#!/usr/bin/perl -w
# $Id: modules.pl 10084 2006-07-04 22:23:29Z mauricio $
#
=head1 NAME
modules.pl - information about modules in BioPerl core
=head1 SYNOPSIS
B<modules.pl> [B<-V|--verbose>] [B<-c|--count>] | [B<-l|--list>] |
[B<-u|--untested>] | [B<-i|--info> class] | [B<-i|--inherit> |
[B<-d|--dir> path ] | [B<-v|--version> | [B<-?|-h|--help>]
=head1 DESCRIPTION
This script counts, lists and provides other information about bioperl
modules. It is mainly meant to be run by bioperl maintainers.
The default action is to count modules in the bioperl core
distribution. Based on the class name it tries to classify them into
categories. The following is a tentative glossary of terms used.
=over 4
=item Base
Synonyms: Generic class, parameterized class, generic module.
A class that you don't instantiate in your scripts, but that it's a
template for other classes.
Examples: Bio::Tools::Run::WrapperBase - a base object for wrappers
around executables. Bio::Tools::Analysis::SimpleAnalysisBase - an
abstract superclass for SimpleAnalysis implementations
This are counted with C</:Base/ | /Base$/>; They have "Base" in the
beginning or end of the name.
=item Interface
Synonyms: protocol, feature set.
Class that defines a set of features that are common to a group of
classes.
Example: Bio::Tree::NodeI - interface describing a Tree Node.
This are counted with C</[^A-Z]I$/>; They have "I" at the end of the
name.
=item Component
A class that implements a small subset of their superclass. They are in
a directory with an identical name of the superclass. There are plenty
of them. You need only a small number of methods to be overridden.
Example: Bio::SeqIO::fasta.
This is counted with C</.*:[a-z]/>; Classes are inside their base directory
and all in lowercase.
=item Instance
The rest of them. It is sometimes helpful to divide them into two
types:
=over 2
=item Algorithmic classes
Example: Bio::AlignIO - Handler for AlignIO formats
=item Storage classes
Example: Bio::SimpleAlign - Multiple alignments held as a set of
sequences
=back
=back
=cut
#
# The helper class to store class status;
#
package BioClass;
sub new {
my $class = shift;
my $name = shift;
die unless $name;
my $self = {};
$self->{'name'} = $name;
$self->{'tested'} = 0;
$self->{'type'} = '';
$self->{'path'} = '';
bless $self, $class;
}
sub name {
my $self = shift;
return $self->{'name'};
}
sub tested {
my $self = shift;
my $value = shift;
$self->{'tested'} = 1 if defined $value && $value;
return $self->{'tested'} || 0;
}
sub type {
my $self = shift;
my $value = shift;
$self->{'type'} = $value if defined $value;
return $self->{'type'};
}
sub path {
my $self = shift;
my $value = shift;
$self->{'path'} = $value if defined $value;
return $self->{'path'};
}
sub add_superclass {
my $self = shift;
my $superclass = shift;
return unless $superclass;
$self->{'superclasses'}->{$superclass} = 1 ;
}
sub each_superclass {
my $self = shift;
return keys %{$self->{'superclasses'}};
}
sub add_used_class {
my $self = shift;
my $used_class = shift;
return unless $used_class;
$self->{'used_classes'}->{$used_class} = 1 ;
}
sub each_used_class {
my $self = shift;
return keys %{$self->{'used_classes'}};
}
package main;
use File::Find;
use Getopt::Long;
use Data::Dumper;
use strict;
# declare subroutines
sub dir;
sub modules;
sub count;
sub list_all;
sub untested;
sub info;
sub inherit;
sub synopsis;
sub version;
# command line options
my ($dir, $count,$list, $verbose,$info,$untested, $inherit, $synopsis,
$version);
GetOptions(
'dir:s' => \$dir,
'count' => \$count,
'list' => \$list,
'test_BioClass' => \&_test_BioClass,
'V|verbose' => \$verbose,
'untested' => \$untested,
'info:s' => \$info,
'inherit' => \$inherit,
'synopsis' => \$synopsis,
'version' => \$version,
'h|help|?' => sub{ exec('perldoc',$0); exit(0) }
);
our %MODULES; # storage structure
# find modules
my $pwd = $ENV{PWD};
my $seachdir = "$pwd/../Bio"; #default
my %FIND_OPTIONS = ( wanted => \&modules );
$seachdir = "$pwd/$dir" if $dir;
find \%FIND_OPTIONS, $seachdir;
# call subroutines
if ($list) { list_all }
elsif ($untested) { untested }
elsif ($info) { info($info) }
elsif ($inherit) { inherit }
elsif ($synopsis) { synopsis }
elsif ($version) { version }
else { count }
################# end main ####################
#
# subroutines;
#
sub _test_BioClass {
$a = new BioClass('Bio::Test');
print "Class name: ", $a->name(), "\n";
$a->add_superclass('Bio::Super');
$a->add_superclass('Bio::Super2');
$a->tested(1);
$a->type('instance');
print Dumper [$a->each_superclass] if $a->tested;
print Dumper $a;
exit;
}
sub modules {
return unless /\.pm$/ ;
#return unless -e $_;
#print "file: $_\n" if $verbose;
open (F, $_) or warn "can't open file $_: $!" && return;
my $class;
while (<F>) {
if (/^package\s+([\w:]+)\s*;/) {
#print $1, "\n" if $verbose;
$_ = $1;
$class = new BioClass($_);
$MODULES{$_} = $class;
if (/.*:[a-z]/) {
$class->type('component');
} elsif (/:Base/ | /Base$/) {
$class->type('base');
} elsif (/[^A-Z]I$/) {
$class->type('interface');
} else {
$class->type('instance');
}
$class->path($File::Find::name);
}
if (/^\w*use/ && /(Bio[\w:]+)\W*;/ && not /base/) {
next unless $class;
#print "\t$1\n" if $verbose;
$class->add_used_class($1);
}
if ((/\@ISA/ || /use base/) && /Bio/) {
next unless $class;
my $line = $_;
while ( $line =~ /(Bio[\w:]+)/g) {
#print "\t$1\n" if $verbose;
$class->add_superclass($1);
}
}
if (/\@ISA/ && /Bio/) {
next unless $class;
my $line = $_;
while ( $line =~ /(Bio[\w:]+)/g) {
#print "\t$1\n" if $verbose;
$class->add_superclass($1);
}
}
}
close F;
}
=head1 OPTIONS
Only one option is processed on each run of the script. The --verbose
is an exception, it modifies the amount of output.
=over 4
=item B<-V | --verbose>
B<INACTIVE>
Set this option if you want to see more verbose output. Often that
will mean seeing warnings normally going into STDERR.
=cut
=item B<-d | --dir> path
Overides the default directories to check by one directory 'path' and
all its subdirectories.
=item B<-c | --count>
The default action if no other option is given. Gives the count of
modules broken to B<instance> ("usable"), B<base> ( (abstract)?
superclass) , B<interface> (the "I" files) and B<component> (used from
instantiable parent) modules, in addition to total number of modules.
Note that abstract superclass in bioperl is not an enforced concept and
they are not clearly indicateded in the class name.
=cut
sub count {
printf "Instance : %3d\n",
scalar (grep $MODULES{$_}->type =~ /instance/ , keys %MODULES);
printf "Base : %3d\n",
scalar (grep $MODULES{$_}->type =~ /base/ , keys %MODULES);
printf "Interface: %3d\n",
scalar (grep $MODULES{$_}->type =~ /interface/ , keys %MODULES);
printf "Component: %3d\n",
scalar (grep $MODULES{$_}->type =~ /component/ , keys %MODULES);
print "--------------\n";
printf "Total : %3d\n", scalar (keys %MODULES);
}
=item B<-l | --list>
Prints all the module names in alphabetical order. The output is a tab
separated list of category (see above) and module name per line. The
output can be processed with standard UNIX command line tools.
=cut
sub list_all {
foreach ( sort keys %MODULES) {
print $MODULES{$_}->type. "\t$_\n";
}
}
=item B<-u | --untested>
Prints a list of instance modules which are I<not> explicitly used by
test files in the directory. Superclasess or any classes used by others
are not reported, either, since their methods are assumed to be tested
by subclass tests.
=cut
sub _used_and_super {
my $name = shift;
# print "-:$name\n" if /Locati/;
foreach ($MODULES{$name}->each_superclass) {
next unless defined $MODULES{$_};
# print "-^$_\n" if /Locati/;
# unless (defined $MODULES{$_} or $MODULES{$_}->tested) {
if (not $MODULES{$_}->tested) {
$MODULES{$_}->tested(1);
_used_and_super($_);
}
}
foreach ($MODULES{$name}->each_used_class) {
next unless defined $MODULES{$_};
# print "--$_\n" if /Locati/;
# unless (defined $MODULES{$_} or $MODULES{$_}->tested) {
if (not $MODULES{$_}->tested) {
$MODULES{$_}->tested(1);
_used_and_super($_);
}
# $MODULES{$_}->tested(1) && _used_and_super($_)
# unless defined $MODULES{$_} or $MODULES{$_}->tested;
}
return 1;
}
sub untested {
foreach (`find ../t -name "*.t" -print | xargs grep -hs "[ur][se][eq]"`) {
s/.*use +//;
s/.*require +//;
next unless /^Bio/;
s/[\W;]+$//;
s/([\w:]+).*/$1/;
my $name = $_;
next unless $MODULES{$_};
$MODULES{$_}->tested(1)
unless defined $MODULES{$_} and $MODULES{$_}->tested;
next if $MODULES{$name}->name eq "Bio::SeqIO::abi"; # exception: requires bioperl ext package
next if $MODULES{$name}->name eq "Bio::SeqIO::ctf"; # exception: requires bioperl ext package
next if $MODULES{$name}->name eq "Bio::SeqIO::exp"; # exception: requires bioperl ext package
next if $MODULES{$name}->name eq "Bio::SeqIO::pln"; # exception: requires bioperl ext package
next if $MODULES{$name}->name eq "Bio::SeqIO::ztr"; # exception: requires bioperl ext package
# print $MODULES{$name}->name, "\n";
# print Dumper $MODULES{$name};
_used_and_super($name);
}
foreach ( sort keys %MODULES) {
# skip some name spaces
next if /^Bio::Search/; # Bio::Search and Bio::SearchIO are extensively tested
# but classes are used by attribute naming
print "$_\n" if
$MODULES{$_}->type eq 'instance' and ($MODULES{$_}->tested == 0) ;
}
}
=item B<-i | --info> class
Dumps information about a class given as an argument.
=cut
sub info {
my $class = shift;
die "" unless $class;
#print Dumper $MODULES{$class};
my $c = $MODULES{$class};
print $c->name, "\n";
printf " Type:\n\t%s\n", $c->type;
print " Superclasses:\n";
foreach (sort $c->each_superclass) {
print "\t$_\n";
}
print " Used classes:\n";
foreach (sort $c->each_used_class) {
print "\t$_\n";
}
}
=item B<-i | --inherit>
Finds interface modules which inherit from an instantiable class.
Could be extended to check other bad inheritance patterns.
=cut
sub inherit {
foreach ( sort keys %MODULES) {
my $c=$MODULES{$_};
next unless $c->type =~ /interface/;
foreach my $super ($c->each_superclass) {
next if $super =~ /I$/;
print "Check this inheritance: ", $c->name, " <-- $super\n";
}
}
}
=item B<-s | --synopsis>
Test SYNOPSIS section of bioperl modules for runnability
=cut
sub synopsis {
foreach ( sort keys %MODULES) {
my $c=$MODULES{$_};
next unless $c->type eq "instance";
next if $c->name eq 'Bio::Root::Version';
next if $c->name eq 'Bio::Tools::HMM';
my $synopsis = '';
open (F, $c->path) or warn "can't open file ".$c->name.": $!" && return;
my $flag = 0;
while (<F>) {
last if $flag && /^=/;
$synopsis .= $_ if $flag;
$flag = 1 if /^=head1 +SYNOPSIS/;
}
# remove comments
$synopsis =~ s/[^\$]#[^\n]*//g;
# allow linking to an other Bio module, e.g.: See L<Bio::DB::GFF>.
$synopsis =~ s/[^\n]*L<Bio[^\n]*//g;
# protect single quotes
$synopsis =~ s/'/"/g;
my $res = `perl -ce '$synopsis' 2>&1 `;
next if $res =~ /syntax OK/;
print $c->path, "\n";
print $synopsis;
print $res;
print "-" x 70, "\n";
# print "SYNOPSIS not runnable\n";
close F;
}
}
=item B<-v | --version>
Test the VERSION of the module against the global one set in
Bio::Root::Variation. Print out the different ones.
=cut
sub version {
use Bio::Root::Version;
my $version = $Bio::Root::Version::VERSION;
my %skip = ( # these are defined together with an other module
# and can not be use independently
'Bio::AnalysisI::JobI' => 1,
'Bio::PrimarySeq::Fasta' => 1,
'Bio::DB::Fasta::Stream' => 1,
'Bio::DB::GFF::ID_Iterator' => 1,
'Bio::DB::GFF::Adaptor::dbi::faux_dbh' =>1,
'Bio::LiveSeq::IO::SRS' =>1 # tries to call an external module
);
foreach ( sort keys %MODULES) {
my $n=$MODULES{$_}->name;
next if $skip{$n};
my $vv= "\$${n}::VERSION";
my $v = `perl -we 'use $n; print $vv;'`;
printf "%50s %-3s\n", $n, $v unless $version eq $v;
}
}
__END__
=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:
http://bugzilla.open-bio.org/
=head1 AUTHOR
Heikki Lehvaslaiho, heikki-at-bioperl-dot-org
=head1 Contributors
Albert Vilella, avilella-AT-gmail-DOT-com
=cut