#
# BioPerl module for fallback HTTP get operations.
#
# Module is proxy-aware
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Chris Dagdigian <dag@sonsorol.org>
# 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.
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
the bugs and their resolution. Bug reports can be submitted via the
web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Lincoln Stein
# Please direct questions and support issues to I<bioperl-l@bioperl.org>
Cared for by Chris Dagdigian <dag@sonsorol.org>
=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;