<?php

$pathToFile = $_POST['file'];
$dataFromFile = file($pathToFile);

$pdo = new \PDO('dsn');

foreach ($dataFromFile as $line) {
    $pdo->exec("INSERT INTO test_table (val1, val2) VALUES ($line[1], $line[2])");

    if (!empty($line[1])) {
        $items = $pdo->query("SELECT * FROM test_table2 WHERE any_filed=$line[1]")
            ->fetchAll();

        foreach ($items as $item) {
            $children = $pdo->query("SELECT * FROM test_table3 WHERE filed={$item['name']}")
                ->fetchAll();

            $pdo->exec("INSERT INTO test_logs (val1, val2) VALUES ($children[0], $children[1])");
        }
    }
}