use strict;
use Data::Dumper;
use Getopt::Long;
use SeedEnv;
use JSON::XS;

my $usage = "usage: get_reaction_keys -d Data\n";
my $dataD;
my $rc  = GetOptions('d=s' => \$dataD,);

if ((! $rc) || (! -d $dataD)) { print STDERR $usage; exit }

#opendir(MODELS,"$dataD/Models") || die "could not open $dataD/Models";
#my @models = grep { $_ !~ /^\./ } readdir(MODELS);
#closedir(MODELS);

open(GAP_JOBS," > $dataD/gapfill_jobs.table") || die "could not open $dataD/gapfill_jobs.table";
foreach $_ (`cat $dataD/MODEL-ID`)
{
    if ($_ =~ /^(\S+)\t(\S+)/) {
        my($genome,$mid) = ($1,$2);
        my $cmd = "kbfba-gapfill $mid --nosubmit --numsol 1 --timepersol 7600 --timelimit 7600";
        my $txt = `$cmd`;
        $txt =~ /Perm ref: (.*)$/m;
        print GAP_JOBS "$mid\t$1\n";
    }
}