#!/usr/bin/perl

use warnings;
use strict;
use Fcntl ':mode';
use Getopt::Long;


#option handling code

#required
my $assm;
#options
my %opt;
my $check = GetOptions(\%opt,
        "d=s",
        "c=s",
        "t"
        );
unless ($check){usage()}

unless ($ARGV[0]){
    usage()
}

$assm = $ARGV[0];
#preset directories
my $dldir = "/hive/groups/encode/dcc/analysis/ftp/pipeline/$assm/";
my $configdir = "/hive/groups/encode/dcc/pipeline/encpipeline_prod/config/";
my $readme = "README.txt";

#options switching
if ($opt{'d'}){
    $dldir = $opt{'d'};
    print STDERR "using download directory: $dldir\n";
}
else {
    print STDERR "using download directory: $dldir\n";
}

if ($opt{'c'}){
    $configdir = $opt{'c'};
    print STDERR "using config directory: $configdir\n";
}
else {
    print STDERR "using config directory: $configdir\n";
}
if ($opt{'t'}){
    $readme = "README.txt.test";
}


my $readmeTemplate = "$configdir/downloadsReadmeTemplate.txt";

open TEMPLATE, "$readmeTemplate" or die "Can't open README template\n";

#grab template to be interpolated;
my @template;
while (<TEMPLATE>){

    my $line = $_;
    chomp $line;
    #skip commented lines
    if ($line =~ m/^\s*#/){next}
    push @template, $line;
    
}

close TEMPLATE;

#find only folders in $dldir that match wgEncode
my $folders = `find $dldir -maxdepth 1 -type d | grep "wgEncode"`;

my @list = split "\n", $folders;

#go through list of folders
foreach my $folder (@list){
    
    my $compname;
    
    #for some reason the search and replace below modifies the original array, so I copied it to prevent that
    my @localtemp = @template;
    #print "folder = $folder\n";    
    #grab composite name from directory
    if ($folder =~ m/\/(wgEncode.*)$/){
        
        $compname = $1;
        #print "compname = $compname\n";
    }
    else {next}
    my @stat = stat($folder);
    #print "$folder:\n";
    my $mode = $stat[2];
    my $writable= ($mode & S_IWGRP) >> 3;
    unless ($writable) {next}
    open README, ">$folder/$readme" or die "Can't open README file to write in directory $folder\n";

    foreach my $line (@localtemp){
        #interpolate in the name of the DB and composite name
        if ($line =~ m/\+\+/){
            $line =~ s/\+\+db\+\+/$assm/;
            $line =~ s/\+\+composite\+\+/$compname/;
            print README "$line\n";
        }
        else {
            print README "$line\n";
        }
    }
    close README;
}

print STDERR "\n\nPlease send out an e-mail reminder that the README.txt has been updated. We wouldn't want to have tracks in QA leaking out an older version.\n\n";



sub usage {
    
    print STDERR  <<END;
usage: encodeDownloadReadme.pl [assembly] [options]

Copies downloadReadmeTemplate.txt to all of the download directories with the proper link per composite 

Options:
    -d\tDownload directory location (default:/hive/groups/encode/dcc/analysis/ftp/pipeline/)
    -c\tConfig directory location (default:/hive/groups/encode/dcc/pipeline_prod/config/)
    -t\t(Boolean) Write README.txt.test instead of README.txt
    
END
exit 1;
}




__END__