read_counts_date.php

<?php
/*
 * read_counts.php
 */
 
include('common_functions.php');
$config_parameters = parse_ini_file("../../config_clearance.ini", true);

//configuration of database
$db_host = $config_parameters['database_setup']['host'];
$db_user = $config_parameters['database_setup']['user'];
$db_password = $config_parameters['database_setup']['password'];
$db = $config_parameters['database_setup']['database'];

$connection_error = False;
$con = mysqli_connect($db_host,$db_user,$db_password,$db);
// Check connection
if (mysqli_connect_errno()){
    $connection_error = True;
    $error_message = '<div class="body_text">Failed to connect to MySQL: ' . mysqli_connect_error() . ' </div>';
}

echo(html_header());

?>

<p>
<form name="date_form" method="post" action="<?php echo $_SERVER['PHP_SELF']; ?>" >
	Dato (yyyymmdd): <input type="text" name="date">
	<input type="submit" name="submit" value="Submit"><br>
</p>

<?php
 
if($connection_error){
    echo $error_message;
    echo html_footer();
} else {

	echo('<div class="datacontainer">');

    $patient_cpr = $_GET['patient_cpr'];
    $patient_exam_date = $_GET['patient_exam_date'];
    $std = $_GET['std'];

    $dir = 'ClearanceResults';
    $files = array();

    //loop over the directory and find .txt files
    if ($handle = opendir($dir)) {
        while (false !== ($entry = readdir($handle))) {
            if ($entry != "." && $entry != ".." && strtolower(substr($entry, strrpos($entry, '.') + 1)) == 'txt') {
                array_push($files, $entry);
            }
        }
        closedir($handle);
    }
    
    //print_r($files);
    
    $number_of_patients_inserted = array();
    $number_of_patients_missing_database = array();
    for($k=0; $k<sizeof($files); $k++){
        //iterate over all the files in the directory
        $file_lines = file($dir . '/' . $files[$k]);

        //get date from the filename and reformat to MySQL standard
        $file_date = date("Y-m-d", filemtime($dir . '/' . $files[$k]));
        //$file_date_reformat = date("Y-m-d", strtotime($file_date . ' + 1 day'));
        if((time()-(60*60*24*31)) < strtotime($file_date) && (time()-(60*60*24*31)) < strtotime($patient_exam_date)){
	        $line_element = array();
	        for($i=0; $i<sizeof($file_lines); $i++){
	            $line_element[$i] = explode("\t", $file_lines[$i]);
	            $line_element[$i] = array_filter($line_element[$i]);
	            $line_element[$i] = array_slice($line_element[$i], 0);
	        }
	    
	        //find well number and the counts associated
	        $counts_well = array();
	        $counts_line = array();
	        for($i=0; $i<sizeof($line_element); $i++){
	            if(preg_grep("/^A.*/", $line_element[$i])) {
	                $counts_well[$line_element[$i][key(preg_grep("/^A.*/", $line_element[$i]))]] = $line_element[$i][key(preg_grep("/^A.*/", $line_element[$i])) + 2];
	                $counts_line[$i] = $line_element[$i][key(preg_grep("/^A.*/", $line_element[$i])) + 2];
	            } elseif(preg_grep("/^B.*/", $line_element[$i])) {
	                $counts_well[$line_element[$i][key(preg_grep("/^B.*/", $line_element[$i]))]] = $line_element[$i][key(preg_grep("/^B.*/", $line_element[$i])) + 2];
	                $counts_line[$i] = $line_element[$i][key(preg_grep("/^B.*/", $line_element[$i])) + 2];
	            } elseif(preg_grep("/^C.*/", $line_element[$i])) {
	                $counts_well[$line_element[$i][key(preg_grep("/^C.*/", $line_element[$i]))]] = $line_element[$i][key(preg_grep("/^C.*/", $line_element[$i])) + 2];
	                $counts_line[$i] = $line_element[$i][key(preg_grep("/^C.*/", $line_element[$i])) + 2];
	            } elseif(preg_grep("/^D.*/", $line_element[$i])) {
	                $counts_well[$line_element[$i][key(preg_grep("/^D.*/", $line_element[$i]))]] = $line_element[$i][key(preg_grep("/^D.*/", $line_element[$i])) + 2];
	                $counts_line[$i] = $line_element[$i][key(preg_grep("/^D.*/", $line_element[$i])) + 2];
	            } else {
	                //not a well match
	            }
	        }
	
	        //find the cpr number in the .txt file    
	        $cpr_array = array();
	        $cpr_lines = array();
	        $cpr_value_lines = array();
	        $std_array = array();
	        $std_array_number = array();
	        $bg_array = array();
	        for($i=0; $i<sizeof($line_element); $i++){
	            if(preg_match("/^\\d{6}-\\d{4}/", $line_element[$i][0])){
	                //array[CPR][line number -1 = array index]
	                $cpr_array[substr($line_element[$i][0],0,11)] = $i;
	        
	                //array with line numbers where we have a CPR
	                array_push($cpr_lines, $i);
	                //array with CPRs (convenience array)
	                array_push($cpr_value_lines, $line_element[$i][0]);
	                
				} elseif(substr($line_element[$i][0],0,3) == 'std' || substr($line_element[$i][0],0,3) == 'Std'){
					//array with counts from standards
					$std_number = preg_replace('/\s+/', '', substr($line_element[$i][0],4,5));
					$std_array_number[$std_number][] = $line_element[$i][3];
					array_push($std_array, $line_element[$i][3]);
				} elseif($line_element[$i][0] == 'bgg' || $line_element[$i][0] == 'bagg' || $line_element[$i][0] == 'bg' || $line_element[$i][0] == 'Bg'){
					array_push($bg_array, $line_element[$i][3]);
	            } else {
	                //there is no preg_match. Line is not a cpr number, bg or standard
	            }
	        }
	    
	        $counts_well = array_slice($counts_well, 1);
	        $counts_line = array_slice($counts_line, 1);
	        //add the end line number of the file
	        array_push($cpr_lines, sizeof($line_element));
	
	        foreach($cpr_value_lines as $key => $value){
	            $cpr_value_lines[$key] = str_replace('-', '', $value);
	        }
	    
	        $patient_data = array();
	        for($i=0; $i<sizeof($cpr_lines); $i++){
	            for($j=$cpr_lines[$i]; $j<=$cpr_lines[$i+1]; $j++){
	                if($j == $cpr_lines[$i]){
	                    $patient_data[$cpr_value_lines[$i]]['sample_0_counts'] = $counts_line[$j-1];
	                } elseif($line_element[$j][0] == '180-1' || $line_element[$j][0] == '120-1'){
	                    $patient_data[$cpr_value_lines[$i]]['sample_1_counts'] = $counts_line[$j-1];
	                } elseif($line_element[$j][0] == '180-2' || $line_element[$j][0] == '120-2'){
	                    $patient_data[$cpr_value_lines[$i]]['sample_2_counts'] = $counts_line[$j-1];
	                } elseif($line_element[$j][0] == '24-1' || $line_element[$j][0] == '24t-1'){
	                    $patient_data[$cpr_value_lines[$i]]['sample_3_counts'] = $counts_line[$j-1];
	                } elseif($line_element[$j][0] == '24-2' || $line_element[$j][0] == '24t-2'){
	                    $patient_data[$cpr_value_lines[$i]]['sample_4_counts'] = $counts_line[$j-1];
	                } elseif($line_element[$j][0] == 'tom'){
	                    $patient_data[$cpr_value_lines[$i]]['background_2_counts'] = $counts_line[$j-1];
	                } elseif($line_element[$j][0] == 'bgg' || $line_element[$j][0] == 'bagg' || $line_element[$j][0] == 'bg'){
	                    $patient_data[$cpr_value_lines[$i]]['background_1_counts'] = $counts_line[$j-1];
	                } elseif(strtolower(substr($line_element[$j][0], 0, 3)) == 'std'){
	                    $patient_data[$cpr_value_lines[$i]]['standard_1_counts'] = $counts_line[$j-1];
	                }
	                //Add the standard counts to the array
	                $patient_data[$cpr_value_lines[$i]]['standard_2_counts'] = $std_array_number[$std][rand(0,sizeof($std_array)-1)];
	            }
	        }
	    
	        //print_r($patient_data);
	        //FIND A BETTER QUERY!!! THIS WILL NOT ALWAYS WORK!
	        //$query_find_patient = "SELECT accession_number FROM patient_data WHERE patient_cpr='$patient_cpr' and patient_exam_date BETWEEN '$file_date_reformat' - INTERVAL 7 DAY and '$file_date_reformat' LIMIT 1";
	        $query_find_patient = "SELECT accession_number FROM patient_data WHERE patient_cpr='$patient_cpr' and patient_exam_date='$patient_exam_date' LIMIT 1";
	        //echo $query_find_patient . '<br>';
	        $result = mysqli_query($con, $query_find_patient);
	        if(mysqli_num_rows($result) > 0  && $std !== ''){
	            $row = mysqli_fetch_array($result);
	            $accession_number = $row['accession_number'];
	            
	            //create the sql queries
				reset($patient_data);
				for($i=0; $i<sizeof($patient_data); $i++){
					//echo $files[$k] . ' : ' . key($patient_data) . ' : ' . $patient_cpr . '<br>';
					if(key($patient_data) == $patient_cpr){
						$query = 'update patient_values set ';
						if(!array_key_exists('background_1_counts', $patient_data[key($patient_data)])){
							$patient_data[key($patient_data)]['background_1_counts'] = $bg_array[rand(0,sizeof($bg_array)-1)];
						}
						if(!array_key_exists('background_2_counts', $patient_data[key($patient_data)])){
							$patient_data[key($patient_data)]['background_2_counts'] = $bg_array[rand(0,sizeof($bg_array)-1)];
						}
						if(!array_key_exists('standard_1_counts', $patient_data[key($patient_data)])){
							$patient_data[key($patient_data)]['standard_1_counts'] = $std_array_number[$std][rand(0,sizeof($std_array)-1)];
						}
						foreach($patient_data[key($patient_data)] as $key => $value){
							$query = $query . $key . '="' . $value . '", ';
						}
						$query = $query . 'counts_file="' . $files[$k] . '"';
						$query = $query . ' where accession_number="' . $accession_number .'"';
						//echo $query . '<br>';
						$result_counts = mysqli_query($con, $query);
						if($result_counts){
	                        echo '<div style="color:#008000">Tællinger indsat på patient (' . $patient_cpr . ') fra filen <a class="txtlink" href="ClearanceResults/' . $files[$k] . '">' . $files[$k] . '</a></div>';
	                    } else {
	                        echo 'Ups. Pinligt! Noget gik galt.<br>';
	                        echo $query;
	                    }
						 
						array_push($number_of_patients_inserted, True);
					} else {
						//echo '<div style="color:#FF0000">Patient-CPR (' . key($patient_data) .') blev ikke fundet i ' . $files[$k] . '</div>';
						array_push($number_of_patients_inserted, False);
					}
					next($patient_data);
					
				}
				array_push($number_of_patients_missing_database, True);
	        } else {
				array_push($number_of_patients_missing_database, False);
	            //echo 'Patienten (' . $patient_cpr .') blev ikke fundet. Er injektionstidspunktet angivet?<br>';
	        }
	    }
	}
    if(count(array_filter($number_of_patients_missing_database)) < 1){
		echo '<div>Mismatch mellem undersøgelsesdato og tidssstemplet på .txt-filen og/eller ingen standard angivet. Forsøger du at hente målinger, der er mere end 14 dage gamle?</div>';
		echo '<div>Vil du selv kigge <a href="list_txtfiles.php">.txt-filerne</a> igennem?</div><br>';
	}
    elseif(count(array_filter($number_of_patients_inserted)) < 1){
		echo '<div style="color:#FF0000">Patient-CPR (' . $patient_cpr . ') blev ikke fundet</div>';
		echo '<div>Vil du selv kigge <a href="list_txtfiles.php">.txt-filerne</a> igennem?</div>';
	}
    echo('<input type="button" class="button" value="Tilbage til arbejdsarket" onclick="window.location.href=\'create_worksheet.php?' . parse_url($_SERVER['REQUEST_URI'], PHP_URL_QUERY) . '\'">');
    echo('</div>');
    echo(html_footer());
}
    
?>