UNIX for Dummies Questions & Answers

#!/usr/bin/perl

use strict;
use warnings;

use HTTP::Request::Common qw(GET);
use LWP::UserAgent;



#-----------------------------------------------------------
# obtaining server access by creating a fake browser
#-----------------------------------------------------------
my $ua = new LWP::UserAgent;
$ua->protocols_allowed( [ 'http' ] );


#-----------------------------------------------------------
# methods
#-----------------------------------------------------------
enter_htmlMain();
my ($name, $address) = grab_samples();
enter_samplePage($address);
grab_files($name);


#-----------------------------------------------------------
# subroutines
#-----------------------------------------------------------
  

# enters the server page with all the sample runs listed
sub enter_htmlMain{

    my $url = 'http://server_name/rundb/';
    open (OUT, ">", "temp.html") or die $!;

    my $user = 'ionuser';
    my $pass = 'ionuser';

    #sets up request
    my $req = GET($url);
    $req->authorization_basic($user, $pass);

    #do it
    my $response = $ua->request($req);

    #check and print to file
    if ($response->is_error())
        {
            printf "%s\n", $response->status_line;
            print "http request error!\n";
        } else {

            my $content = $response->content();
            print OUT $content;
        }
    close OUT;

} #end of enter_htmlMain


#-----------------------------------------------------------
# grabs the names and location of the samples currently on 
#the server from temp.html and prints them for user selection
#-----------------------------------------------------------
sub grab_samples{

    my %sample;
    my $i = 1;

    open (IN, "<", "temp.html");

    while (<IN>){

        if ($_=~/<a href=\"(\/output\/Home\/.*\.php)\"/){
        my $holder = $1;
        my $sample_name;
        my $address = "http://server_name$holder";
    
            if ($holder=~/\/output\/Home\/(.*)\//){$sample_name = $1;}

        my $info = "$sample_name\t$address";
        print "$i\t$sample_name\n";
        $sample{$i} = $info;
        $i++;

        } #end of original 'if' statement    

    } #end of 'while' loop

    close IN;

    print "\n\nPlease select sample.\t";
    my $input = <>;
    chomp $input;
    
    my @temp = split(/\t/,$sample{$input});
    my $n = $temp[0];
    my $a = $temp[1];

    return ($n, $a);

    #remove temp.html
    my $cmd = "rm temp.html";
    system ($cmd);
    if ($?) {die "command: $cmd failed\n"};
    
} # end of grab_samples

#-----------------------------------------------------------
# copies the html page from the sample of intrest to temp.html
#-----------------------------------------------------------
sub enter_samplePage{

    my @destination = @_;

    my $url = $destination[0];
    open (OUT, ">", "temp.html") or die $!;

    my $user = 'ionuser';
    my $pass = 'ionuser';

    #sets up request
    my $req = GET($url);
    $req->authorization_basic($user, $pass);

    #do it
    my $response = $ua->request($req);

    #check and print to file
    if ($response->is_error())
        {
            printf "%s\n", $response->status_line;
            print "http request error!\n";
        } else {

            my $content = $response->content();
            print OUT $content;
        }
    close OUT;

} #end of enter_samplePage

#-----------------------------------------------------------
# grabs the barcode sff files and downloads them from the server
#-----------------------------------------------------------
sub grab_files{

    my @name = @_;
    my $barcode_sff;

    open (IN, "<", "temp.html");
    my @file = <IN>;
    close IN;

    foreach my $j (@file){
        if ($j=~/\(BAI\).*href\=\'(.*\.barcode\.sff\.zip)\'/){$barcode_sff = $1;}
    }

    #remove temp.html
    my $cmd = "rm temp.html";
    system ($cmd);
    if ($?) {die "command: $cmd failed\n"};


    #downloading .zip file
    my $barcode_sff_url = "http://server_name/output/Home/$name[0]/$barcode_sff";
    open (OUT, ">", $barcode_sff) or die $!;

    my $user = 'ionuser';
    my $pass = 'ionuser';

    #sets up request
    my $req = GET($barcode_sff_url);
    $req->authorization_basic($user, $pass);

    #do it
    my $response = $ua->request($req);

    #check and print to file
    if ($response->is_error())
        {
            printf "%s\n", $response->status_line;
            print "http request error!\n";
        } else {

            my $content = $response->content();
            print OUT $content;
        }
    close OUT;

    #change permissions on .zip
    $cmd = "chmod 775 $barcode_sff";
    system ($cmd);
    if ($?) {die "command: $cmd failed\n"};

    #unzip barcode.sff.zip
    $cmd = "unzip $barcode_sff";
    system ($cmd);
    if ($?) {die "command: $cmd failed\n"};

    #remove barcode.sff.zip
    $cmd = "rm $barcode_sff";
    system ($cmd);
    if ($?) {die "command: $cmd failed\n"};
        
} #end of grab_files