Bio::Root HTTPget
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Root::HTTPget - module for fallback HTTP get operations when
LWP:: is unavailable
Package variables
No package variables defined.
Included modules
Bio::Root::Root
IO::Socket qw ( :DEFAULT :crlf )
Inherit
Bio::Root::Root
Synopsis
 Use Bio::Root::HTTPget;

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

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

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

 $response    = get('http://localhost/images/navauthors.gif');
 $response    = get(-url=>'http://www.google.com',
 		    -proxy=>'http://www.modperl.com');
Description
This is basically an last-chance module for doing network HTTP get requests in
situations where more advanced external CPAN modules such as LWP:: are not
installed.
The particular reason this module was developed was so that the Open Bio
Database Access code can fallback to fetching the default registry files
from http://open-bio.org/registry/ without having to depend on
external dependencies like Bundle::LWP for network HTTP access.
The core of this module was written by Lincoln Stein. It can handle proxies
and HTTP-based proxy authentication.
Methods
getDescriptionCode
getFHDescriptionCode
_http_parse_urlDescriptionCode
_http_connectDescriptionCode
_encode_base64DescriptionCode
Methods description
getcode    nextTop
 Title   : get
 Usage   : 
 Function:
 Example :
 Returns : string
 Args    :
getFHcodeprevnextTop
 Title   : getFH
 Usage   : 
 Function:
 Example :
 Returns : string
 Args    :
_http_parse_urlcodeprevnextTop
 Title   :
 Usage   : 
 Function:
 Example :
 Returns :
 Args    :
_http_connectcodeprevnextTop
 Title   :
 Usage   : 
 Function:
 Example :
 Returns :
 Args    :
_encode_base64codeprevnextTop
 Title   :
 Usage   : 
 Function:
 Example :
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Methods code
getdescriptionprevnextTop
sub get {
  my ($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 = $headers{Location} or __PACKAGE__->throw("invalid redirect: no Location header");
    return get($location,$proxy,$timeout);  # 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;
  }

  $response;
}
getFHdescriptionprevnextTop
sub getFH {
  my ($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 = $headers{Location} or __PACKAGE__->throw("invalid redirect: no Location header");
    return get($location,$proxy,$timeout);  # 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;
}
_http_parse_urldescriptionprevnextTop
sub _http_parse_url {
  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,$pass);
}
_http_connectdescriptionprevnextTop
sub _http_connect {
  my ($host,$port,$timeout) = @_;
  my $sock = IO::Socket::INET->new(Proto     => 'tcp',
                                   Type      => SOCK_STREAM,
				   PeerHost  => $host,
				   PeerPort  => $port,
				   Timeout   => $timeout,
				  );
  $sock;
}
_encode_base64descriptionprevnextTop
sub _encode_base64 {
    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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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://bio.perl.org/MailList.html     - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution.
Bug reports can be submitted via email or the web:
  bioperl-bugs@bio.perl.org
  http://bugzilla.bioperl.org/
AUTHOR - Lincoln SteinTop
 Cared for by Chris Dagdigian <dag@sonsorol.org>
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _