What best practices should be followed when handling file uploads in PHP, especially with PDF files?

When handling file uploads in PHP, especially with PDF files, it is important to validate the file type, size, and ensure secure storage to prevent any malicious uploads. One best practice is to use the `move_uploaded_file()` function to move the uploaded file to a secure directory on the server. Additionally, consider using a unique filename to prevent overwriting existing files.

// Check if the file is a PDF
if ($_FILES['file']['type'] == 'application/pdf') {
    // Check file size
    if ($_FILES['file']['size'] < 5000000) {
        // Move the uploaded file to a secure directory
        $uploadDir = 'uploads/';
        $uploadFile = $uploadDir . basename($_FILES['file']['name']);
        
        if (move_uploaded_file($_FILES['file']['tmp_name'], $uploadFile)) {
            echo 'File uploaded successfully.';
        } else {
            echo 'Error uploading file.';
        }
    } else {
        echo 'File is too large.';
    }
} else {
    echo 'Invalid file type.';
}