File Coverage

Bio/Root/HTTPget.pm

Criterion	Covered	Total	%
statement	12	146	8.2
branch	0	92	0.0
condition	0	83	0.0
subroutine	4	12	33.3
pod	5	5	100.0
total	21	338	6.2

#
# BioPerl module for fallback HTTP get operations.
#
# Module is proxy-aware
#
# Please direct questions and support issues to
#
#  Cared for by Chris Dagdigian
#  but all of the good stuff was written by
#  Lincoln Stein.
#
# You may distribute this module under the same terms as perl itself

# POD documentation - main docs before the code

=head1 NAME

Bio::Root::HTTPget - module for fallback HTTP get operations when
LWP:: is unavailable

=head1 SYNOPSIS

 use Bio::Root::HTTPget;
 my $web = Bio::Root::HTTPget->new();

 my $response = $web->get('http://localhost');
 $response    = $web->get('http://localhost/images');

 $response    = eval { $web->get('http://fred:secret@localhost/ladies_only/')
                     } or warn $@;

 $response    = eval { $web->get('http://jeff:secret@localhost/ladies_only/')
                     } or warn $@;

 $response    = $web->get('http://localhost/images/navauthors.gif');
 $response    = $web->get(-url=>'http://www.google.com',
 		                    -proxy=>'http://www.modperl.com');

=head1 DESCRIPTION

This is basically an last-chance module for doing network HTTP get
requests in situations where more advanced external CPAN modules such
as LWP:: are not installed.

The particular reason this module was developed was so that the Open
Bio Database Access code can fallback to fetching the default registry
files from http://open-bio.org/registry/ without having to depend on
external dependencies like Bundle::LWP for network HTTP access.

The core of this module was written by Lincoln Stein. It can handle proxies
and HTTP-based proxy authentication.

=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 one of the Bioperl mailing lists.
Your participation is much appreciated.

  [e-mail]                  - 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
the bugs and their resolution.  Bug reports can be submitted via the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Lincoln Stein

# Please direct questions and support issues to I

 Cared for by Chris Dagdigian

=head1 APPENDIX

The rest of the documentation details each of the object
methods. Internal methods are usually preceded with a _

=cut


# Let the code begin...

package Bio::Root::HTTPget;

use strict;
use warnings;
use IO::Socket qw(:DEFAULT :crlf);

use base qw(Bio::Root::Root);

{
    # default attributes, in case used as a class/sub call
    my %attributes;

=head2 get

 Title   : get
 Usage   : my $resp = get(-url => $url);
 Function:
 Returns : string
 Args    : -url     => URL to HTTPGet
           -proxy   => proxy to use
           -user    => username for proxy or authentication
           -pass    => password for proxy or authentication
           -timeout => timeout

=cut

sub get {
    my $self;
    if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) {
	$self = shift;
    }

    my ($url,$proxy,$timeout,$auth_user,$auth_pass) =
	__PACKAGE__->_rearrange([qw(URL PROXY TIMEOUT USER PASS)],@_);
    my $dest  = $proxy || $url;

    my ($host,$port,$path,$user,$pass)
	= _http_parse_url($dest) or __PACKAGE__->throw("invalid URL $url");
    $auth_user ||= $user;
    $auth_pass ||= $pass;
    if ($self) {
        unless ($proxy) {
            $proxy = $self->proxy;
        }
        unless ($auth_user) {
            ($auth_user, $auth_pass) = $self->authentication;
        }
    }
    $path = $url if $proxy;

    # set up the connection
    my $socket = _http_connect($host,$port) or __PACKAGE__->throw("can't connect: $@");

    # the request
    print $socket "GET $path HTTP/1.0$CRLF";
    print $socket "User-Agent: Bioperl fallback fetcher/1.0$CRLF";
    # Support virtual hosts
    print $socket "HOST: $host$CRLF";

    if ($auth_user && $auth_pass) { # authentication information
	my $token = _encode_base64("$auth_user:$auth_pass");
	print $socket "Authorization: Basic $token$CRLF";
    }
    print $socket "$CRLF";

    # read the response
    my $response;
    {
	local $/ = "$CRLF$CRLF";
	$response = <$socket>;
    }

    my ($status_line,@other_lines) = split $CRLF,$response;
    my ($stat_code,$stat_msg) = $status_line =~ m!^HTTP/1\.[01] (\d+) (.+)!
	or __PACKAGE__->throw("invalid response from web server: got $response");

    my %headers = map {/^(\S+): (.+)/} @other_lines;
    if ($stat_code == 302 || $stat_code == 301) { # redirect
	my $location = $headers{Location} or
            __PACKAGE__->throw("invalid redirect: no Location header");
	return get(-url => $location, -proxy => $proxy, -timeout => $timeout, -user => $auth_user, -pass => $auth_pass); # recursive call
    }

    elsif ($stat_code == 401) { # auth required
	my $auth_required = $headers{'WWW-Authenticate'};
	$auth_required =~ /^Basic realm="([^\"]+)"/
	    or __PACKAGE__->throw("server requires unknown type of".
                                  " authentication: $auth_required");
	__PACKAGE__->throw("request failed: $status_line, realm = $1");
    }

    elsif ($stat_code != 200) {
	__PACKAGE__->throw("request failed: $status_line");
    }

    $response = '';
    while (1) {
	my $bytes = read($socket,$response,2048,length $response);
	last unless $bytes > 0;
    }

    $response;
}

=head2 getFH

 Title   : getFH
 Usage   :
 Function:
 Example :
 Returns : string
 Args    :

=cut

sub getFH {
  my $self;
    if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) {
	$self = shift;
    }
  my ($url,$proxy,$timeout,$auth_user,$auth_pass) =
    __PACKAGE__->_rearrange([qw(URL PROXY TIMEOUT USER PASS)],@_);
  my $dest  = $proxy || $url;

  my ($host,$port,$path,$user,$pass)
    = _http_parse_url($dest) or __PACKAGE__->throw("invalid URL $url");
  $auth_user ||= $user;
  $auth_pass ||= $pass;
  $path = $url if $proxy;

  # set up the connection
  my $socket = _http_connect($host,$port) or __PACKAGE__->throw("can't connect: $@");

  # the request
  print $socket "GET $path HTTP/1.0$CRLF";
  print $socket "User-Agent: Bioperl fallback fetcher/1.0$CRLF";
  # Support virtual hosts
  print $socket "HOST: $host$CRLF";

  if ($auth_user && $auth_pass) {  # authentication information
    my $token = _encode_base64("$auth_user:$auth_pass");
    print $socket "Authorization: Basic $token$CRLF";
  }
  print $socket "$CRLF";

  # read the response
  my $response;
  {
    local $/ = "$CRLF$CRLF";
    $response = <$socket>;
  }

  my ($status_line,@other_lines) = split $CRLF,$response;
  my ($stat_code,$stat_msg) = $status_line =~ m!^HTTP/1\.[01] (\d+) (.+)!
    or __PACKAGE__->throw("invalid response from web server: got $response");

  my %headers = map {/^(\S+): (.+)/} @other_lines;
  if ($stat_code == 302 || $stat_code == 301) {  # redirect
    my $location = $headers{Location} or
        __PACKAGE__->throw("invalid redirect: no Location header");
    return getFH(-url => $location, -proxy => $proxy, -timeout => $timeout, -user => $auth_user, -pass => $auth_pass);  # recursive call
  }

  elsif ($stat_code == 401) { # auth required
    my $auth_required = $headers{'WWW-Authenticate'};
    $auth_required =~ /^Basic realm="([^\"]+)"/
      or __PACKAGE__->throw("server requires unknown type of ".
                            "authentication: $auth_required");
    __PACKAGE__->throw("request failed: $status_line, realm = $1");
  }

  elsif ($stat_code != 200) {
    __PACKAGE__->throw("request failed: $status_line");
  }

  # Now that we are reasonably sure the socket and request
  # are OK we pass the socket back as a filehandle so it can
  # be processed by the caller...

  $socket;

}


=head2 _http_parse_url

 Title   :
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

=cut

sub _http_parse_url {
  my $self;
    if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) {
	$self = shift;
    }
  my $url = shift;
  my ($user,$pass,$hostent,$path) =
    $url =~ m!^http://(?:([^:]+):([^:]+)@)?([^/]+)(/?[^\#]*)! or return;
  $path ||= '/';
  my ($host,$port) = split(':',$hostent);
  return ($host,$port||80,$path,$user,$pass);
}

=head2 _http_connect

 Title   :
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

=cut

sub _http_connect {
  my ($host,$port,$timeout) = @_;
  my $sock = IO::Socket::INET->new(Proto     => 'tcp',
                                   Type      => SOCK_STREAM,
				   PeerHost  => $host,
				   PeerPort  => $port,
				   Timeout   => $timeout,
				  );
  $sock;
}


=head2 _encode_base64

 Title   :
 Usage   :
 Function:
 Example :
 Returns :
 Args    :

=cut

sub _encode_base64 {
    my $self;
    if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) {
	$self = shift;
    }
    my $res = "";
    my $eol = $_[1];
    $eol = "\n" unless defined $eol;
    pos($_[0]) = 0;                          # ensure start at the beginning

    $res = join '', map( pack('u',$_)=~ /^.(\S*)/, ($_[0]=~/(.{1,45})/gs));

    $res =~ tr|` -_|AA-Za-z0-9+/|;               # `# help emacs
    # fix padding at the end
    my $padding = (3 - length($_[0]) % 3) % 3;
    $res =~ s/.{$padding}$/'=' x $padding/e if $padding;
    # break encoded string into lines of no more than 76 characters each
    if (length $eol) {
        $res =~ s/(.{1,76})/$1$eol/g;
    }
    return $res;
}


=head2 proxy

 Title   : proxy
 Usage   : $httpproxy = $db->proxy('http')  or
           $db->proxy(['http','ftp'], 'http://myproxy' )
 Function: Get/Set a proxy for use of proxy. Defaults to environment variable
           http_proxy if present.
 Returns : a string indicating the proxy
 Args    : $protocol : string for the protocol to set/get
           $proxyurl : url of the proxy to use for the specified protocol
           $username : username (if proxy requires authentication)
           $password : password (if proxy requires authentication)

=cut

sub proxy {
    my $self;
    if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) {
	$self = shift;
    }
    my ($protocol,$proxy,$username,$password) = @_;
    my $atts = ref($self) ? $self : \%attributes;
    $protocol ||= 'http';
    if (!$proxy) {
        if (defined $ENV{http_proxy}) {
            $proxy = $ENV{http_proxy};
            if ($proxy =~ /\@/) {
                ($username, $password, $proxy) = $proxy =~ m{http://(\S+):(\S+)\@(\S+)};
                $proxy = 'http://'.$proxy;
            }
        }
    }
    if (defined $proxy) {
        # default to class method call
        __PACKAGE__->authentication($username, $password)
        if ($username && $password);
        $atts->{'_proxy'}->{$protocol} = $proxy;
    }
    return $atts->{'_proxy'}->{$protocol};
}

=head2 clear_proxy

 Title   : clear_proxy
 Usage   : my $old_prozy = $db->clear_proxy('http')
 Function: Unsets (clears) the proxy for the protocol indicated
 Returns : a string indicating the old proxy value
 Args    : $protocol : string for the protocol to clear

=cut

sub clear_proxy {
    my $self;
    if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) {
        $self = shift;
    }
    my ($protocol) = @_;
    my $atts = ref($self) ? $self : \%attributes;
    $protocol ||= 'http';
    delete $atts->{'_proxy'}->{$protocol};
}

=head2 authentication

 Title   : authentication
 Usage   : $db->authentication($user,$pass)
 Function: Get/Set authentication credentials
 Returns : Array of user/pass
 Args    : Array or user/pass


=cut

sub authentication {
    my $self;
    if($_[0] && (ref($_[0]) or $_[0] =~ /^Bio::/)) {
	$self = shift;
    }
    my $atts = ref($self) ? $self : \%attributes;
    if (@_) {
	my ($u,$p) = @_;
	my $atts = ref($self) ? $self : \%attributes;

	$atts->{'_authentication'} = [ $u,$p];
    }
    return @{$atts->{'_authentication'} || []};
}

}

1;