From pieter at dev.open-bio.org Sun Dec 2 12:15:49 2007 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Sun, 2 Dec 2007 12:15:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200712021715.lB2HFnaS010440@dev.open-bio.org> pieter Sun Dec 2 12:15:49 EST 2007 Update of /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl In directory dev.open-bio.org:/tmp/cvs-serv10387/Perl/MOBY/Adaptor/moby/Impl Modified Files: FetaQueryAdaptor.pm Log Message: Removed redundancy from Makefile.PL. Fixed small POD errors in FetaQueryAdaptor.pm, MobyException.pm and MobyExceptionCodes.pm moby-live/Perl/MOBY/Adaptor/moby/Impl FetaQueryAdaptor.pm,1.1,1.2 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm,v retrieving revision 1.1 retrieving revision 1.2 diff -u -r1.1 -r1.2 --- /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm 2005/08/03 16:33:55 1.1 +++ /home/repository/moby/moby-live/Perl/MOBY/Adaptor/moby/Impl/FetaQueryAdaptor.pm 2007/12/02 17:15:49 1.2 @@ -3,6 +3,15 @@ use vars qw(@ISA); use XML::LibXML; @ISA = qw{MOBY::Adaptor::moby::DataAdapterI}; # implements the interface + +=head1 NAME + +MOBY::Adaptor::moby::impl::FetaQueryAdaptor.pm - FetaQueryAdaptor + +=head1 DESCRIPTION + +Todo + =head2 _queryServiceInstanceHash Title : _queryServiceInstanceHash @@ -21,6 +30,7 @@ description => String, signatureURL => String, lsid => String} + =cut sub queryServiceInstanceHash { From pieter at dev.open-bio.org Sun Dec 2 12:15:49 2007 From: pieter at dev.open-bio.org (Pieter Neerincs) Date: Sun, 2 Dec 2007 12:15:49 -0500 Subject: [MOBY-guts] biomoby commit Message-ID: <200712021715.lB2HFnmg010422@dev.open-bio.org> pieter Sun Dec 2 12:15:49 EST 2007 Update of /home/repository/moby/moby-live/Perl In directory dev.open-bio.org:/tmp/cvs-serv10387/Perl Modified Files: Makefile.PL Log Message: Removed redundancy from Makefile.PL. Fixed small POD errors in FetaQueryAdaptor.pm, MobyException.pm and MobyExceptionCodes.pm moby-live/Perl Makefile.PL,1.31,1.32 =================================================================== RCS file: /home/repository/moby/moby-live/Perl/Makefile.PL,v retrieving revision 1.31 retrieving revision 1.32 diff -u -r1.31 -r1.32 --- /home/repository/moby/moby-live/Perl/Makefile.PL 2007/09/24 18:53:32 1.31 +++ /home/repository/moby/moby-live/Perl/Makefile.PL 2007/12/02 17:15:49 1.32 @@ -248,205 +248,3 @@ # #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. - -