tbr

use strict;
use Bio::KBase::AppService::BinningReport;
use Bio::KBase::AppService::AppConfig qw(data_api_url db_host db_user db_pass db_name seedtk);
use DBI;
use Data::Dumper;
use JSON::XS;
use Bio::P3::Workspace::WorkspaceClientExt;
use IPC::Run 'run';

my $ws = Bio::P3::Workspace::WorkspaceClientExt->new();

my $dsn = "DBI:mysql:database=" . db_name . ";host=" . db_host;
my $dbh = DBI->connect($dsn, db_user, db_pass, { RaiseError => 1, AutoCommit => 0 });

my $job_id = '3d13b98a-fdd2-4085-9400-b4bd04883911';
my($params_txt) = $dbh->selectrow_array(qq(SELECT app_params
				      FROM JobGroup
				      WHERE parent_job = ?), undef, $job_id);
my $params = decode_json($params_txt);

my $qual_path = join("/", $params->{output_path}, "." . $params->{output_file}, "quality.json");
my $qual = load_workspace_json($ws, $qual_path);

my $ppr_path = join("/", $params->{output_path}, "." . $params->{output_file}, "ppr_report.json");
my $ppr = load_workspace_json($ws, $ppr_path);

my $bins_path = join("/", $params->{output_path}, "." . $params->{output_file}, "bins.json");
my $bins = load_workspace_json($ws, $bins_path);

Bio::KBase::AppService::BinningReport::write_report($job_id, $params, $qual, $ppr, $bins, \*STDOUT);

sub load_workspace_json
{
    my($ws, $path) = @_;

    my $str;
    open(my $fh, ">", \$str) or die "Cannot open string reference filehandle: $!";

    eval {
	$ws->copy_files_to_handles(1, $ws->{token}, [[$path, $fh]]);
    };
    if ($@)
    {
	my($err) = $@ =~ /_ERROR_(.*)_ERROR_/;
	$err //= $@;
	die "load_workspace_json: failed to load $path: $err\n";
    }
    close($fh);

    my $doc = eval { decode_json($str) };

    if ($@)
    {
	die "Error parsing json: $@";
    }
    return $doc;
}