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#!/usr/bin/perl
#
=head1 NAME
authors.pl - check modules and scripts for authors not in AUTHORS file
=head1 SYNOPSIS
B<authors.pl> [B<-d|--dir> path ] [B<-v|--verbose>] B<-a|--authorsfile>
[B<-?|-h|--help>]
=head1 DESCRIPTION
Checks Plain Old Documentation (POD) of all bioperl live modules for
AUTHORS and CONTRIBUTORS tags and prints out any emails missing from
the AUTHORS file
=cut
use Data::Dumper;
use File::Find;
use Getopt::Long;
use strict;
sub findauthors;
#
# command line options
#
my ($verbose, $dir, $authorsfile, $help) = (0, undef, "../AUTHORS", undef);
GetOptions(
'v|verbose' => \$verbose,
'dir:s' => \$dir,
'authorsfile:s' => \$authorsfile,
'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
);
#
# global variables
#
# known authors from the AUTHORS file are read into
# the hash which is initialized with known synonymes
our %AUTHORS = map {$_=>1} qw{
birney@sanger.ac.uk
jinsana@gmx.net
Insana@ebi.ac.uk
fugui@worf.fugu-sg.org
cjm@fruitfly.bdgp.berkeley.edu
elia@tll.org.sg
heikki-at-bioperl-dot-org
bioinformatics@dieselwurks.com
bioinformatics1@dieselwurks.com
bioperl-l@bio.perl.org
paul@systemsbiology.org
gattiker@isb-sib.ch
elia@fugu-sg.org
jason@cgt.mc.duke.edu
jason@chg.mc.duke.edu
jason@open-bio.org
hilmar.lapp@pharma.novartis.com
richard.adams@ed.ac.uk
dblock@gene.pbi.nrc.ca
ak@ebi.ac.uk
day@cshl.org
bala@tll.org.sg
mrp@sanger.ac.uk
m.w.e.j.fiers@plant.wag-ur.nl
cmzmasek@yahoo.com
fuguteam@fugu-sg.org
shawnh@gmx.net
};
our %NEWAUTHORS; # new authors
our %FIND_OPTIONS = ( wanted => \&findauthors, no_chdir => 1 );
# Directories to check
my @dirs = qw( ../Bio/ ../scripts . );
#print Dumper \%AUTHORS;
#
# Read the AUTHORS file
#
open (F, $authorsfile) || die "can't open file $authorsfile: $!";
while (<F>) {
my ($email) = /([\.\w_-]+ at [\.\w_-]+)/;
next unless $email;
#print $email, "\n";
$email =~ s/ at /@/;
$AUTHORS{$email} = 1;
}
close F;
#
# run
#
if ($dir) {
find \%FIND_OPTIONS, $dir;
} else {
find \%FIND_OPTIONS, @dirs;
}
#
# results
#
print Dumper \%NEWAUTHORS;
#
##
### end main
##
#
#
# this is where the action is
#
sub findauthors {
return unless /\.PLS$/ or /\.p[ml]$/ ;
return unless -e $_;
print "$_\n" if $verbose;
my $filename = $_;
#local $/=undef;
open F, $_ || die "Could not open file $_";
while (<F>) {
#print;
last if /=head1 +AUTHOR/;
}
my $authorblock;
while (<F>) {
last if /=head/ and not /CONTRIBUTORS/;
$authorblock .= $_;
}
return unless $authorblock;
while ( $authorblock =~ /([\.\w_-]+@[\.a-z_-]+)/g) {
#my $email = $1;
#$email =~ //
next if $AUTHORS{$1};
#print "$filename\t$1\n";
push @{$NEWAUTHORS{$1}}, $filename;
}
}
=head1 OPTIONS
=over 3
=item B<-d | --dir> path
Overides the default directories to check by one directory 'path' and
all its subdirectories.
=item B<-a | --authorsfile>
path from working directory the AUTHORS file.
Redundant as this information could be had from --dir option butI am
feeling too lazy to change the code.
=cut
sub blankline {
return unless /\.PLS$/ or /\.p[ml]$/ ;
return unless -e $_;
my $file = $_;
open (F, $_) or warn "can't open file $_: $!" && return;
local $/="";
while (<F>) {
print "$file: +|$1|\n" if /[ \t]\n(=[a-z][^\n]+$)/m and $verbose;
print "$file: ++|$1|\n" if /\w\n(=[a-z][^\n]+$)/m and $verbose;
print "$file:|$1|+\n" if /(^=[a-z][^\n]+)\n[\t ]/m;
#print "$file:|$1|++\n" if /(^=[^\n]+)\n\w/m;
}
close F;
}
__END__
=item B<-v | --verbose>
Show the progress through files during the POD checking.
=item B<-? | -h | --help>
This help text.
=back
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Heikki Lehvaslaiho
Email heikki-at-bioperl-dot-org
=cut
# find . -name '*.pm' -print | xargs perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|" if /(\s\s^=[^\n]+$)/m ; }' ;
# find . -name '*.pm' -print | xargs perl -e '$/=""; while (<>) {$n = $1 if /^package\s+([\w:]+)/; print "$n:|$1|\n" if /(^=[^\n]+\n[\t ])/m ; }' ;
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