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<?php
//set content type and xml tag
header("Content-type: text/xml");
/**************************/
// replace these information if needed
$db_name = "test";
$table_name = "";
$host_name = "localhost";
$user_name = "root";
$password = "";
$DBlink = mysqli_connect($host_name, $user_name, $password);
$currentRow = 0;
/***************************/
if (isset($_POST["upload"])){
$timestamp = (new DateTime())->getTimestamp();
$timestamp = "upload".$timestamp;
$data = parseData($_POST["upload"]);
if(isset($_POST["tableName"])){
$result = insertToDb($_POST["tableName"], $_POST["header"],$data);
ajaxReturn($result);
}
else{
$result = insertToDb($timestamp, $_POST["header"],$data);
ajaxReturn($result);
}
}
else if (isset($_POST["processData"])){
$serviceUrl = $_POST["processData"];
$processFileHandle = $_POST["processFileHandle"];
$result = processData($serviceUrl,$processFileHandle);
ajaxReturn($result);
}
else if (isset($_POST["getData"])){
if (isset($_POST["getStart"])&&isset($_POST["getEnd"])){
$result = getData($_POST["getData"],$_POST["getStart"],$_POST["getEnd"]);
ajaxReturn($result);
}
else {
$result = getData($_POST["getData"],"","");
ajaxReturn($result);
}
}
else if (isset($_POST["getCurrentData"])){
$result = getData($_POST["getCurrentData"], $currentRow, 17);
ajaxReturn($result);
}
else if (isset($_POST["getTrackData"])){
$result = getTrackData($_POST["fileHandle"], $_POST["type"], $_POST["chrom"], $_POST["start"], $_POST["end"]);
ajaxReturn($result);
}
else if (isset($_POST["getRange"])){
$result = getRange($_POST["fileHandle"], $_POST["type"], $_POST["chrom"]);
ajaxReturn($result);
}
else if (isset($_POST["loadTooltip"])){
$result = loadTooltip($_POST["chrom"], $_POST["type"], $_POST["min"],$_POST["max"],$_POST["fileHandle"]);
ajaxReturn($result);
}
else if (isset($_POST["loadFastaData"])){
$result = loadFastaData($_POST["chrom"],$_POST["start"], $_POST["length"], $_POST["file"]);
ajaxReturn($result);
}
else if (isset($_POST["getFastaRange"])){
$result = getFastaRange($_POST["chrom"],$_POST["file"]);
ajaxReturn($result);
}
else if (isset($_POST["getFullTrackData"])){
$result = getFullTrackData($_POST["fileHandle"]);
ajaxReturn($result);
}
else if (isset($_POST["checkTable"])){
$result = checkTable($_POST["tableName"],$_POST["filePath"]);
ajaxReturn($result);
}
else {
loadTable();
}
function checkTable($tableName,$filePath){
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$sql = "SELECT * FROM {$db_name}.{$tableName} LIMIT 1";
$res = mysqli_query ($link,$sql);
$firstRow = mysqli_fetch_row($res);
if($firstRow)
return $tableName;
else{
uploadWithFilePath($tableName, $filePath);
return $tableName;
}
}
function uploadWithFilePath($tableName, $filePath){
$tempNames = explode("_", $tableName);
$data = file_get_contents($filePath);
if($tempNames[0] == "shelve" || $tempNames[0] == "shoer"){
$header = ["CHROM","START","END"];
$parsedData = [$header];
$rows = explode("\n", $data);
foreach($rows as $row){
$rowArray = explode("\t", $row);
$firstRow = [$rowArray[0],$rowArray[1],$rowArray[2]];
$secRow = [$rowArray[0],$rowArray[3],$rowArray[4]];
array_push($parsedData, $firstRow);
array_push($parsedData, $secRow);
}
insertToDb($tableName, $header,$parsedData);
}
else{
$parsedData = parseData($data);
$header = $parsedData[0];
insertToDb($tableName, $header,$parsedData);
}
}
function loadFastaData($chrom, $start, $length, $file){
// $indexFile = fopen($indexFile, "r");
// $indexArray = [];
// while (($line = fgets($indexFile))) {
// if($line !== ""){
// $lineArray = explode("\t", $line);
// array_push($indexArray,$lineArray);
// }
// }
// fclose($indexFile);
// foreach ($indexArray as $key => $value) {
// if ($value[0] == $chrom){
// $chromStart = $value[2];
// $chromLength = $value[1];
// $lineLength = $value[3];
// }
// }
$chromStart = strlen($chrom) + 2;
$lineNum = floor($start/$lineLength); //the line number of the starting bit
$startBit = $chromStart + $lineNum + $start; //starting bit position
if($file == "")
$filePath = $file.$chrom.".fa";
else
$filePath = $file."/".$chrom.".fa";
//echo filesize($filePath);
// echo $filePath;
// $file = new SplFileObject($file);
// $file->fseek($startBit);
// $resultLine1 = $file->current();
// $file->next();
// $nextLine2 = $file->current();
// $file->next();
// $nextLine3 = $file->current();
$fp = fopen($filePath, 'r');
if($fp){
fseek($fp, $startBit);
$line = fread($fp, $length+2);
// $composeLine = $resultLine1 . $nextLine2 . $nextLine3;
$returnString = str_replace("\n", "", $line);
return substr($returnString,0,$length);
}
else{
return "";
}
}
function my_fseek($fp,$pos,$first=0) {
// set to 0 pos initially, one-time
if($first) fseek($fp,0,SEEK_SET);
// get pos float value
$pos=floatval($pos);
// within limits, use normal fseek
if($pos<=PHP_INT_MAX)
fseek($fp,$pos,SEEK_CUR);
// out of limits, use recursive fseek
else {
fseek($fp,PHP_INT_MAX,SEEK_CUR);
$pos -= PHP_INT_MAX;
my_fseek($fp,$pos);
}
}
function getFastaRange($chrom, $file){
if($file == "")
$filePath = $file.$chrom.".fa";
else
$filePath = $file."/".$chrom.".fa";
$fileSize = filesize($filePath);
$fileSize = $fileSize - (strlen($chrom) + 2);
$numOfLine = ceil($fileSize/51);
$range = $fileSize - $numOfLine - 1;
// $indexFile = fopen($indexFile, "r");
// $indexArray = [];
// while (($line = fgets($indexFile))) {
// if($line !== ""){
// $lineArray = explode("\t", $line);
// array_push($indexArray,$lineArray);
// }
// }
// fclose($indexFile);
// foreach ($indexArray as $key => $value) {
// if ($value[0] == $chrom){
// $chromLength = $value[1];
// }
// }
return [0,$range];
}
function processData($serviceUrl,$processFileHandle){
$data = getData($processFileHandle,"","");
//print_r($data);
$result = httpCurlPost("http://localhost/loadingtable/data_process_service.php", $data);
$resultArray = json_decode(trim($result), TRUE);
//print_r($resultArray) ;
$timestamp = (new DateTime())->getTimestamp();
$header = $resultArray[0];
//print_r($header);
//array_pop($resultArray);
$tableName = insertToDb($timestamp,$header, $resultArray);
return $tableName;
}
function httpCurlPost($url, $params) {
//$postData = "data=";
//$postData = http_build_query($params);
// print_r($postData);
$postData = json_encode($params);
// print_r($postData);
//echo $postData;
//create name value pairs seperated by &
// foreach ($params as $k => $v) {
// $postData .= $k . '=' . $v . '&';
// }
// rtrim($postData, '&');
$ch = curl_init();
curl_setopt($ch, CURLOPT_URL, $url);
curl_setopt($ch, CURLOPT_RETURNTRANSFER, true);
curl_setopt($ch, CURLOPT_HEADER, false);
// curl_setopt($ch, CURLOPT_POST, count($postData));
curl_setopt($ch, CURLOPT_POST, 1);
curl_setopt($ch, CURLOPT_POSTFIELDS, "data=".$postData);
$output = curl_exec($ch);
//var_dump($output);
//echo $output;
curl_close($ch);
return $output;
}
function parseData($data){
$result = [];
$rows = explode("\n", $data);
foreach($rows as $row){
$rowArray = explode("\t", $row);
array_push($result, $rowArray);
}
return $result;
}
function getData($fileHandle,$start,$end){
$count = $end - $start;
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$resArray = [];
if ($start !== "" && $end !== ""){
$sql = "SELECT * FROM {$db_name}.{$fileHandle} LIMIT ".$start.",".$count;
}
else {
$sql = "SELECT * FROM {$db_name}.{$fileHandle}";
}
$res = mysqli_query ($link,$sql);
$header = [];
$firstRow = mysqli_fetch_assoc($res);
$firstRowArray = [];
foreach ($firstRow as $key => $value) {
array_push($header, $key);
array_push($firstRowArray, $value);
}
array_push($resArray, $firstRowArray);
while($row = mysqli_fetch_row($res)){
array_push($resArray, $row);
}
array_unshift($resArray, $header);
return $resArray;
//echo json_encode($resArray);
}
function mergeExonsArray($exons, $scale){
$resArray = [];
$mergedExon = $exons[0];
for ($i=1; $i < count($exons); $i++) {
if ($exons[$i][1] - $mergedExon[2] > 1/$scale){
array_push($resArray, $mergedExon);
$mergedExon[1] = $exons[$i][1];
$mergedExon[2] = $exons[$i][2];
}
else{
if ($exons[$i][2] > $mergedExon[2]){
$mergedExon[2] = $exons[$i][2];
}
}
}
$LastElement = end($resArray);
reset($resArray);
if ($mergedExon[2] != $LastElement[2] || count($resArray) == 0){
array_push($resArray, $mergedExon);
}
return $resArray;
}
function mergeExons($geneStart, $geneEnd, $Exstart, $Exend, $start,$end, $scale){
$ExStartArray = explode(",",trim($Exstart, '"'));
$ExEndArray = explode(",",trim($Exend, '"'));
if ($geneEnd-$geneStart < 1/$scale){
return [["", $ExStartArray[0],max($ExEndArray)]];
}
else{
$resArray = [];
if(count($ExStartArray) > 1){
$mergedExon = ["", $ExStartArray[0],$ExEndArray[0]];
for ($i=1; $i < count($ExStartArray); $i++) {
if ($ExStartArray[$i] - $ExEndArray[$i-1] > 1/$scale){
array_push($resArray, $mergedExon);
$mergedExon[1] = $ExStartArray[$i];
$mergedExon[2] = $ExEndArray[$i];
}
else{
if ($ExEndArray[$i] > $ExEndArray[$i-1]){
$mergedExon[2] = $ExEndArray[$i];
}
}
}
$LastElement = end($resArray);
reset($resArray);
if ($mergedExon[2] != $LastElement[2]){
array_push($resArray, $mergedExon);
}
}
else{
array_push($resArray, ["", $ExStartArray[0],$ExEndArray[0]]);
}
return $resArray;
}
}
function getGeneTrackData($fileHandle,$chrom,$start,$end){
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$resArray = [];
$exonArray = [];
$scale = 1000/($end - $start);
$sql = "SELECT `chrom`, `txStart`, `txEnd`, `name2`, `score`, `exonStarts`, `exonEnds` FROM {$db_name}.{$fileHandle}";
$sql .= " WHERE `chrom` = '".$chrom."'";
$sql .= " AND (((`txStart` BETWEEN $start AND $end) OR (`txEnd` BETWEEN $start AND $end))";
$sql .= " OR (`txStart` <= $start AND `txEnd` >= $end))";
$sql .= " ORDER BY `txStart` * 1 ASC";
$res = mysqli_query ($link,$sql);
$mergedRect = [];
$firstRow = mysqli_fetch_row($res);
$exons = mergeExons($firstRow[1],$firstRow[2],$firstRow[5], $firstRow[6], $start,$end, $scale);
//print_r($exons);
foreach ($exons as $key => $value) {
array_push($exonArray, $value);
}
$mergedRect = [$chrom,$firstRow[1],$firstRow[2],"",""];
$noMergedRect = false;
while($row = mysqli_fetch_row($res)){
$tempStartPix = ($row[1] - $start) * $scale;
$tempEndtPix = ($row[2] -$start)* $scale;
$mergedRectStartPix = ($mergedRect[1] - $start) * $scale;
$mergedRectEndtPix = ($mergedRect[2] - $start) * $scale;
$exons = mergeExons($row[1],$row[2],$row[5], $row[6], $start,$end, $scale);
foreach ($exons as $key => $value) {
array_push($exonArray, $value);
}
if ($noMergedRect){
$mergedRect = [$chrom,$row[1],$row[2],"",$row[4]];
$noMergedRect = false;
continue;
}
//print_r($row);
if (is_numeric($row[4])){
array_push($resArray, $mergedRect);
array_push($resArray, [$chrom,$row[1],$row[2],"",$row[4]]);
$noMergedRect = true;
continue;
}
if ($tempStartPix - $mergedRectEndtPix > 1){
//$mergedRect[5] = mergeExonsArray($mergedRect[5],$scale);
array_push($resArray, $mergedRect);
$mergedRect[1] = $row[1];
$mergedRect[2] = $row[2];
//$mergedRect[5] = [$exons];
}
else{
if ($mergedRect[2] < $row[2]){
$mergedRect[2] = $row[2];
}
// foreach ($exons as $key => $value) {
// array_push($mergedRect[5], $value);
// }
}
}
$LastElement = end($resArray);
reset($resArray);
if ($mergedRect[1] != $LastElement[1]){
array_push($resArray, $mergedRect);
}
$resExon = mergeExonsArray($exonArray,$scale);
return [$resArray,$resExon];
}
function getCpgTrackData($fileHandle,$chrom,$start,$end){
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$resArray = [];
$scale = 1000/($end - $start);
$fileHangleArray = explode(",", $fileHandle);
$cpgFile = $fileHangleArray[0];
$shelveFile = $fileHangleArray[1];
$shoreFile = $fileHangleArray[2];
foreach ($fileHangleArray as $key => $handle) {
$type = "";
if ($key == 0){
$type = "cpg";
}
else if ($key == 1){
$type = "shelve";
}
else {
$type = "shore";
}
$sql = "SELECT `CHROM`, `START`, `END` FROM {$db_name}.{$handle}";
$sql .= " WHERE `CHROM` = '".$chrom."'";
$sql .= " AND (((`START` BETWEEN $start AND $end) OR (`END` BETWEEN $start AND $end))";
$sql .= " OR (`START` <= $start AND `END` >= $end))";
$sql .= " ORDER BY `START` * 1 ASC";
$res = mysqli_query ($link,$sql);
$mergedRect = [];
$firstRow = mysqli_fetch_row($res);
$mergedRect = [$chrom,$firstRow[1],$firstRow[2],$type];
while($row = mysqli_fetch_row($res)){
if ($row[1] - $mergedRect[2] > 1/$scale){
array_push($resArray, $mergedRect);
$mergedRect[1] = $row[1];
$mergedRect[2] = $row[2];
$mergedRect[3] = $type;
}
else{
if ($mergedRect[2] < $row[2]){
$mergedRect[2] = $row[2];
$mergedRect[3] = $type;
}
}
}
$LastElement = end($resArray);
reset($resArray);
if ($mergedRect[1] != $LastElement[1]){
array_push($resArray, $mergedRect);
}
}
return $resArray;
}
function getTrackData($fileHandle,$type,$chrom,$start,$end){
# code...
if ($type == "gene"){
$resArray = getGeneTrackData($fileHandle,$chrom,$start,$end);
return $resArray;
}
else if ($type == "cpg"){
$resArray = getCpgTrackData($fileHandle,$chrom,$start,$end);
return $resArray;
}
//$fileHandle = $value;
else{
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$resArray = [];
$scale = 1000/($end - $start);
$sql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle}";
$sql .= " WHERE `CHROM` = '".$chrom."'";
$sql .= " AND (((`CHROM_START` BETWEEN $start AND $end) OR (`CHROM_END` BETWEEN $start AND $end))";
$sql .= " OR (`CHROM_START` <= $start AND `CHROM_END` >= $end))";
$sql .= " ORDER BY `CHROM_START` * 1 ASC";
$res = mysqli_query ($link,$sql);
$mergedRect = [];
$firstRow = mysqli_fetch_row($res);
$mergedRect = [$chrom,$firstRow[1],$firstRow[2],"",""];
$noMergedRect = false;
while($row = mysqli_fetch_row($res)){
$tempStartPix = ($row[1] - $start) * $scale;
$tempEndtPix = ($row[2] -$start)* $scale;
$mergedRectStartPix = ($mergedRect[1] - $start) * $scale;
$mergedRectEndtPix = ($mergedRect[2] - $start) * $scale;
if ($noMergedRect){
$mergedRect = [$chrom,$row[1],$row[2],"",$row[4]];
$noMergedRect = false;
continue;
}
//print_r($row);
if (is_numeric($row[4])){
array_push($resArray, $mergedRect);
array_push($resArray, [$chrom,$row[1],$row[2],"",$row[4]]);
$noMergedRect = true;
continue;
}
if ($tempStartPix - $mergedRectEndtPix > 1){
//array_push($result, $mergedRect);
array_push($resArray, $mergedRect);
$mergedRect[1] = $row[1];
$mergedRect[2] = $row[2];
}
else{
if ($mergedRect[2] < $row[2]){
$mergedRect[2] = $row[2];
}
}
}
$LastElement = end($resArray);
reset($resArray);
if ($mergedRect[1] != $LastElement[1]){
array_push($resArray, $mergedRect);
}
// $resArray = [$resArray];
// $returnArray[$name[$key]] = $resArray;
//$array = [$resArray];
return $resArray;
}
}
function getFullTrackData($fileHandle){
$returnArray = [];
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$sql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE`, `STRAND` FROM {$db_name}.{$fileHandle}";
$sql .= " ORDER BY LENGTH(`CHROM`), `CHROM`, `CHROM_START` * 1 ASC";
$res = mysqli_query ($link,$sql);
while($row = mysqli_fetch_row($res)){
array_push($returnArray, [$row[0],$row[1],$row[2],$row[3],$row[4],$row[5]]);
}
return $returnArray;
}
function getRange($fileHandle,$type,$chrom){
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$returnArray = [];
$sql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle}";
$sql .= " WHERE `CHROM` = '".$chrom."'";
$sql .= " ORDER BY `CHROM_START` * 1 ASC";
# code...
$minsql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle} ORDER BY `CHROM_START` * 1 ASC LIMIT 1";
if ($type == "gene"){
$minsql = "SELECT `chrom`, `txStart`, `txEnd`, `name2`, `score` FROM {$db_name}.{$fileHandle} ORDER BY `txStart` * 1 ASC LIMIT 1";
}
if ($type == "cpg"){
$temp = explode(",", $fileHandle);
$shelveFile = $temp[1];
$minsql = "SELECT `CHROM`, `START`, `END` FROM {$db_name}.{$shelveFile} ORDER BY `START` * 1 ASC LIMIT 1";
}
$minres = mysqli_query ($link,$minsql);
$row = mysqli_fetch_row($minres);
$min = $row[1];
array_push($returnArray, $min);
$maxsql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle} ORDER BY `CHROM_END` * 1 DESC LIMIT 1";
if ($type == "gene"){
$maxsql = "SELECT `chrom`, `txStart`, `txEnd`, `name2`, `score` FROM {$db_name}.{$fileHandle} ORDER BY `txEnd` * 1 DESC LIMIT 1";
}
if ($type == "cpg"){
$temp = explode(",", $fileHandle);
$shelveFile = $temp[1];
$maxsql = "SELECT `CHROM`, `START`, `END` FROM {$db_name}.{$shelveFile} ORDER BY `END` * 1 DESC LIMIT 1";
}
$maxres = mysqli_query ($link,$maxsql);
$row = mysqli_fetch_row($maxres);
$max = $row[2];
array_push($returnArray, $max);
return $returnArray;
}
function loadTooltip($chrom, $type, $min, $max, $fileHandle){
//return $chrom.$trackName.$type.$xCoordinate.$scale.$fileHandle;
if($type == "cpg" || $type == "shore" || $type == "shelve"){
return loadCPGTooltip($chrom,$type, $min,$max,$fileHandle);
}
else if($type == 'gene' || $type == "exon"){
return loadGeneTooltip($chrom,$type, $min,$max,$fileHandle);
}
else{
return loadBEDTooltip($chrom,$type, $min,$max,$fileHandle);
}
}
function loadCPGTooltip($chrom,$type, $min,$max,$fileHandle){
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$sql = "SELECT `START`, `END` FROM {$db_name}.{$fileHandle}";
$sql .= " WHERE `CHROM` = '".$chrom."'";
$sql .= " AND (((`START` BETWEEN $min AND $max) OR (`END` BETWEEN $min AND $max))";
$sql .= " OR (`START` <= $min AND `END` >= $max))";
$sql .= " ORDER BY `START` * 1 ASC";
$res = mysqli_query ($link,$sql);
$returnArray = [];
$compString = "";
$count = 0;
while($row = mysqli_fetch_row($res)){
$start = (string)$row[0];
$end = (string)$row[1];
//$compString.(string)$row[0]."-".(string)$row[1].", ";
$count++;
if($count > 5){
$compString = substr($compString,0,-2);
$compString .= " ... zoom in to see more ";
break;
}
else{
$compString .= $start." - ".$end.", ";
}
}
$compString = substr($compString,0,-2);
return $chrom." ".$type.": ".$compString;
}
function loadGeneTooltip($chrom,$type, $min,$max,$fileHandle){
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$sql = "SELECT `txStart`, `txEnd`, `name2`, `exonStarts`, `exonEnds` FROM {$db_name}.{$fileHandle}";
$sql .= " WHERE `chrom` = '".$chrom."'";
$sql .= " AND (((`txStart` BETWEEN $min AND $max) OR (`txEnd` BETWEEN $min AND $max))";
$sql .= " OR (`txStart` <= $min AND `txEnd` >= $max))";
$sql .= " ORDER BY `txStart` * 1 ASC";
$res = mysqli_query ($link,$sql);
$returnArray = [];
$compString = "";
$count = 0;
while($row = mysqli_fetch_row($res)){
$count++;
if($type == "gene"){
$start = (string)$row[0];
$end = (string)$row[1];
$name = (string)$row[2];
if($count > 5){
$compString = substr($compString,0,-2);
$compString .= " ... zoom in to see more ";
break;
}
else{
//$compString.(string)$row[0]."-".(string)$row[1].", ";
$compString .= $name." (".$start." - ".$end."), ";
}
}
else{
if($count > 1){
$compString = substr($compString,0,-2);
$compString .= " ... zoom in to see more ";
break;
}
else{
$name = (string)$row[2];
$start = substr((string)$row[3],0,-1);
$end = substr((string)$row[4],0,-1);
$start_array = explode(",",$start);
$end_array = explode(",",$end);
$exons = "";
foreach ($start_array as $key => $value) {
$exons .= "(".$value." - ".$end_array[$key]."), ";
}
$compString .= $name." ".$exons;
}
}
}
$compString = substr($compString,0,-2);
return $chrom." ".$type.": ".$compString;
}
function loadBEDTooltip($chrom,$type, $min,$max,$fileHandle){
$db_name = $GLOBALS['db_name'];
$link = $GLOBALS['DBlink'];
$sql = "SELECT `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle}";
$sql .= " WHERE `CHROM` = '".$chrom."'";
$sql .= " AND (((`CHROM_START` BETWEEN $min AND $max) OR (`CHROM_END` BETWEEN $min AND $max))";
$sql .= " OR (`CHROM_START` <= $min AND `CHROM_END` >= $max))";
$sql .= " ORDER BY `CHROM_START` * 1 ASC";
$res = mysqli_query ($link,$sql);
$returnArray = [];
$compString = "";
while($row = mysqli_fetch_row($res)){
$start = (string)$row[0];
$end = (string)$row[1];
$name = (string)$row[2];
$score = (string)$row[3];
//$compString.(string)$row[0]."-".(string)$row[1].", ";
$compString .= $name. " (".$start."-".$end.") Score: ".$score.", ";
}
$compString = substr($compString,0,-2);
return $chrom." ".$type.": ".$compString;
}
function ajaxReturn($result){
echo json_encode($result);
}
function insertToDb($timestamp,$header, $data){
$db_name = $GLOBALS['db_name'];
$table_name = $GLOBALS['table_name'];
$host_name = $GLOBALS['host_name'];
$user_name = $GLOBALS['user_name'];
$password = $GLOBALS['password'];
$link = mysqli_connect($host_name, $user_name, $password, $db_name);
$tableName = $timestamp;
$sql = "CREATE TABLE IF NOT EXISTS `".$tableName."` (
ID VARCHAR(10)
)";
mysqli_query ($link,$sql);
foreach($header as $colName){
$sql = "ALTER TABLE `".$tableName."` ADD $colName VARCHAR( 255 )";
mysqli_query ($link,$sql);
}
//$rows = explode("\n", $data);
array_shift($data);
$length = sizeof($data);
//sql for insert columes, this line includes column names, values will be added in the loop
$sql = "INSERT INTO ".$tableName." (ID";
$headerColumnCount = 0;
$comma = ", ";
foreach ($header as $title){
$headerColumnCount++;
$sql.= $comma . $title;
}
$sql.= ") VALUES";
$sqlCopy = $sql;
//echo $sql;
$rowNo = 1;
$countDown = 1000;
//sql for values to be inserted
// $sqlForValue = " ('". $counter ."',";
// foreach ($rowArray as $key=>$title){
// $sqlForValue.= "'". $rowArray[$key] ."',";
// }
// $sqlForValue = rtrim($sqlForValue, ",");
// $sqlForValue.= "),";
// echo $sqlForValue;
// foreach($rows as $row){
// $counter++;
// $rowArray = explode("\t", $row);
// if ($countDown !== 0){
// $sqlForValue = " ('". $counter ."',";
// foreach ($rowArray as $key=>$title){
// $sqlForValue.= "'". $rowArray[$key] ."',";
// }
// $sqlForValue = rtrim($sqlForValue, ",");
// $sqlForValue.= "),";
// $sql.= $sqlForValue;
// $countDown--;
// }
// else {
// $result = rtrim($sql, ",");
// mysqli_query ($link,$result);
// $countDown = 1000;
// $sql = $sqlCopy;
// $sqlForValue = " ('". $counter ."',";
// foreach ($rowArray as $key=>$title){
// $sqlForValue.= "'". $rowArray[$key] ."',";
// }
// $sqlForValue = rtrim($sqlForValue, ",");
// $sqlForValue.= "),";
// $sql.= $sqlForValue;
// }
// if ($counter == $length){
// $result = rtrim($sql, ",");
// mysqli_query ($link,$result);
// }
// }
foreach($data as $rowArray){
//echo $rowArray;
//$rowArray = explode("\t", $row);
$sqlForValue = " ('". $rowNo ."'";
$dataColumnCount = 0;
$comma = ", ";
foreach ($rowArray as $key=>$title){
$dataColumnCount++;
$sqlForValue.= $comma . "'". $rowArray[$key]. "'";
}
if($dataColumnCount != $headerColumnCount){
continue;
}
// $sqlForValue = rtrim($sqlForValue, ",");
$sqlForValue.= "),";
$sql.= $sqlForValue;
$rowNo++;
$countDown--;
if ($countDown == 0){
$result = rtrim($sql, ",");
mysqli_query ($link,$result);
// echo $result . "<br>";
$countDown = 1000;
$sql = $sqlCopy;
}
}
if ($sql !== $sqlCopy){
$result = rtrim($sql, ",");
// echo $result;
mysqli_query ($link,$result);
}
$sql = "SELECT @n:=0";
mysqli_query ($link,$sql);
$sql = "UPDATE ".$tableName." SET ID = @n := @n + 1";
mysqli_query ($link,$sql);
return $tableName;
//echo json_encode($tableName);
}
function loadTable(){
global $currentRow;
$db_name = $GLOBALS['db_name'];
$table_name = $GLOBALS['table_name'];
$host_name = $GLOBALS['host_name'];
$user_name = $GLOBALS['user_name'];
$password = $GLOBALS['password'];
//define variables from incoming values
if (isset($_GET["tableRef"])){
if ($_GET["tableRef"] !== ""){
$table_name = $_GET["tableRef"];
}
}
if(isset($_GET["posStart"]))
$posStart = $_GET['posStart'];
else
$posStart = 0;
if(isset($_GET["count"]))
$count = $_GET['count'];
else
$count = 100;
$currentRow = $posStart;
$totalCount = 0;
//connect to database
$link = mysqli_connect($host_name, $user_name, $password);
//$db = mysqli_select_db ("test");
//create query to products table
$sql = "SELECT * FROM {$db_name}.{$table_name}";
//if this is the first query - get total number of records in the query result
if($posStart==0){
$sqlCount = "Select count(*) as cnt from ($sql) as tbl";
$resCount = mysqli_query ($link,$sqlCount);
$rowCount=mysqli_fetch_assoc($resCount);
$totalCount = $rowCount["cnt"];
}
if(isset($_GET["name_mask"]) && isset($_GET["filter_attribute"])){
$p = $_GET['filter_attribute'];
$sql.=" Where {$p} = '".$_GET["name_mask"]."'";
$sqlCount = "Select count(*) as cnt from ($sql) as tbl";
$resCount = mysqli_query ($link,$sqlCount);
$rowCount=mysqli_fetch_assoc($resCount);
$totalCount = $rowCount["cnt"];
}
if (isset($_GET["order"]) && isset($_GET["sort_attribute"])){
$order = $_GET['order'];
$sort_attribute = $_GET['sort_attribute'];
$ifNumeric = "SELECT `".$sort_attribute."` FROM {$db_name}.{$table_name} LIMIT 1";
$res = mysqli_query ($link, $ifNumeric);
$resArray = mysqli_fetch_row($res);
if( is_numeric($resArray[0])){
$sql.=" ORDER BY $sort_attribute * 1 $order";
}
else {
$sql.=" ORDER BY $sort_attribute $order";
}
}
//add limits to query to get only rows necessary for the output
$sql.= " LIMIT ".$posStart.",".$count;
//query database to retrieve necessary block of data
$res = mysqli_query ($link,$sql);
//output data in XML format
print("<rows pos='".$posStart."' total_count='".$totalCount."'>");
while($row=mysqli_fetch_row($res)){
print("<row ID='".$row[0]."'>");
// print("<cell>");
// print($row[0]);
// print("</cell>");
// print("<cell>");
// print($row[1]);
// print("</cell>");
// print("<cell>");
// print($row[2]);
// print("</cell>");
// print("<cell>");
// print($row[3]);
// print("</cell>");
// print("<cell>");
// print($row[4]);
// print("</cell>");
// print("<cell>");
// print($row[5]);
// print("</cell>");
// print("<cell>");
// print($row[6]);
// print("</cell>");
foreach ($row as $key=>$title){
print("<cell>");
print($row[$key]);
print("</cell>");
}
print("</row>");
}
print("</rows>");
}
?>
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