#!/usr/bin/perl -w
use strict;
use File::Basename;
use Net::SSH::Perl;
use IO::Handle;
use Net::SCP::Expect;
use Data::Dumper;

#person in charge of this script
#this should be the person currently in charge of scripts for this project
my $script_maintainer='Teri Solow <tms45@cornell.edu>';


#Program designed to log in and retrieve sequences from the PSU (Penn State University) LIMS system
#Logs into the PSU machine via ssh using key-based authentication to retrieve the list of files, and uses scp with the same authentication mechanism to do the actual copying



@ARGV or print "No input parameters, proceeding with default.\n";

my @arg_pairs = split (/\-/, (join ' ', @ARGV));

my %args=();

foreach (@arg_pairs){

    $_ or next;
    my ($flag, $val)=split /\s+/;
    $args{$flag}=$val;
}

my $new_dir=$args{'i'};
my $done_dir=$args{'d'};

my $username = 'transfer';
my $password = 'cornell2fgp!';
my $login_identification = '/data/shared/pgn_data_processing/scripts/processing_components/data_files/fgn_psu_ssh/identification';
my $psu_machine_ip = '146.186.172.248';

#set defaults for io, script filename, etc
$new_dir ||= "/data/shared/pgn_data_processing/incoming_files/fgn/new_files/";
$done_dir ||= "/data/shared/pgn_data_processing/incoming_files/fgn/done_files/";


#uniform trailing slashes
$new_dir=~/\/$/ or $new_dir.='/';
$done_dir=~/\/$/ or $done_dir.='/';

# ssh login information
my $ssh = Net::SSH::Perl->new($psu_machine_ip);
$ssh->login($username, $password);
my $scp = Net::SCP::Expect->new(host=>$psu_machine_ip,user=>$username,password=>$password,verbose=>'1',auto_yes=>'1');
$scp->login($username,$password);

#main body of script
#####################


#Get a list of files we already have
my @local_files=&traverse_dir($done_dir);
my %local_filenames=();
foreach (@local_files){
    /\/([^\/]+\.zip)/
	and $local_filenames{ucfirst $1}++;
}

#Get a list of the remote files
my $files;
($files, undef, undef) = $ssh->cmd("ls /home/fgp/transfer/tracefiles/tocornell/*.zip");
my @files_array = split(/\n/, $files);

#get a list of the new ones
my @files_toget=();

foreach(@files_array){
    chomp;
    $local_filenames{ucfirst basename($_)} and next;
    push @files_toget, $_;

}
#print Dumper(@files_toget);
#exit;

#get the new files
my $filecounter=0;
my $totalcount=@files_toget;


if ($totalcount){
    print "Retrieving $totalcount new files.\n";
}
else{
    print "No new files to transfer.\n";
    exit;
}

foreach (@files_toget){
    $filecounter++;
    print "Getting $_ (file $filecounter of $totalcount)\n";
    my $format_fname = ucfirst basename($_);
	$scp->scp(":$_", "${new_dir}${format_fname}");
}



print "Done retrieving sequences\n";


#sub to recursively traverse directories and build a list of file names
#######################
sub traverse_dir{
    my ($dirarg)=@_;
    opendir (THISDIR, $dirarg) or die "Couldn't open directory $dirarg\n";
#skip any files starting with .
    my @dir_list= grep !/^\./, readdir THISDIR;
    my ($filename, @filelist);
    foreach $filename (@dir_list){
	$filename=$dirarg.$filename;
	if(-d $filename){
	    $filename.='/';
	   push @filelist,  &traverse_dir($filename); 
       }
	else{
	    push @filelist, $filename;
	}
    }
    return @filelist;
}