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Search_R_php.php
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Search_R_php.php
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<?php
/* Excel reader setup to read from CTV flat file */
//require_once 'Excel/reader.php';
//echo "Hello";
// print_r($_POST);
// exit;
$time_start = time();
$time_lapse = 0;
require_once 'Excel/excel_reader2.php';
$data = new Spreadsheet_Excel_Reader("CTV_data_2016-xls.xls");
// $data = new Spreadsheet_Excel_Reader("ctv_data.xls");
error_reporting(E_ALL ^ E_NOTICE);
$search_var=$_POST['compoundName']; //Retrieve compound name from user
$mol_Weight =$_POST['MolWeight']; //Retrieve molecular weight
$search= $_POST['searchType'];
$chem_rowspan = 0;
// Search data table
for ($i = 1; $i <= $data->rowcount($sheet_index=0); $i++) {
$compound_match = 0;
if(strcasecmp(strtolower($data->val($i,3)), strtolower($_POST['compoundName'])) ==0) {
// if the compound name matches
$compound_match = 1;
$value_RfD = $data->val($i, 15);
$source_RfD = $data->val($i, 20);
$value_RfC = $data->val($i, 23);
$source_RfC = $data->val($i, 28);
$value_OSF = $data->val($i, 31);
$source_OSF = $data->val($i, 36);
$value_IUR = $data->val($i, 39);
$source_IUR = $data->val($i, 44);
$value_CPV = $data->val($i, 47);
$source_CPV = $data->val($i, 52);
$has_a_value = 0;
if(($_POST['refDose'] == "true" && $value_RfD != 0 )|| ($_POST['refConc'] == "true" && $value_RfC != 0 ) || ($_POST['oralSlope'] == "true" && $value_OSF != 0 ) || ($_POST['ihalUnit'] == "true" && $value_IUR != 0 ) || ($_POST['cancPot'] == "true" && $value_CPV != 0 )) {
// if there is any value available.
$has_a_value = 1;
}
break;
} // end of text match, if(strcasecmp($data->val($i,2), $_POST['compoundName']) ==0) {}
} // end of going through rows, for ($i = 1; $i <= $data->rowcount($sheet_index=0); $i++) {}
// if any model is needed
$any_model_needed = $_POST['refDose'] == "true" && $value_RfD == 0;
$any_model_needed = $any_model_needed || ($_POST['refConc'] == "true" && $value_RfC == 0);
$any_model_needed = $any_model_needed || ($_POST['oralSlope'] == "true" && $value_OSF == 0);
$any_model_needed = $any_model_needed || ($_POST['ihalUnit'] == "true" && $value_IUR == 0);
$any_model_needed = $any_model_needed || ($_POST['cancPot'] == "true" && $value_CPV == 0);
$any_model_needed = $any_model_needed || $_POST['onbd'] == "true";
$any_model_needed = $any_model_needed || $_POST['noel'] == "true" || $_POST['onbdl'] == "true";
if ($any_model_needed){
// Start model
$smilesValue = $_POST['smilee'];
$process_id = "pi_". rand ( 100000 , 999999);
$file = 'C:\\4_R\\ToxValue\\Prediction\\Prediction_temp_files\\'. $process_id. '_input.txt';
// Write the contents back to the file
file_put_contents($file, $smilesValue);
$R_command =
'cmd.exe /c C:\"Program Files"\R\R-3.4.1\bin\Rscript C:\4_R\ToxValue\Prediction\Prediction_Script\Predict_new_chemical_Rscript_v3.R '. $process_id;
// execute shell command.
shell_exec ( $R_command );
$warning_file = 'C:\\4_R\\ToxValue\\Prediction\\Prediction_temp_files\\'. $process_id. '_warn.txt';
$warning = file_exists($warning_file);
// echo "Warning: ". $warning;
$warn_message = file_get_contents($warning_file);
$warn_message = str_replace ("use" , "use. <br>" , $warn_message);
$warn_message = str_replace ("imputed" , "imputed." , $warn_message);
}
if($warning){
$display_status = "none";
}
echo '<link href="css/bootstrap.css" rel="stylesheet">';
echo '<script type="text/javascript" src="js/customScript.js"></script>';
echo ' <style>
td {
border: 1px solid black;
padding-left: 1px;
padding-right: 1px;
}
#title{border-top: 10px;}
</style>';
echo '<br><br><div class="row">';
echo ' <h2 style="background-color:;">Step 4<small>: Results</small></h2>';
echo '<div class="col-lg-3 col-md-3 col-sm-3 col-xs-3" style="background-color: ;">';
$imageValue = $_POST[' '];
echo '';// ' <div style="text-align: left;"> ';
// echo ' <img src="data:image/png;base64,' . $imageValue . '" />';
if($search=='name' || $search=='cas')
{
echo '<img src="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/'.$search_var.'/png" />';
}
elseif ($search=='smiles')
{
echo '<img src="https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/'.$search_var.'/png" />';
}
echo ' </div>'; // end first div in row.
echo ' <div class="col-lg-1 col-md-1 col-sm-1 col-xs-1"></div>';
echo ' <div class="col-lg-8 col-md-8 col-sm-8 col-xs-8" style="background-color:;"><br><br><br>';
echo " <p><b>Common Name: $search_var </b></p>";
echo ' <ul id="legend_ul" class="legend" style="display: '. $display_status. ';">';
echo ' <li><span class="superawesome" style="background-color: Beige;" ></span>';
echo ' <B style="text-indent: -30px;">';
echo 'These value were retrieved from publicly available sources ';
echo ' (<a href="CTV_data_2016-xls.xls" target="_blank">Data Table</a>).</B></li>';
echo ' <li><span class="superawesome" style="background-color: LightCyan;">';
echo ' </span> <b>These values were predicted.</B></li>';
echo ' </ul>';
echo ' </div>'; // end of second div in row
echo '</div>'; // end of row
echo '<div class="row">
<div class="col-lg-12 col-md-12 col-sm-12 col-xs-12" style="background-color:;">';
echo '<div style = "width-max: 500px; margin:auto; background-color:; ">';
// this div holds the table.
if($warning){
echo <<< EOT
<div id="warning_div" style="margin-left: 20px; font-weight: bold; background-color: Salmon; padding: 50px; padding-top: 30px;
padding-bottom: 30px;">
$warn_message
<br><br>
<button class="btn btn-primary" onclick="Continue_Function()">Continue</button>
<a class="btn btn-success" href="index_R.php">Start Over</a>
</div>
<script>
function Continue_Function(){
// alert("h");
// $("#compResults").show();
$("#compResults_display").show();
$("#legend_ul").show();
$("#two_buttons").show();
$("#notes").show();
$("#warning_div").hide();
};
</script>
EOT;
}
for ($j = 0; $j < 2; $j++) { // produce two tables one for display and one for download.
if($j==0){
echo '<table id="compResults" border="2" style="text-align: center; margin: auto; padding-right: 3px; padding-left: 3px; display: none;">';
if($has_a_value == 1){
echo '<tr style = "border-top: 8px solid black;"><td>Chemical name</td>';
echo '<td colspan="2">Endpoint</td><td colspan="2">Toxicity value</td>';
echo '<td>Unit</td><td colspan="2">Source</td></tr>';
}
}
if($j==1){
$GLOBALS['chem_rowspan'] = $chem_rowspan;
echo '<table id="compResults_display" border="2" style="text-align: center; margin: auto; padding-right: 3px; padding-left: 3px; display: '. $display_status. ';">';
if($compound_match == 1 && $has_a_value == 1){
echo '<tr style = "border-top: 8px solid black;">';
echo '<td>Chemical name</td>';
echo '<td colspan="2">Endpoint</td><td colspan="2">Toxicity value</td>';
echo '<td>Unit</td><td colspan="2">Source</td></tr>';
}
}
$GLOBALS['chem_display'] = 1;
if(($_POST['refDose'] == "true" || $_POST['refDose'] == "true_2") && $value_RfD != 0 ){
Display_exist_value($_POST['compoundName'], "Reference Dose", $value_RfD, $source_RfD, 'mg/(kg·day)');
$_POST['refDose'] = "true_2";
if($j==0){$chem_rowspan += 1;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if(($_POST['refConc'] == "true" || $_POST['refConc'] == "true_2") && $value_RfC != 0 ){
Display_exist_value($_POST['compoundName'], "Reference Concentration", $value_RfC, $source_RfC, 'mg/m<sup>3</sup>');
$_POST['refConc'] = "true_2";
if($j==0){$chem_rowspan += 1;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if(($_POST['oralSlope'] == "true" || $_POST['oralSlope'] == "true_2") && $value_OSF != 0 ){
Display_exist_value($_POST['compoundName'], "Oral Slope Factor", $value_OSF, $source_OSF, 'risk per mg/(kg·day)');
$_POST['oralSlope'] = "true_2";
if($j==0){$chem_rowspan += 1;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if(($_POST['cancPot'] == "true" || $_POST['cancPot'] == "true_2") && $value_CPV != 0 ){
Display_exist_value($_POST['compoundName'], "Cancer Potency Value", $value_CPV, $source_CPV, 'risk per mg/(kg·day)');
$_POST['cancPot'] = "true_2";
if($j==0){$chem_rowspan += 1;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if(($_POST['ihalUnit'] == "true" || $_POST['ihalUnit'] == "true_2") && $value_IUR != 0 ){
Display_exist_value($_POST['compoundName'], "Inhalation Unit Risk", $value_IUR, $source_IUR, 'risk per µg/m<sup>3</sup>');
$_POST['ihalUnit'] = "true_2";
if($j==0){$chem_rowspan += 1;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if ($any_model_needed){
if($warning){
echo '<tr><td colspan="7" bgcolor="Salmon" align = "left" style="color:;"><div style="margin-left: 20px; font-weight: bold;"> ';
echo $warn_message;
echo '</div></tr></td> ';
}
// display table header
echo '<tr ';
echo 'style = "all: none; border: 5px; border-top: 8px solid black; ';
echo 'border-bottom: 2px solid black; ">';
if ($GLOBALS['chem_display'] == 1){echo '<td>Chemical name</td>';}
echo '<td>Model Name</td><td>Unit</td><td>Prediction</td>';
echo '<td>Lower 95%<sup>*</sup></td><td>Upper 95%<sup>*</sup></td><td>Appl Domain<sup>**</sup></td>';
echo '</tr>';
$csv = array_map('str_getcsv', file('C:\\4_R\\ToxValue\\Prediction\\Prediction_temp_files\\'. $process_id. '_output.csv'));
if($_POST['refDose'] == "true"){
$log_value = $csv[1][1];
$Lower_CI = $csv[1][2];
$Upper_CI = $csv[1][3];
$sigma_value = $csv[1][4];
Prediction_Display($_POST['compoundName'], 'CTV Reference Dose (RfD)', $log_value, $mol_Weight, ' -Log<sub>10</sub>Mol/(kg·day)', 'mg/(kg·day)', $Lower_CI, $Upper_CI, $sigma_value);
if($j==0){$chem_rowspan += 2;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if($_POST['noel'] == "true") {
$log_value = $csv[2][1];
$Lower_CI = $csv[2][2];
$Upper_CI = $csv[2][3];
$sigma_value = $csv[2][4];
Prediction_Display($_POST['compoundName'], 'CTV Reference Dose NO(A)EL', $log_value, $mol_Weight, ' -Log<sub>10</sub>Mol/(kg·day)', 'mg/(kg·day)', $Lower_CI, $Upper_CI, $sigma_value);
if($j==0){$chem_rowspan += 2;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if($_POST['onbd'] == "true"){
$log_value = $csv[4][1];
$Lower_CI = $csv[4][2];
$Upper_CI = $csv[4][3];
$sigma_value = $csv[4][4];
Prediction_Display($_POST['compoundName'], 'CTV Reference Dose (RfD) BMD', $log_value, $mol_Weight, ' -Log<sub>10</sub>Mol/(kg·day)', 'mg/(kg·day)', $Lower_CI, $Upper_CI, $sigma_value);
if($j==0){$chem_rowspan += 2;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if($_POST['onbdl'] == "true"){
$log_value = $csv[3][1];
$Lower_CI = $csv[3][2];
$Upper_CI = $csv[3][3];
$sigma_value = $csv[3][4];
Prediction_Display($_POST['compoundName'], 'CTV Reference Dose (RfD) BMDL', $log_value, $mol_Weight, ' -Log<sub>10</sub>Mol/(kg·day)', 'mg/(kg·day)', $Lower_CI, $Upper_CI, $sigma_value);
if($j==0){$chem_rowspan += 2;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if($_POST['refConc'] == "true"){
$log_value = $csv[7][1];
$Lower_CI = $csv[7][2];
$Upper_CI = $csv[7][3];
$sigma_value = $csv[7][4];
Prediction_Display($_POST['compoundName'], 'CTV Reference Concentration (RfC)', $log_value, $mol_Weight, ' -Log<sub>10</sub>Mol/m<sup>3</sup>', 'mg/m<sup>3</sup>', $Lower_CI, $Upper_CI, $sigma_value);
if($j==0){$chem_rowspan += 2;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if($_POST['oralSlope'] == "true"){
$log_value = $csv[5][1];
$Lower_CI = $csv[5][2];
$Upper_CI = $csv[5][3];
$sigma_value = $csv[5][4];
Prediction_Display($_POST['compoundName'], 'CTV Oral Slope Factor (OSF)', $log_value, $mol_Weight, 'Log<sub>10</sub>(risk per Mol/(kg·day))', 'risk per mg/(kg·day)', $Lower_CI, $Upper_CI, $sigma_value);
if($j==0){$chem_rowspan += 2;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if($_POST['cancPot'] == "true"){
$log_value = $csv[6][1];
$Lower_CI = $csv[6][2];
$Upper_CI = $csv[6][3];
$sigma_value = $csv[6][4];
// echo 'CPV: '. $log_value_1. ', '. $log_value_2. ', '. $log_value;
Prediction_Display($_POST['compoundName'], 'CTV Cancer Potency Value (CPV)', $log_value, $mol_Weight,'Log<sub>10</sub>(risk per Mol/(kg·day))', 'risk per mg/(kg·day)', $Lower_CI, $Upper_CI, $sigma_value);
if($j==0){$chem_rowspan += 2;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
if($_POST['ihalUnit'] == "true"){
$log_value = $csv[8][1];
$Lower_CI = $csv[8][2];
$Upper_CI = $csv[8][3];
$sigma_value = $csv[8][4];
Prediction_Display($_POST['compoundName'], 'CTV Inhalation Unit Risk (IUR)', $log_value, $mol_Weight, 'Log<sub>10</sub>(m<sup>3</sup>/Mol)', 'risk per µg/m<sup>3</sup>', $Lower_CI, $Upper_CI, $sigma_value);
if($j==0){$chem_rowspan += 2;}
if($j==1){$GLOBALS['chem_display'] = 0; }
}
// function Prediction_Display($Chemical_name, $model_name, $model_value, $mol_Weight, $model_unit, $converted_unit, $Lower_CI, $Upper_CI, $sigma_value)
} // end of if ($any_model_needed){}
echo '</table><br><br>';
} // end of for ($j = 0; $j <= 2; $j++)
echo '</div></div>';
echo '</div></div><br>'; // end of div row, and end of div colum
echo '<div id="two_buttons" style="display: '. $display_status. ';">';
echo ' <p align="center">'; // 2 buttons
echo ' <input type="button" class="btn btn-primary" id = "Export_CSV" value="Export as CSV">';
echo ' <a class="btn btn-success" href="index_R.php">Start Over</a>';
echo ' </p>';
echo '</div>'; // end of div for 2 buttons
echo '<script>
$("#Export_CSV").click(function() {
// alert("");
$("#compResults").show();
$("#compResults").table2CSV();
$("#compResults").hide();
})</script>
';
echo '<br><br>';
echo '<div id = "notes" style="display: '. $display_status. ';">';
echo '* One-tailed confidence bounds, based on residuals from cross validation.<br>';
echo '** Number of σ. Typical applicability domain cutoffs are <3σ for a less restrictive domain and <1σ for a more restrictive domain. A negative value indicates the chemical is within the applicability domain. <br><div>';
function E_or_point($input_value){
if ((abs($input_value) >= 1000 || abs($input_value) < 0.001) && $input_value <> 0){
$output_value = sprintf("%.2e", $input_value);}
elseif(abs($input_value) >= 100 && abs($input_value) < 1000){
$output_value = round($input_value, 0);
}
elseif(abs($input_value) >= 10 && abs($input_value) < 100){
$output_value = sprintf("%01.1f", round($input_value, 1));
}
elseif((abs($input_value) >= 1 && abs($input_value) < 10) || $input_value == 0){
$output_value = sprintf("%01.2f", round($input_value, 2));
}
elseif(abs($input_value) >= 0.1 && abs($input_value) < 1){
$output_value = sprintf("%01.3f", round($input_value, 3));
}
elseif(abs($input_value) >= 0.01 && abs($input_value) < 0.1){
$output_value = sprintf("%01.4f", round($input_value, 4));
}
elseif(abs($input_value) >= 0.001 && abs($input_value) < 0.01){
$output_value = sprintf("%01.5f", round($input_value, 5));
}
else{$output_value = round($input_value, 3);}
return $output_value;
}
function Prediction_Display($Chemical_name, $model_name, $model_value, $mol_Weight, $model_unit, $converted_unit, $Lower_CI, $Upper_CI, $sigma_value)
{
// echo '<br>$model_value: '. $model_value.'<br>';
global $j;
if ($model_value != 0){
$sigma_value_f = E_or_point($sigma_value);
$Lower_95 = $Lower_CI;
$Upper_95 = $Upper_CI;
// echo '$Upper_95 = $model_value + $Upper_CI: '. $Upper_95, $model_value, $Upper_CI;;
if ($model_name == 'CTV Oral Slope Factor (OSF)' || $model_name== 'CTV Cancer Potency Value (CPV)' || $model_name == 'CTV Inhalation Unit Risk (IUR)' ){ // three models that mole is on bottom.
$mole_model = 1/pow(10, $model_value);
$mole_lower = 1/pow(10, $Lower_95);
$mole_upper = 1/pow(10, $Upper_95);
if ($model_name == 'Oral Slope Factor'){
$Inverted_converted = $mole_model * (1000 * 1000 * $mol_Weight);
$Inverted_converted_lower = $mole_lower * (1000 * 1000 * $mol_Weight);
$Inverted_converted_upper = $mole_upper * (1000 * 1000 * $mol_Weight);
}
else{
$Inverted_converted = $mole_model * (1000 * $mol_Weight);
$Inverted_converted_lower = $mole_lower * (1000 * $mol_Weight);
$Inverted_converted_upper = $mole_upper * (1000 * $mol_Weight);
}
$converted_value = 1/$Inverted_converted;
$converted_lower = 1/$Inverted_converted_lower;
$converted_upper = 1/$Inverted_converted_upper;
// echo '$model_value. $Lower_95. $Upper_95: '.$model_value. ' '. $Lower_95. $Upper_95. ' '. $converted_value. ' '. $converted_lower. ' '. $converted_upper;
} // end of three models that mole is on bottom.
elseif($model_name == 'CTV Reference Dose (RfD)' || $model_name== 'CTV Reference Concentration (RfC)' || $model_name == 'CTV Reference Dose (RfD) BMDL' || $model_name == 'CTV Reference Dose (RfD) BMD' || $model_name == 'CTV Reference Dose NO(A)EL'){
$converted_value = pow(10, $model_value*(-1)) * 1000 * $mol_Weight;
$converted_lower = pow(10, $Lower_95*(-1)) * 1000 * $mol_Weight;
$converted_upper = pow(10, $Upper_95*(-1)) * 1000 * $mol_Weight;
} // end of three models that mole is on top.
$model_value_f = E_or_point($model_value);
$converted_value_f = E_or_point($converted_value);
if ($Lower_95 > $Upper_95){ // switch lower and higher
$middle = $Lower_95;
$Lower_95 = $Upper_95;
$Upper_95 = $middle;
}
if ($converted_lower > $converted_upper){ // switch lower and higher
$middle = $converted_lower;
$converted_lower = $converted_upper;
$converted_upper = $middle;
}
$Lower_95_f = E_or_point($Lower_95);
$Upper_95_f = E_or_point($Upper_95);
$converted_lower_f = E_or_point($converted_lower);
$converted_upper_f = E_or_point($converted_upper);
echo '<tr bgcolor="LightCyan" style = "border: 2px; border-collapse: separate; ">';
if ($GLOBALS['chem_display'] == 1) {
if ($j == 0){ echo '<td>'. $Chemical_name. '</td>'; }
if ($j == 1){ echo '<td rowspan = '. $GLOBALS["chem_rowspan"]. '>'. $Chemical_name. '</td>'; }
}
if ($j == 0){echo '<td>'. $model_name. '</td>';}
if ($j == 1){echo '<td rowspan = "2">'. $model_name. '</td>';}
echo '<td>'. $model_unit. '</td><td>';
echo $model_value_f. '</td><td>'. $Lower_95_f. '</td><td>'. $Upper_95_f. '</td>';
if ($j == 0){echo '<td>'. $sigma_value_f. '</td></tr>';}
if ($j == 1){echo '<td rowspan = "2">'. $sigma_value_f. '</td></tr>';}
echo '<tr bgcolor="LightCyan" style = "border: 2px; border-collapse: separate; ">';
if ($GLOBALS['chem_display'] == 1 && $j == 0){
echo '<td style = "text-align: center; text-indent: 3px; padding-right: 3px;">'. $Chemical_name. '</td>';}
if ($j == 0){echo '<td>'. $model_name. '</td>';}
echo '<td>'. $converted_unit. '</td><td>';
echo $converted_value_f. '</td><td>'. $converted_lower_f. '</td><td>'. $converted_upper_f. '</td>';
if ($j == 0){echo '<td>'. $sigma_value_f. '</td>';}
echo '</tr>';
} // end of if ($model_value != 0){ )
else{ // $model_value == 0
echo'<tr style = "border: 2px;" bgcolor="LightCyan">';
if ($GLOBALS['chem_display'] == 1) {
if ($j == 0){echo '<td>'. $Chemical_name. '</td>';}
elseif ($j == 1){echo '<td rowspan = '. $GLOBALS["chem_rowspan"]. '>'. $Chemical_name. '</td>';}}
echo '<td>'. $model_name. '</td>';
echo '<td colspan="6" > Prediction not available</td>';
}
}
//Display_exist_value("Reference Dose", $value_RfD, $mol_Weight, 'mg/(kg x day)');
function Display_exist_value($Chemical_name, $model_name, $value, $source, $converted_unit){
echo'<tr bgcolor="Beige" style = "all: none; border: 5px; border-right: 2px; border-bottom: 2px solid black; ">';
$field_1 = E_or_point($value);
global $j;
if ($GLOBALS['chem_display'] == 1) {
if ($j == 0){echo '<td>'. $Chemical_name. '</td>';}
elseif ($j == 1){echo '<td rowspan = '. ($GLOBALS["chem_rowspan"] + 1). '>'. $Chemical_name. '</td>';}}
echo '<td colspan="2">'. $model_name. '</td>';
// echo '<td rowspan="2">'. $Chemical_name. '</td><td colspan="2">'. $model_name. '</td>';
echo '<td colspan="2">'. $field_1. '</td>';
echo "<td> $converted_unit</td><td colspan='2'>". $source .'</td></tr>';
}
?>