<?php

require ("../lib/genopar.lib.php");

if(!doAuth(LVLADM)) {
	$genopar->fechaPagina(); exit;
}

$genopar = new Genopar(__FILE__);

$genopar->abrePagina("BLAST databases management");

verGetPost(array('mtg', 'submit', 'orgsToBlast', 'runCOG', 'runPFAM', 'evalue'));
print_r($orgsToBlast);
if (!$mtg && !($orgsToBlast || $runCOG || $runPFAM)){
	/*  */
	$mtgs = $genopar->obtemMtgs();

	$genopar->abreForm();
	echo "<TABLE CELLSPACING=5 CELLPADDING=5 BORDER=1 RULES=ROWS FRAME=BOX>";
	echo "<TR>";
	echo "<TD>";
	echo "Assembly: ";
	echo "</TD>";
	echo "<TD>";
	$genopar->select("mtg", $mtgs, "","", TRUE);
	echo "</TD>";
	echo "</TR>";
	echo "<TD align=center colspan=2>";
	$genopar->submit();
	echo "</TD>";
	echo "</TABLE>";
	$genopar->fechaForm();

	$genopar->fechaPagina();
}elseif(!($orgsToBlast || $runCOG || $runPFAM)){
	$genopar->abreForm();

	$genopar->input("mtg", "hidden", $mtg);
	$genopar->mostraListaBact();

	$genopar->fechaForm();
}else{
	$genopar->abreBanco();
	
	if ($orgsToBlast){
		foreach ($orgsToBlast as $id => $name){
			
			$query = "SELECT * FROM orgsToBlast WHERE idOrg=$id";
			
			$genopar->queryBanco($query);
			$break=0;
			$download=1;
			while($lin = $genopar->getArray()){
				if ($lin['idMontagem'] == $mtg){
					$break = 1;
					break;
				}else
					$download=0;
			}
			
			if ($break) break;
			
			if ($download){
				$orgDir = "../BlastDatabases/$id";
				$ext = "faa";
				$localFile = "$orgDir/$id.$ext";
				
				if(!is_file($localFile)){
					$sql = "SELECT ftpFolder FROM taxonomy WHERE id=$id";
					$genopar->queryBanco($sql);
					$lin = $genopar->getArray();
					
					$orgFolder = $lin['ftpFolder'];				
					getFile($genopar,$id, $orgFolder, $ext);

					if (!is_file($localFile))
						$genopar->error("Nao foi possivel fazer o download do arquivo FASTA");

					$blastDB = formatDB($localFile);
				}
			}
			
			$blastOutDir = "../BlastReports/$mtg";
			if (!is_dir($blastOutDir)) mkdir($blastOutDir);
			
			$blastOutDirOrg = $blastOutDir."/".$id;
			mkdir($blastOutDirOrg);
			
// 			echo $blastOutDirOrg; exit;
			
// 			$nomeOrganismo = addslashes($name); \"".$nomeOrganismo."\"
			$orfDir = "../Fasta/$mtg/ORFs/p"; 
			if ($handle = opendir($orfDir)) {
				$query = "INSERT INTO orgsToBlast VALUES ('$mtg', $id, '".$evalue['nr']."')";
				$genopar->queryBanco($query);
				while (false !== ($file = readdir($handle))) {
					if ($file != "." && $file != "..") {
						system("cd ../bin && perl runOrfsBlast.pl ".$genopar->MySQL_Default_DBname." $mtg $orfDir/$file ../BlastDatabases/$id/$id $blastOutDirOrg");
					 }
				}
			}
		}
	}
	$blastOutDir = "../BlastReports/$mtg";

	if ($runCOG){
		$query = "INSERT INTO orgsToBlast VALUES ('$mtg', 'COG', '".$evalue['COG']."')";
		$genopar->queryBanco($query);
		$orfDir = "../Fasta/$mtg/ORFs/p";
		if ($handle = opendir($orfDir)) {
			/* This is the correct way to loop over the directory. */
			while (false !== ($file = readdir($handle))) {
				if ($file != "." && $file != "..") {
					system("cd ../bin && perl runOrfsBlastCOG.pl ".$genopar->MySQL_Default_DBname." $mtg $orfDir/$file $blastOutDir");
				}
			}
		}
	}
	
	if ($runPFAM){
		$query = "INSERT INTO orgsToBlast VALUES ('$mtg', 'PFAM', '".$evalue['COG']."')";
		$genopar->queryBanco($query);
		$orfDir = "../Fasta/$mtg/ORFs/p";
		if ($handle = opendir($orfDir)) {
			/* This is the correct way to loop over the directory. */
			while (false !== ($file = readdir($handle))) {
				if ($file != "." && $file != "..") {
					system("cd ../bin && perl runOrfsBlastPFAM.pl ".$genopar->MySQL_Default_DBname." $mtg $orfDir/$file $blastOutDir");
				}
			}
		}
	}
	
	echo '<H3>Done...</H3>';
}

$genopar->fechaPagina();

function formatDB($file){
	$dbName = substr($file, 0, -4);
	$formatDB = "/usr/local/blast/bin/formatdb -i $file -p T -n $dbName";

	system($formatDB);

	return $dbName;
}

# Conecta via FTP ao NCBI e baixa o arquivo "nome.ext"
function getFile($genopar, $idOrg, $folder, $ext){
	$ncbi = "ftp.ncbi.nih.gov";
	$USER = "anonymous";
	$PASS = "nada@lugar.algum";

	$con = ftp_connect($ncbi) or $genopar->error("NCBI indisponível.");
	ftp_login($con, $USER, $PASS);
	ftp_pasv($con, TRUE);
	
	ftp_chdir($con, "genomes/Bacteria/$folder") or $genopar->error("Nao foi possivel mudar de diretorio.");
	
	$pattern = "/.$ext$/";
	foreach(ftp_nlist($con, ".") as $file){
		if (preg_match($pattern, $file)){
			$rmtFile = $file;
			break;
		}
	}
	
	mkdir("../BlastDatabases/$idOrg");
	
	$file = "../BlastDatabases/$idOrg/$idOrg.$ext";
	$handle = fopen($file, "w");

	if (!ftp_fget($con, $handle, $rmtFile, FTP_ASCII, 0))
		$file = NULL;
	
	fclose($handle);
	ftp_close($con);

	return $file;
}
"; echo "Assembly: "; echo "	"; $genopar->select("mtg", $mtgs, "","", TRUE); echo "
"; $genopar->submit(); echo "