#!/usr/bin/perl -w

use strict;
use DBI;



my $in = $ARGV[0];
my $out = $ARGV[1];

my $go_db_name = $ARGV[2];
my $go_db_username = $ARGV[3];
my $go_db_password = $ARGV[4];

# Major categories of GO terms
# ----------------------------

# Processes
my @processes = ("metabolic process", "electron transport", "photosynthesis", "cell cycle", "cellular component organization and biogenesis", "cell communication", "cellular response to stimulus", "localization");

# Compnents
my @components = ("nucleus", "mitochondrion", "plastid", "endoplasmic reticulum", "cytosol", "ribosome", "chromosome", "cytoskeleton", "membrane", "Golgi apparatus", "lysosome");

# Functions
my @functions = ("catalytic activity", "enzyme regulator activity", "signal transducer activity", "antioxidant activity", "structural molecule activity", "transporter activity", "transcription regulator activity", "translation regulator activity", "DNA binding", "RNA binding", "nucleotide binding");

my $unknown = "_UNKNOWN_";
my $others = "_OTHERS_";

open IN, "< $in" or die "Error opening input file $in: $!";
open OUT, "> $out" or die "Error opening output file $out: $!";

# Flush immediately to the output file (i.e. no buffering)
my $old_fh = select(OUT);
$| = 1;
select($old_fh);

# Connect to the database that holds the schema and data of GO
my $dbh = DBI->connect("dbi:mysql:$go_db_name",$go_db_username, $go_db_password) or die "Error connecting to GO database:",  $DBI::errstr;

my $line;

my $index = 0;

while ($line = <IN>) {
    
    chomp($line);
    
    if ($line =~ m/^([^\s]+)\s+([^\s]+)\s+([^\s]+)$/) {
	$index++;

	print "$index\t$1\t$2\t$3\n";

	my $id = $1;
	my $db = $2;
	my $key = $3;

	print OUT $id;
	
	my $name = get_go($db, $key, 'biological_process', @processes);
	
	print OUT "\t", $name;
	
	$name = get_go($db, $key, 'cellular_component', @components);
	
	print OUT "\t", $name;
	
	$name = get_go($db, $key, 'molecular_function', @functions);
	
	print OUT "\t", $name;
	
	print OUT "\n";
    }
}

$dbh->disconnect();
close(OUT);

sub get_go {
    my ($db, $key, $type, @parents) = @_;
    
    my $sql = qq {
	select term.id, term.name
	    from dbxref
	    inner join gene_product on (dbxref.id = gene_product.dbxref_id)
	    inner join association on (association.gene_product_id=gene_product.id)
	    inner join term on (association.term_id = term.id)
	    where dbxref.xref_dbname = '$db'
	    and dbxref.xref_key = '$key'
	    and term.term_type = '$type'
	    and term.name <> '$type'
	};
    
    my $sth = $dbh->prepare($sql) or die "Error prepare: ", $dbh->errstr;
    $sth->execute or die "Error execute: ", $dbh->errstr;
    
    my $id = -1;
    my $name = $unknown;
    $sth->bind_columns(\$id, \$name);
    
    if ($sth->fetch()) {
	$name = get_parent($id, @parents);
    }
    
    $sth->finish();


    $name =~ tr/ /_/;

    return $name;
}

sub get_parent {

    my ($child, @list) = @_;
    
    my $parent = $others;
    
    my $found = 0;
    
    for (my $i = 0; $i < @list && !$found; $i++) {
	my $item = $list[$i];
	if (belongs($child, $item)) {
	    $parent = $item;
	    $found = 1;
	}
    }
    
    return $parent;
}

sub belongs {

    my ($child, $parent) = @_;
    
    my $sql = qq {
	select p.id
	from graph_path
	inner join term as t on (t.id = graph_path.term2_id)
	inner join term as p on (p.id = graph_path.term1_id)
	where t.id = $child
	and p.id in (select term.id
		     from term
		     where name = '$parent')
    };
    
    my $sth = $dbh->prepare($sql) or die "Error prepare: ", $dbh->errstr;
    $sth->execute or die "Error execute: ", $dbh->errstr;

    my $val = 0;

    if ($sth->fetch()) {
	return $val = 1;
    }

    $sth->finish();
    
    return $val;
}