/**
* Get the ids and the names of all cities
*
* @return array with objects
*/
public function getAllCities()
{
require '../database_connection/database_connect.php';
$databaseConnection = new DatabaseConnect();
$connection = $databaseConnection->connect();
$stmt = $connection->query("SET NAMES 'utf8';");
$stmt = $connection->prepare("SELECT id, name FROM cities ORDER BY name;");
$stmt->execute();
return $stmt->fetchAll(PDO::FETCH_OBJ);
}
public function getEventCategories()
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
mysql_query("set names 'utf8'");
$query = mysql_query("SELECT * FROM `EventCatigories` ") or die(mysql_error());
$stack = array();
while ($row = mysql_fetch_array($query, MYSQL_ASSOC)) {
array_push($stack, $row);
}
echo json_encode($stack);
$dbConnect->close();
}
public function getGroupList($inputs)
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
$query = mysql_query("SELECT * FROM `groups` LIMIT " . $inputs->limit . "") or die(mysql_error());
$stack = array();
while ($row = mysql_fetch_array($query)) {
$respond = array('id' => $row['Gid'], 'name' => $row['Gname'], 'ProfilePic' => $row['GProfilePic'], 'Royal' => $row['Royal']);
array_push($stack, $respond);
}
echo json_encode($stack);
$dbConnect->close();
}
public function GetFullNews($inputs)
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
mysql_query("set names 'utf8'");
$query = mysql_query("SELECT * FROM News WHERE NewsID=" . $inputs->NewsID . "");
if ($query) {
$row = mysql_fetch_array($query, MYSQL_ASSOC);
echo json_encode($row);
} else {
$respond = array('sucess' => false);
echo json_encode($respond);
}
$dbConnect->close();
}
static function getInstance()
{
if (self::$_instance == null) {
self::$_instance = new DatabaseConnect();
}
return self::$_instance;
}
public function SendFeedback($inputs)
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
$sql = "INSERT INTO `" . DB_DATABASE . "`.`Feedbacks` (`SenderID`, `FeedbackType`, `Subject`, `Message`)\n VALUES ('" . $inputs->SenderID . "', '" . $inputs->FeedbackType . "', '" . $inputs->Subject . "', '" . $inputs->Message . "');";
if (mysql_query($sql)) {
$respond = array('sucess' => true);
echo json_encode($respond);
//successfully Registering new user
} else {
$respond = array('success' => false);
echo json_encode($respond);
//an error has been accourd
}
$dbConnect->close();
}
public function GetUserBlockList($inputs)
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
$sql = mysql_query("SELECT InvitationID FROM BlockList WHERE memberID=" . $inputs->memberID . " ORDER BY InvitationID");
if ($sql) {
$stack = array();
while ($row = mysql_fetch_array($sql, MYSQL_ASSOC)) {
array_push($stack, $row);
}
echo json_encode($stack);
} else {
$respond = array('sucess' => false);
echo json_encode($respond);
}
$dbConnect->close();
}
public function retriveComments($inputs)
{
$tableName = $inputs->POSTType == 0 ? "EventsComments" : "NewsComments";
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
$sql = mysql_query("SELECT `" . $tableName . "`.`CommentID`,`members`.`name` ,`members`.`id`, `members`.`ProfilePic`\n , `" . $tableName . "`.`comment` from `" . $tableName . "` INNER JOIN `members`\n ON `members`.`id`=`" . $tableName . "`.`memberID`\n WHERE `" . $tableName . "`.`POSTID` = \"" . $inputs->POSTID . "\"\n LIMIT " . $inputs->start . ", " . $inputs->limit . " ") or die(mysql_error());
if ($sql) {
$stack = array();
while ($row = mysql_fetch_array($sql, MYSQL_ASSOC)) {
array_push($stack, $row);
}
echo json_encode($stack);
} else {
$respond = array('sucess' => false);
echo json_encode($respond);
}
$dbConnect->close();
}
public function getInvitationList($inputs)
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
$query = mysql_query("SELECT * FROM `invitationPackages` LIMIT " . $inputs->limit . "") or die(mysql_error());
$stack = array();
while ($row = mysql_fetch_array($query)) {
$invitations = new invitationPackages();
$invitations->id = $row['Packageid'];
$invitations->number = $row['number'];
$invitations->packageName = $row['packageName'];
//$invitations->VIP=$row['VIP'];
$invitations->price = $row['price'];
array_push($stack, $invitations);
}
echo json_encode($stack);
$dbConnect->close();
}
function RegisterUser($username, $password, $name, $parentEmail, $avatarSetup, $avatarImage)
{
include_once '../config/Config.php';
$conn = new DatabaseConnect();
$mysqli = $conn->connect($db_host, $db_username, $db_password, $mysql_db);
//check valid email address if entered
if (!filter_var($parentEmail, FILTER_VALIDATE_EMAIL) && $parentEmail != null) {
echo "Please try your parent's email address again";
die;
}
$md5_password = md5($password);
$hash = md5(rand(1, 10000));
$add = new Child_Functions();
//Function which either adds or creates new family entry
$add->childFamilyAdd($parentEmail, $username);
//NEED TO INSERT ID NOT USERNAME
$queryEmReg = "SELECT '" . $username . "' FROM Child_Account WHERE email ='" . $email . "'";
$emailCheck = $mysqli->query($queryEmReg);
if (!mysqli_num_rows($emailCheck) < 1) {
echo 'Username already in use';
echo $queryEmReg;
} else {
$sql = "INSERT INTO Child_Account (Username,Password,Name,ParentsEmail,hash)\n\t\t\t\t\tVALUES (?,?,?,?,?)";
//avatarSetup,avatarImage,
$mail = new Child_Functions();
//prepared query statements
if ($stmt = $mysqli->prepare($sql)) {
$stmt->bind_param("sssss", $username, $md5_password, $name, $parentEmail, $hash);
$stmt->execute();
$stmt->bind_result($result);
if ($stmt->affected_rows > 0) {
echo 'Email sent';
$mail->VerificationParent($parentEmail, $name, $hash);
} else {
echo 'Error - could not register';
}
$stmt->close();
} else {
echo 'Failed register child database query';
echo $stmt->errno;
}
}
$connect->close();
}
/**
* create connection
*/
public function __construct()
{
if (is_null(self::$_connection)) {
try {
$dbConfig = Config::getConfig()['database'];
self::$_connection = new ExtendedPdo("mysql:host={$dbConfig['host']};dbname={$dbConfig['database']};port={$dbConfig['port']}", $dbConfig['user'], $dbConfig['pass']);
self::$_connection->connect();
} catch (\Exception $e) {
Log::addError($e->getMessage(), 'db connection');
}
}
}
/**
* Selects the images for the most rated 4 landmarks
*
* @return array Array with arrays of objects
*/
public function selectLandmarkHomepageItemsImages($type)
{
$mostRated = $this->selectLandmarkHomepageItems();
$ids = array();
foreach ($mostRated as $value) {
$ids[] = (int) $value->id;
}
require 'database_connection/database_connect.php';
$databaseConnect = new DatabaseConnect();
$connection = $databaseConnect->connect();
$stmt = $connection->query("SET NAMES 'utf8';");
$images = array();
foreach ($ids as $id) {
$stmt = $connection->prepare("SELECT image FROM landmark_images WHERE place_id = :id AND type = :type LIMIT 1;");
$stmt->bindParam(':id', $id, PDO::PARAM_INT);
$stmt->bindParam(':type', $type, PDO::PARAM_STR);
$stmt->execute();
$images["{$id}"] = $stmt->fetch(PDO::FETCH_OBJ);
}
return $images;
}
function RegisterParent($email, $password, $title, $sex, $nickname, $firstname, $lastname)
{
include_once '../config/Config.php';
$conn = new DatabaseConnect();
$mysqli = $conn->connect($db_host, $db_username, $db_password, $mysql_db);
//check valid email address
if (!filter_var($email, FILTER_VALIDATE_EMAIL)) {
echo "Please enter a valid email address";
die;
} else {
//md5 level password encryption
$md5_password = md5($password);
$hash = md5(rand(1, 10000));
$queryEmReg = "SELECT * FROM parents WHERE email ='" . $email . "'";
$emailCheck = $mysqli->query($queryEmReg);
if (!mysqli_num_rows($emailCheck) < 1) {
echo 'Email address in use';
} else {
$sql = "INSERT INTO parents (email,password,title,sex,nickname,firstname,lastname,hash)\n\t\t\t\t\t\tVALUES (?,?,?,?,?,?,?,?)";
$mail = new Parents();
//prepared query statements
if ($stmt = $mysqli->prepare($sql)) {
$stmt->bind_param("ssssssss", $email, $md5_password, $title, $sex, $nickname, $firstname, $lastname, $hash);
$stmt->execute();
$stmt->bind_result($result);
if ($stmt->affected_rows > 0) {
echo 'Email sent';
$mail->VerificationEmail($email, $firstname, $hash);
} else {
echo 'Error - could not register';
}
$stmt->close();
} else {
echo 'Failed query';
}
}
}
$connect->close();
}
public function cycler($ncicli)
{
$db = new DatabaseConnect("a22docente", "softuser", "_s0ft*", "allievo17");
$select = "SELECT numero FROM numeriPrimi WHERE numero = {$ncicli}";
//da modificare
if ($db->select($select) == 0) {
for ($i = 2; $i <= $ncicli; $i++) {
$primo = $this->isPrime($i);
if ($primo == 1) {
$query = "INSERT INTO numeriPrimi (numero,primo) VALUES ({$i},{$primo})";
$db->insert($query);
}
}
$secondSelect = "SELECT sum(primo) AS quanti FROM numeriPrimi";
$res = mysql_query($secondSelect);
while ($row = mysql_fetch_assoc($res)) {
$quanti = $row['quanti'];
}
return "Trovati {$quanti} numeri primi nel database";
} else {
return "Valore {$ncicli} già presente";
}
}
/**
* Get the id of the logged in user
*
* @param string $userName
*
* @return int
*/
public function getUserId($userName)
{
require 'database_connection/database_connect.php';
$databaseConnect = new DatabaseConnect();
$connection = $databaseConnect->connect();
$stmt = $connection->prepare("SELECT id FROM users WHERE username = :userName");
$stmt->bindParam(':userName', $userName, PDO::PARAM_STR);
$stmt->execute();
while ($row = $stmt->fetch()) {
return $row['id'];
}
}
<?php
include_once '../functions/Parents.php';
include_once '../functions/DatabaseConnect.php';
$conn = new DatabaseConnect();
include '../config/Config.php';
$mysqli = $conn->connect($db_host, $db_username, $db_password, $mysql_db);
//if(isset($_GET['email']) && !empty($_GET['email']) AND isset($_GET['hash']) && !empty($_GET['hash'])){
// Verify data
//$email = mysql_escape_string($_GET['email']); // Set email variable
//$hash = mysql_escape_string($_GET['hash']); // Set hash variable
$updatePass = md5(mysql_escape_string($_POST["password"]));
$email = '*****@*****.**';
$hash = '4ef30115b941a1bcd71ffebb50c69ece';
$query = "SELECT password FROM parents WHERE email='" . $email . "' AND hash='" . $hash . "' ";
if (!($search = $mysqli->query($query))) {
echo 'Could not update password: '******'" . $updatePass . "' \n\t\t\tWHERE email ='" . $email . "' \n\t\t\tAND hash='" . $hash . "'";
$mysqli->query($update);
echo 'Thank you, your new password has been saved.';
} else {
echo 'Could not find account. Please copy and paste link from email in your browser.';
}
}
mysqli_close($conn);
public function getUserInvNumber($inputs)
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
mysql_query("set names 'utf8'");
$MembersQuery = mysql_query("SELECT `inNOR` , `inVIP` FROM `members` WHERE `id` = \"" . $inputs->id . "\" ") or die(mysql_error());
$membersRow = mysql_fetch_array($MembersQuery);
if ($membersRow) {
$respond = array('success' => true, 'inNOR' => $membersRow['inNOR'], 'inVIP' => $membersRow['inVIP']);
echo json_encode($respond);
} else {
$respond = array('success' => false);
echo json_encode($respond);
}
$dbConnect->close();
}
function taskServer()
{
include_once '../config/Config.php';
$conn = new DatabaseConnect();
$mysqli = $conn->connect($db_host, $db_username, $db_password, $mysql_db);
$time = time() / 86400;
$rounded = floor($time);
$frequency = 2;
date_default_timezone_set("Europe/London");
$time = time() / 86400;
$today = round($time);
$expiry = round($time + $frequency);
$insertTask = "INSERT INTO Child_Tasks (parenttask_id, User, Description, Reward, repeat_frequency, time_of_day, expiry)\n\t\t\t\t\tSELECT id, Child, Description, Reward, repeat_frequency, time_of_day, expiry\n\t\t\t\t\tFROM Parent_Tasks\n\t\t\t\t\tWHERE expiry = '" . $today . "'";
$updateParentExpiry = "UPDATE Parent_Tasks SET expiry = '" . $expiry . "' WHERE expiry = '" . $today . "'";
$updateChildExpiry = "UPDATE Child_Tasks SET expiry = '" . $expiry . "' WHERE expiry = '" . $today . "'";
if ($mysqli->query($insertTask)) {
if ($mysqli->query($updateParentExpiry)) {
if ($mysqli->query($updateChildExpiry)) {
echo 'Set new expiry- both child and parent';
}
}
} else {
echo 'Could not update fields';
}
//need to find number of tasks complete/failed for x days, auto destroy tasks,
//if today+1 = expiry then delete (deletes after final day)
//if completed = 1 before expiry - completed
//if completed = 0 before expiry - failed
$expired = $expiry + 1;
$deleteCompleted = "SELECT FROM Child_Tasks\n\t\t\t\tWHERE completed = 1 AND expiry = '" . $expired . "'";
$deleteFailed = "SELECT FROM Child_Tasks\n\t\t\t\tWHERE completed = 0 AND expiry = '" . $expired . "'";
//check for any expired tasks
//seperate failed and completed
//count if deleted or completed
//delete after counted
if ($result = $mysqli->query($deleteCompleted)) {
if (mysqli_num_rows($result) > 0) {
while ($row = $result->fetch_assoc()) {
$countComplete = "UPDATE Parent_Tasks SET Completed = Completed + 1\n\t\t\t\t\t\t\tWHERE id = '" . $row['id'] . "'";
if ($mysqli->query($countComplete)) {
echo 'Completed task';
$deleteQuery = "DELETE FROM Child_Tasks WHERE parenttask_id = '" . $row['id'] . "'";
if ($mysqli->query($deleteQuery)) {
echo 'Deleted completed task';
}
}
}
}
} else {
die("N/A: Database Error:" . $mysqli->error . "");
}
if ($resultF = $mysqli->query($deleteFailed)) {
if (mysqli_num_rows($resultF) > 0) {
while ($row = $resultF->fetch_assoc()) {
$countDelete = "UPDATE Parent_Tasks SET Failed = Failed + 1\n\t\t\t\t\t\t\tWHERE id = '" . $row['id'] . "'";
if ($mysqli->query($countDelete)) {
echo 'Failed task';
$deleteQuery = "DELETE FROM Child_Tasks WHERE parenttask_id = '" . $row['id'] . "'";
if ($mysqli->query($deleteQuery)) {
echo 'Deleted failed task';
}
}
}
}
} else {
die("N/A: Database Error:" . $mysqli->error . "");
}
$deleteCompleted = "DELETE FROM Child_Tasks \n\t\t\t\tWHERE completed = 1 AND expiry = '" . $expired . "'";
$deleteFailed = "DELETE FROM Child_Tasks\n\t\t\t\tWHERE completed = 0 AND expiry = '" . $expired . "'";
//have to insert into table which and then delete
$query = "SELECT id FROM Child_Tasks WHERE Confirmed = 1";
$updateQuery = "DELETE FROM Child_Tasks WHERE Confirmed = 1";
if ($upd = $mysqli->prepare($updateQuery)) {
$upd->bind_param('s', $taskID);
$upd->execute();
$upd->bind_result($login);
$upd->fetch();
echo '';
} else {
echo 'Could not delete task';
}
$mysqli->close();
}
$phpro_password = sha1($phpro_password);
/*** connect to database ***/
/*** mysql hostname ***/
$mysql_hostname = DB_HOST;
//'localhost';
/*** mysql username ***/
$mysql_username = DB_USER;
//'mysql_username';
/*** mysql password ***/
$mysql_password = DB_PASSWORD;
//'mysql_password';
/*** database name ***/
$mysql_dbname = DB_DATABASE;
//'phpro_auth';
//echo "dbname: " . $mysql_hostname . $mysql_dbname . $mysql_username . $mysql_password;
$abc = new DatabaseConnect();
#$abc->executeQuery("select count(*) from phpro_users");
$abc->executeQuery("select count(*) from addresses");
try {
$dbh = new PDO("mysql:host={$mysql_hostname};dbname={$mysql_dbname}", $mysql_username, $mysql_password);
echo "connected";
/*** $message = a message saying we have connected ***/
/*** set the error mode to excptions ***/
$dbh->setAttribute(PDO::ATTR_ERRMODE, PDO::ERRMODE_EXCEPTION);
/*** prepare the insert ***/
$stmt = $dbh->prepare("INSERT INTO phpro_users (phpro_username, phpro_password ) VALUES (:phpro_username, :phpro_password )");
/*** bind the parameters ***/
$stmt->bindParam(':phpro_username', $phpro_username, PDO::PARAM_STR);
$stmt->bindParam(':phpro_password', $phpro_password, PDO::PARAM_STR, 40);
/*** execute the prepared statement ***/
$stmt->execute();
public function DisapproveEventbyID($inputs)
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
$sql = mysql_query("SELECT `VIP` FROM `Events` WHERE `Events`.`id`=" . $inputs->Eventid) or die(mysql_error());
if ($sql) {
$row = mysql_fetch_array($sql);
if ($row["VIP"] == 1) {
//Give the user back his points
} else {
// Just Send the dissaproval messege ي
}
}
$dbConnect->close();
}
$dbConnect = new DatabaseConnect();
mysql_query("DELETE FROM `Images` WHERE `imageID`=" . $TicketId . "");
$dbConnect->close();
// if everything is ok, try to upload file
} else {
if (move_uploaded_file($_FILES["fileToUpload"]["tmp_name"], $target_file)) {
$respond = array('success' => true, 'id' => $TicketId);
createthumb($target_file, $FileName . "150x150." . $imageFileType, 150, 150);
$dbConnect = new DatabaseConnect();
mysql_query("UPDATE `" . DB_DATABASE . "`.`Images` SET `imageSrc` = '" . $FileNameOnline . "', `ext` = '" . $imageFileType . "' WHERE `Images`.`imageID` = " . $TicketId . "");
echo json_encode($respond);
//SUCESS uploading
} else {
$respond = array('success' => false);
echo json_encode($respond);
$dbConnect = new DatabaseConnect();
mysql_query("DELETE FROM `Images` WHERE `imageID`=" . $TicketId . "");
$dbConnect->close();
}
}
}
}
function createthumb($name, $filename, $new_w, $new_h)
{
$system = explode(".", $name);
if (preg_match("/jpg|jpeg/", $system[1])) {
$src_img = imagecreatefromjpeg($name);
}
if (preg_match("/png/", $system[1])) {
$src_img = imagecreatefrompng($name);
}
public function getEvents($inputs)
{
//$inputs->groupID;// -1:home page anyother value i am on a group
//$inputs->catID;//-1 uncatigorized , anyother value catigorized
//$inputs->start;
//$inputs->limit;
$timeNow = Date("Y-m-d h:m:s");
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
mysql_query("set names 'utf8'");
$Filters = "";
if ($inputs->groupID == -1) {
$Filters .= "AND `Events`.`VIP` = 1";
//Homepage
} else {
$Filters .= "AND `members`.`groupID` = " . $inputs->groupID . " ";
//Group page
}
if ($inputs->catID != -1) {
$Filters .= " AND `Events`.`eventType` = " . $inputs->catID . " ";
//catigorized
}
if (1) {
$Filters .= " AND `Events`.`TimeEnded` >= '" . $timeNow . "' ";
//catigorized
}
$query = mysql_query("SELECT\n `Events`.`id` ,\n `members`.`name`,\n `members`.`groupID` ,\n `members`.`ProfilePic` ,\n `Events`.`subject` ,\n `Events`.`VIP` ,\n `Events`.`eventType` ,\n `Events`.`picture` ,\n `Events`.`TimeEnded` ,\n `Events`.`approved`\n from `Events` INNER JOIN `members` ON `Events`.`CreatorID`=`members`.`id`\n WHERE `Events`.`approved`=1 " . $Filters . "\n ORDER BY `Events`.`VIP` DESC,\n `Events`.`timeCreated` DESC\n LIMIT " . $inputs->start . ", " . $inputs->limit . " ") or die(mysql_error());
$stack = array();
while ($row = mysql_fetch_array($query)) {
$user = array('Eventid' => $row['id'], 'CreatorName' => $row['name'], 'CreatorPic' => $row['ProfilePic'], 'subject' => $row['subject'], 'EventPic' => $row['picture'], 'catID' => $row['eventType'], 'VIP' => $row['VIP'], 'TimeEnded' => $row['TimeEnded']);
array_push($stack, $user);
}
echo json_encode($stack);
$dbConnect->close();
}
public function isInvited($inputs)
{
require_once "DataBaseConnection.php";
$dbConnect = new DatabaseConnect();
$query = mysql_query("SELECT * FROM `invitationsLog` WHERE `EventID` = \"" . $inputs->eventID . "\" AND\n `memberID` = \"" . $inputs->memberID . "\" ") or die(mysql_error());
$row = mysql_fetch_array($query);
$respond = array('sucess' => false);
if (!empty($row)) {
$respond = array('sucess' => true);
}
echo json_encode($respond);
$dbConnect->close();
}
function SendCharmsToRelative($parentID, $Charms, $ownEmail)
{
include_once '../config/Config.php';
$conn = new DatabaseConnect();
$mysqli = $conn->connect($db_host, $db_username, $db_password, $mysql_db);
$query = "UPDATE users\n\t\t\t\tSET charms = \n\t\t\t\tWHERE Username = '******'\n\t\t\t\t";
if (!($result = $mysqli->query($query))) {
die("N/A: Database Error:" . $mysqli->error . "");
}
while ($row = $result->fetch_assoc()) {
echo $row['Charms'];
}
}
/**
* Adds the place in the database
*
* @param array $data The data for the place
*/
public function addBar($data)
{
$cityId = (int) $data['city'];
$type = $data['types'];
$url = trim($data['url']);
require '../database_connection/database_connect.php';
$databaseConnect = new DatabaseConnect();
$connection = $databaseConnect->connect();
$stmt = $connection->query("SET NAMES 'utf8';");
$stmt = $connection->prepare("INSERT INTO landmark_restaurants(city_id, type, review) VALUES(:cityId, :type, :url);");
$stmt->bindParam(':type', $type, PDO::PARAM_STR);
$stmt->bindParam(':url', $url, PDO::PARAM_STR);
$stmt->bindParam(':cityId', $cityId, PDO::PARAM_INT);
$stmt->execute();
}
function __construct()
{
parent::__construct();
}
/**
* Gets the landmarks from given city
*
* @param int $id
*
* @return array
*/
public function searchLandmarkByCity($id)
{
require '../database_connection/database_connect.php';
$databaseConnect = new DatabaseConnect();
$connection = $databaseConnect->connect();
$stmt = $connection->query("SET NAMES 'utf8';");
$stmt = $connection->prepare("SELECT id, name FROM landmarks WHERE city_id = :id;");
$stmt->bindParam(':id', $id, PDO::PARAM_INT);
$stmt->execute();
return $stmt->fetchAll(PDO::FETCH_OBJ);
}
<?php include '../REDTools/REDLog.php'; include '../database/DatabaseManager.php'; include '../database/DatabaseConnect.php'; include '../filters/denovo/RepeatRegionsFilter.php'; include '../database/TableCreator.php'; include '../REDTools/REDTools.php'; include '../REDTools/SiteBean.php'; $con = DatabaseConnect::mysqlConnect(); $args = array(0); $previousTable = "bj22n_etfilter_qcffilter"; $rrFilterName = RepeatRegionsFilter::getName(); $currentTable = "bj22n_qcfilter_" . $rrFilterName; RepeatRegionsFilter::performRepeatRegionsFilter($con, $previousTable, $currentTable, $args);
static function executeFilters()
{
$startInfo = "RNA Editing Detector start\r\n" . "--------------------------\r\n" . "--------------------------\r\n";
REDLog::writeInfoLog($startInfo);
$infoPath = "../infoFile";
if (($lineArray = REDTools::readInfoFile($infoPath)) != false) {
$con = DatabaseConnect::mysqlConnect();
$userid = $lineArray[0];
$rnaVcfName = $lineArray[1];
$dnaVcfName = $lineArray[2];
$etArgs = $lineArray[3];
$qcArray = explode('/', $lineArray[4]);
$qcArgs = array($qcArray[0], $qcArray[1]);
$rrArgs = array(0);
$sjArgs = array($lineArray[5]);
$ksArgs = array(0);
$drArgs = array();
//assignment in DRMode
$lrArgs = array();
$storgePath = "G:/Taruca/data/";
$rnaVcfFilePath = $storgePath . $rnaVcfName;
$dnaVcfFilePath = $storgePath . $dnaVcfName;
if ($rnaVcfName !== "null") {
//denove mode
//load RNAVcfFile
$rnaVcfTableNameArray = RNAVCFParser::parseMultiRNAVCFFile($con, $rnaVcfFilePath, $userid);
if ($dnaVcfName !== "null") {
$dnaVcfTableNameArray = DNAVCFParser::parseMultiDNAVCFFile($con, $dnaVcfFilePath, $userid);
}
if (count($rnaVcfTableNameArray) != 0) {
$i = 0;
foreach ($rnaVcfTableNameArray as $rnaVcfTableName) {
$etTableName = REDTools::getFirstHalfTableName($rnaVcfTableName) . EditingTypeFilter::getName() . "_" . date("Ymdhisa");
EditingTypeFilter::performEditingTypeFilter($con, $rnaVcfTableName, $etTableName, $etArgs);
$qcTableName = REDTools::getFirstHalfTableName($etTableName) . QualityControlFilter::getName() . "_" . date("Ymdhisa");
QualityControlFilter::performQualityControlFilter($con, $etTableName, $qcTableName, $qcArgs);
$rrTableName = REDTools::getFirstHalfTableName($qcTableName) . RepeatRegionsFilter::getName() . "_" . date("Ymdhisa");
RepeatRegionsFilter::performRepeatRegionsFilter($con, $qcTableName, $rrTableName, $rrArgs);
$sjTableName = REDTools::getFirstHalfTableName($rrTableName) . SpliceJunctionFilter::getName() . "_" . date("Ymdhisa");
SpliceJunctionFilter::performSpliceJunctionFilter($con, $rrTableName, $sjTableName, $sjArgs);
$ksTableName = REDTools::getFirstHalfTableName($sjTableName) . KnownSNPFilter::getName() . "_" . date("Ymdhisa");
KnownSNPFilter::performKnownSNPFilter($con, $sjTableName, $ksTableName, $ksArgs);
if ($dnaVcfName == "null") {
REDTools::writeTableIntoDb($con, $userid, $ksTableName);
} else {
if (count($dnaVcfTableNameArray) == count($rnaVcfTableNameArray)) {
$drTableName = REDTools::getFirstHalfTableName($ksTableName) . DNARNAFilter::getName() . "_" . date("Ymdhisa");
$drArgs[0] = $dnaVcfTableNameArray[$i];
$drArgs[1] = $lineArray[6];
DNARNAFilter::performDNARNAFilter($con, $ksTableName, $drTableName, $drArgs);
$lrTableName = REDTools::getFirstHalfTableName($drTableName) . LikelihoodRateFilter::getName() . "_" . date("Ymdhisa");
$lrArgs[0] = $dnaVcfTableNameArray[$i];
$lrArgs[1] = $lineArray[7];
LikelihoodRateFilter::performLikelihoodRateFilter($con, $drTableName, $lrTableName, $lrArgs);
REDTools::writeTableIntoDb($con, $userid, $lrTableName);
} else {
REDLog::writeErrLog("The num of DNA sample is different from RNA sample, please check your vcf file");
}
}
$i++;
}
} else {
REDLog::writeErrLog("There is no rnaVcfTables");
}
}
$endInfo = "------------------------\r\n" . "------------------------\r\n" . "RNA Editing Detector end\r\n";
REDLog::writeInfoLog("{$endInfo}");
} else {
//sleep 10 minute，20s to test
sleep(20);
self::executeFilters();
}
}
