAD
- for (my $i = 0; $i < @{$pms}; $i++) {
- print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
- }
-print INDEX <
-
-
-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++) {
+ $postamble .= <index.html" or die "Couldn't open index.html ($!)";
+ print INDEX <
+
+
+
+ MOBY-S Perl Module Documentation
+
+
+
+
MOBY-S Perl Modules Documentation
+
+For an overview of how to do various things in Perl, see the
+Perl Tutorial
+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.
+
+
+HEAD
+ for (my $i = 0; $i < @{$pms}; $i++) {
+ print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
+ }
+print INDEX <
+
+
+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++) {
+ $postamble .= <index.html" or die "Couldn't open index.html ($!)";
+ print INDEX <
+
+
+
+ MOBY-S Perl Module Documentation
+
+
+
+
MOBY-S Perl Modules Documentation
+
+For an overview of how to do various things in Perl, see the
+Perl Tutorial
+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.
+
+
+HEAD
+ for (my $i = 0; $i < @{$pms}; $i++) {
+ print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
+ }
+print INDEX <
+
+
+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.
-
+
This document is broken down into the following sections:
Getting Started
@@ -86,7 +87,7 @@
These variable must be set for the agent to work properly with these scripts.
- Also, note that it is important to place the variable JAVA_HOME in the environment of the web server you are using so that Mobycentral can access it!
+ Also, note that it is important to place the variable JAVA_HOME in the environment of the web server you are using so that Mobycentral can access it!
Add the path to the RDFagent to the [mobycentral] section of your mobycentral.config file:
@@ -411,7 +412,7 @@
This file must be called '.htaccess'.
- 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:
+ 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:
AllowOverride AuthConfig
i.e.
@@ -440,11 +441,11 @@
file at /path/that/exists/
username would be the newly created login name
-You will be prompted for a password.
+
You will be prompted for a password.
This login name and password will have to be entered into the agents
configuration file.
-
+Don't forget to restart apache each and every time that you modify the httpd.conf file!
Uses for the Agent
The following are some uses for the agent:
@@ -472,6 +473,20 @@
If you have any other uses for the agent, please let me know.
+
+FAQ
+Below are the frequently asked questions. If you have a question not on this list, please let me know!
+
+ - I have installed everything according to this document, but when I run the agent, I get an error stating:
+
+
+ "An empty value was found where a yes or no was expected in the config file ..."
+ What did I do wrong?
+ A.
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:
+ agent.output.flatfile = yes
+ Once you have added that value to the config file, try testing the agent again.
+
+
@@ -480,6 +495,7 @@
Last modified: Tue May 17 15:49:04 2005
+ $Date$
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 = "\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 =~ /[^\]]+))\]\]>/ ) {
$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 :
-
+
your at email.here
authority.uri.here
+ parentTypeName
...
...
@@ -2716,7 +2717,14 @@
if ( $desc =~ /[^\]]+))\]\]>/ ) {
$desc = $1;
}
- $types .="\n\n$contact\n$auth\n\n"; #UNCOMMENT
+ $isa_type ||="";
+ $isa_lsid ||="";
+ $types .="
+
+ $contact
+ $auth
+ $isa_type
+ \n"; #UNCOMMENT
}
$types .= "\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 =~ /[^\]]+))\]\]>/ ) {
+ $email = $1;
+ }
+ $ISA_LSID = $elem->getAttributeNode('lsid')->getValue;
+ }
+
$desc =~ s/[^\]]+))\]\]>/$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 =~ /[^\]]+))\]\]>/ ) {
$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 @@
your at email.here
authority.uri.here
- parentTypeName
+ parentTypeName
...
...
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 @@
...
...
-
+
=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 = <
+
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++) {
- $postamble .= <index.html" or die "Couldn't open index.html ($!)";
- print INDEX <
-
-
-
- MOBY-S Perl Module Documentation
-
-
-
-
MOBY-S Perl Modules Documentation
-
-For an overview of how to do various things in Perl, see the
-Perl Tutorial
-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.
-
-
-HEAD
- for (my $i = 0; $i < @{$pms}; $i++) {
- print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
- }
-print INDEX <
-
-
-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++) {
- $postamble .= <index.html" or die "Couldn't open index.html ($!)";
- print INDEX <
-
-
-
- MOBY-S Perl Module Documentation
-
-
-
-
MOBY-S Perl Modules Documentation
-
-For an overview of how to do various things in Perl, see the
-Perl Tutorial
-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.
-
-
-HEAD
- for (my $i = 0; $i < @{$pms}; $i++) {
- print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
- }
-print INDEX <
-
-
-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++) {
+ $postamble .= <index.html" or die "Couldn't open index.html ($!)";
+ print INDEX <
+
+
+
+ MOBY-S Perl Module Documentation
+
+
+
+
MOBY-S Perl Modules Documentation
+
+For an overview of how to do various things in Perl, see the
+Perl Tutorial
+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.
+
+
+HEAD
+ for (my $i = 0; $i < @{$pms}; $i++) {
+ print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
+ }
+print INDEX <
+
+
+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++) {
+ $postamble .= <index.html" or die "Couldn't open index.html ($!)";
+ print INDEX <
+
+
+
+ MOBY-S Perl Module Documentation
+
+
+
+
MOBY-S Perl Modules Documentation
+
+For an overview of how to do various things in Perl, see the
+Perl Tutorial
+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.
+
+
+HEAD
+ for (my $i = 0; $i < @{$pms}; $i++) {
+ print INDEX "- [$i]\">MOBY::$mod_names->[$i]
\n";
+ }
+print INDEX <
+
+
+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.
-
+
This document is broken down into the following sections:
Getting Started
@@ -86,7 +87,7 @@
These variable must be set for the agent to work properly with these scripts.
- Also, note that it is important to place the variable JAVA_HOME in the environment of the web server you are using so that Mobycentral can access it!
+ Also, note that it is important to place the variable JAVA_HOME in the environment of the web server you are using so that Mobycentral can access it!
Add the path to the RDFagent to the [mobycentral] section of your mobycentral.config file:
@@ -411,7 +412,7 @@
This file must be called '.htaccess'.
- 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:
+ 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:
AllowOverride AuthConfig
i.e.
@@ -440,11 +441,11 @@
file at /path/that/exists/
username would be the newly created login name
-You will be prompted for a password.
+
You will be prompted for a password.
This login name and password will have to be entered into the agents
configuration file.
-
+Don't forget to restart apache each and every time that you modify the httpd.conf file!
Uses for the Agent
The following are some uses for the agent:
@@ -472,6 +473,20 @@
If you have any other uses for the agent, please let me know.
+
+FAQ
+Below are the frequently asked questions. If you have a question not on this list, please let me know!
+
+ - I have installed everything according to this document, but when I run the agent, I get an error stating:
+
+
+ "An empty value was found where a yes or no was expected in the config file ..."
+ What did I do wrong?
+ A.
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:
+ agent.output.flatfile = yes
+ Once you have added that value to the config file, try testing the agent again.
+
+
@@ -480,6 +495,7 @@
Last modified: Tue May 17 15:49:04 2005
+ $Date$
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 = "\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 =~ /[^\]]+))\]\]>/ ) {
$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 :
-
+
your at email.here
authority.uri.here
+ parentTypeName
...
...
@@ -2716,7 +2717,14 @@
if ( $desc =~ /[^\]]+))\]\]>/ ) {
$desc = $1;
}
- $types .="\n\n$contact\n$auth\n\n"; #UNCOMMENT
+ $isa_type ||="";
+ $isa_lsid ||="";
+ $types .="
+
+ $contact
+ $auth
+ $isa_type
+ \n"; #UNCOMMENT
}
$types .= "\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 =~ /[^\]]+))\]\]>/ ) {
+ $email = $1;
+ }
+ $ISA_LSID = $elem->getAttributeNode('lsid')->getValue;
+ }
+
$desc =~ s/[^\]]+))\]\]>/$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 =~ /[^\]]+))\]\]>/ ) {
$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 @@
your at email.here
authority.uri.here
- parentTypeName
+ parentTypeName
...
...
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 @@
...
...
-
+
=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 = <
+
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