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VQI_GenomeBrowser/dynamic_loading.php
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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(); | |
| $data = parseData($_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["fileHandles"], $_POST["name"], $_POST["chrom"], $_POST["start"], $_POST["end"]); | |
| ajaxReturn($result); | |
| } | |
| else if (isset($_POST["getRange"])){ | |
| $result = getRange($_POST["fileHandles"], $_POST["name"], $_POST["chrom"]); | |
| ajaxReturn($result); | |
| } | |
| else if (isset($_POST["loadTooltip"])){ | |
| $result = loadTooltip($_POST["chrom"],$_POST["trackName"], $_POST["type"], $_POST["min"],$_POST["max"],$_POST["fileHandle"]); | |
| ajaxReturn($result); | |
| } | |
| else if (isset($_POST["loadFastaData"])){ | |
| $result = loadFastaData($_POST["chrom"],$_POST["start"], $_POST["length"], $_POST["file"],$_POST["indexFile"]); | |
| ajaxReturn($result); | |
| } | |
| else if (isset($_POST["getFastaRange"])){ | |
| $result = getFastaRange($_POST["chrom"],$_POST["indexFile"]); | |
| ajaxReturn($result); | |
| } | |
| else if (isset($_POST["getFullTrackData"])){ | |
| $result = getFullTrackData($_POST["fileHandles"]); | |
| ajaxReturn($result); | |
| } | |
| else { | |
| loadTable(); | |
| } | |
| function loadFastaData($chrom, $start, $length, $file, $indexFile){ | |
| $indexFile = fopen($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]; | |
| } | |
| } | |
| $lineNum = floor($start/$lineLength); //the line number of the starting bit | |
| $startBit = $chromStart + $lineNum + $start; //starting bit position | |
| $file = new SplFileObject($file); | |
| $file->fseek($startBit); | |
| $resultLine1 = $file->current(); | |
| $file->next(); | |
| $nextLine2 = $file->current(); | |
| $file->next(); | |
| $nextLine3 = $file->current(); | |
| $composeLine = $resultLine1 . $nextLine2 . $nextLine3; | |
| $returnString = str_replace("\n", "", $composeLine); | |
| return substr($returnString,0,$length); | |
| } | |
| function getFastaRange($chrom, $indexFile){ | |
| $indexFile = fopen($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 = $value[1]; | |
| } | |
| } | |
| return [0,$chromLength]; | |
| } | |
| 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){ | |
| $ExStartArray = explode(",",substr($Exstart,0,-1)); | |
| $ExEndArray = explode(",",substr($Exend,0,-1)); | |
| 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 $resArray; | |
| } | |
| } | |
| function getHG19TrackData($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 $resArray; | |
| } | |
| function getTrackData($fileHandles,$name,$chrom,$start,$end){ | |
| $returnArray = []; | |
| foreach ($fileHandles as $key => $value) { | |
| # code... | |
| if ($name[$key] == "HG19"){ | |
| $resArray = getHG19TrackData($fileHandles[$key],$chrom,$start,$end); | |
| $returnArray["HG19"] = $resArray; | |
| continue; | |
| } | |
| if ($name[$key] == "cpg"){ | |
| $resArray = getCpgTrackData($fileHandles[$key],$chrom,$start,$end); | |
| $returnArray["cpg"] = $resArray; | |
| continue; | |
| } | |
| $fileHandle = $value; | |
| $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; | |
| } | |
| return $returnArray; | |
| } | |
| function getFullTrackData($fileHandles){ | |
| $returnArray = []; | |
| foreach ($fileHandles as $key => $value) { | |
| $fileHandle = $value; | |
| $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 $returnArray; | |
| } | |
| function getRange($fileHandles,$name,$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."'"; | |
| $sql .= " ORDER BY `CHROM_START` * 1 ASC"; | |
| foreach ($fileHandles as $key => $value) { | |
| # code... | |
| $fileHandle = $value; | |
| $minsql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle} ORDER BY `CHROM_START` * 1 ASC LIMIT 1"; | |
| if ($name[$key] == "HG19"){ | |
| $minsql = "SELECT `chrom`, `txStart`, `txEnd`, `name2`, `score` FROM {$db_name}.{$fileHandle} ORDER BY `txStart` * 1 ASC LIMIT 1"; | |
| } | |
| if ($name[$key] == "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,$minsql); | |
| while($row = mysqli_fetch_row($minres)) | |
| { | |
| $min = $row[1]; | |
| array_push($returnArray, $min); | |
| } | |
| $maxsql = "SELECT `CHROM`, `CHROM_START`, `CHROM_END`, `GENESYMBOL`, `SCORE` FROM {$db_name}.{$fileHandle} ORDER BY `CHROM_END` * 1 DESC LIMIT 1"; | |
| if ($name[$key] == "HG19"){ | |
| $maxsql = "SELECT `chrom`, `txStart`, `txEnd`, `name2`, `score` FROM {$db_name}.{$fileHandle} ORDER BY `txEnd` * 1 DESC LIMIT 1"; | |
| } | |
| if ($name[$key] == "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,$maxsql); | |
| while($row = mysqli_fetch_row($maxres)) | |
| { | |
| $max = $row[2]; | |
| array_push($returnArray, $max); | |
| } | |
| } | |
| return $returnArray; | |
| } | |
| function loadTooltip($chrom,$trackName, $type, $min, $max, $fileHandle){ | |
| //return $chrom.$trackName.$type.$xCoordinate.$scale.$fileHandle; | |
| if($trackName == "cpg"){ | |
| return loadCPGTooltip($chrom,$type, $min,$max,$fileHandle); | |
| } | |
| else if($trackName == 'HG19'){ | |
| return loadHG19Tooltip($chrom,$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.": ".$compString; | |
| } | |
| function loadHG19Tooltip($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); | |
| $tableName = "upload".$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>"); | |
| } | |
| ?> |