#!/usr/bin/perl -w

# POD documentation - main docs before the code

=head1 NAME

parseUNIPROT4MySQL

=head1 DESCRIPTION

This script parse the XML file containing uniprot knowledgebase, fetch informations ad insert them
into a MySQL db.

=head1 CONTACT

TEXTORIS Julien , <julien.textoris@gmail.com>

=head1 USAGE

./parseUNIPROT4MySQL.pl <XML_filename> <function>

function :
	- 'coordinate'
	- 

=cut

use strict;
use warnings;
use DBI;
use XML::SAX;
use lib './';
use MySAXHandler;

$|=1;

=head1 Variables Declaration

=over 3
 =item $filename : XML file to parse
 =item $function : implemented function to use
 =item $dbd : MySQL connection
 =item $dbname : DB Name
 =item $host : computer which host the database
 =item $user / $pass : user and password to connect DB
 =item $insert_ensembl = Insert EnsEMBL_ID into ensEMBL_ID table if it doesn't exists
 =item $insert_uniprot = Insert Uniprot_ID into Uniprot_ID table if it doesn't exists
 =item $insert_relEnsemblUniprot = insert values into the relational table (n:m relation)
 =item $parser = new XML parser object
 =item $doc = XML object loaded from $filename, option strip whitespace make parsing 30% faster
 =item $rootNode = XML root tag
 =item $AccNumber = store Uniprot Accession number of entry being processed
 =item $type = type argument of <comment> tag
 =item $value = value of <text> tag of a given comment tag

=back
 
=cut

my $filename = $ARGV[0];
my $function = $ARGV[1];
my $dbname   = "AnnotationDB";
my $host     = "localhost";
my $user     = "jtextori";
my $pass     = "marcel";

#my $dbd = DBI->connect( "DBI:mysql:$dbname;host=$host",
#	$user, $pass, { RaiseError => 1 } )
#  or die
#  "can't connect : \nerror1 ==> $DBI::errstr\nerror1 ==> $@\nerror1 ==> $!\n\n";
#
#my $insert_ensembl = $dbd->prepare('INSERT INTO ensEMBL_ID (`ensEMBL_ID`) VALUES (?)');
#my $insert_uniprot = $dbd->prepare('INSERT INTO Uniprot_ID (`Uniprot_ID`) VALUES (?)');
#my $insert_relEnsemblUniprot = $dbd->prepare('INSERT INTO ensEMBL_ID_has_Uniprot_ID (`ensEMBL_ID_ensEMBL_ID`,`Uniprot_ID_Uniprot_ID`) VALUES(?,?)');

my $parser = XML::SAX::ParserFactory->parser(Handler => MySAXHandler->new);
$parser->parse_uri($filename);

exit(0)