inventarioSustancias/public_html/scripts/extract.php

<?php
/*  Authors         :   Carlos C. Corrada-Bravo
                        David J. Ortiz-Rivera

    Organization    :   Centro de Desarrollo y Consultoria Computacional
    Project         :   OPASO Material Registry   
    File            :   extract.php
    Description     :   Extract and insert data from tsv */

	/* database connection */
	include_once "../config/database.php";
	error_reporting(E_ALL);
	ini_set("display_errors",1);

	/* for each file: open and explode each row by tabs */
	foreach (glob("") as $file){
		$laboratory = array();
		$pi = array();
		$cho = array();
		$register = array();
		$success = 0;
		$null = "n/a";
		$row = 1;

		/* Parse tsv file */
		if(($fhandle = fopen($file,"r")) !== FALSE){
	  		while(($data = fgetcsv($fhandle,1000,"\t")) !== FALSE){
				/* extract department and personnel in columns B(1) and I(8) */ 
				if($row > 6 and $row < 12){
					/* avoid null keys */
					if($data[0]){
						$laboratory[$data[0]] = $data[1];
					}
					if($row < 10){
						$pi[$data[7]] = $data[8];
					}
					else{
						$cho[$data[7]] = $data[8];
					}
				}

				/* cho phone */ 
				elseif($row == 12){
					$cho[$data[7]] = $data[8];
				}

				/* generate register keys */ 
				elseif($row == 14){
					for($index=0; $index < count($data); $index++){
						if($data[$index]){
							$register[$data[$index]] = "";
						}
					}

					foreach($pi as $key=>&$value){
						if(!$value){
							$value = $null;
						}
					}

					foreach($cho as $key=>&$value){
						if(!$value){
							$value = $null;
						}
					}

					/* person entries */
					$person = $db->stmt_init();
					if($person = $db->prepare("INSERT INTO Person(pname,email,password,phone,privileges) VALUES (?,?,?,?,?)")){
						$person->bind_param("sssss",$pi["pi"],$pi["piemail"],$null,$pi["piphone"],$null);
						if($person->execute()){
							$pi = $db->insert_id;
						}
						/* duplicate entry */ 
						else{
							$email = $pi['piemail'];
							if ($person = $db->prepare("SELECT pid FROM Person WHERE email=?")){
							    $person->bind_param("s",$email);
							    if($person->execute()){
								    $person->bind_result($pi);
								    $person->fetch();
							    }
							}
						}
					}

					/* cho */
					$person = $db->stmt_init();
					if($person = $db->prepare("INSERT INTO Person(pname,email,password,phone,privileges) VALUES (?,?,?,?,?)")){
						$person->bind_param("sssss",$cho["cho"],$cho["choemail"],$null,$cho["chophone"],$null);
						
						if($person->execute()){
							$cho = $db->insert_id;
						}

						/* duplicate entry */ 
						else{
							$email = $cho['choemail'];
							if ($person = $db->prepare("SELECT pid FROM Person WHERE email=?")){
							    $person->bind_param("s",$email);
							    if($person->execute()){
								    $person->bind_result($cho);
								    $person->fetch();
							    }
							}
						}
					}
					$person->close();

					/* lab entry */
					$lab = $db->stmt_init();
					if($lab = $db->prepare("INSERT INTO Laboratory(lname,lab,department,building,extension,pi,cho) VALUES (?,?,?,?,?,?,?)")){
						$lab->bind_param("sssssii",$laboratory["lname"],$laboratory["lab"],$laboratory["department"],$laboratory["building"],$laboratory["extension"],$pi,$cho);
						$lab->execute();
						$lab->close();
						/* extract generated lab_id */
						$lab_id = $db->insert_id;
					}
				}

				/* extract register data by row */ 
				elseif($row > 15){
					/* reset index */
					$d = 0;
					foreach($register as $key=>&$value){
						if($data[$d]){
							$value = $data[$d];
						}
						else{
							$value = $null;
						}

						$d += 1;

						/* avoid seg fault */ 
						if($d >= count($register)){
							break;	
						}
					}

					/* inventory entries */ 
					$inventory = $db->stmt_init();
					if($register['chemical'] != "null entry"){
						if($inventory = $db->prepare("INSERT INTO Inventory(chemical,manufacturer,sds,cas,state,hazard,type,amount,quantity,total,location,ghs,lid) VALUES (?,?,?,?,?,?,?,?,?,?,?,?,?)")){
					 		$inventory->bind_param("ssssssssssssi",$register["chemical"],$register["manufacturer"],$register["sds"],$register["cas"],$register["state"],$register["hazard"],$register["type"],$register["amount"],$register["quantity"],$register["total"],$register["location"],$register["ghs"],$lab_id);

							/* query failed */ 
							if(!($inventory->execute())){
								echo "Entry error:";
								echo "<br>";
					 			print_r($inventory);
					 			echo "<br>";
					 			print_r($register);
					 			echo "<br>";
								echo "PI id: " . $pi . "<br>";
								echo "CHO id: " . $cho . "<br>";
								echo "LAB id: " . $lab_id . "<br>";
							}

							/* successful entries */ 
							else{
								$success += 1;
								$inventory->close();
							}
						}
					}
				}

				/* update row */ 
		    	$row += 1;
		  	}

		  	fclose($fhandle);
			echo "<br>FILE: " . $file . "<br>";
			echo "PI id: " . $pi . "<br>";
			echo "CHO id: " . $cho . "<br>";
			echo "LAB id: " . $lab_id . "<br>";
			echo $success . " successful entries." . "<br><br>";
		}
	}

	$db->close();
?>