Communicating to and from a microSD card

Hi! My name is Renato and I am an apprentice with regards to the Arduino. I have this project that I am doing for school which requires me to have a website that can send commands to the arduino board to have its motor spin. I m having a problem figuring out how I can have a function or something on this website code to call into the arduino code to make the motor move. How do I communicate from the website in the SD. card and the Arduino code outside of it? I just want to have a function that moves the motor when the alarm on the website sounds. As in this snippet of the website:

 if (typeof this.hourwake!="undefined"){ //if alarm is set
                        if (this.ctref.title==(this.hourwake+":"+this.minutewake+":"+this.secondwake)){
                                clearInterval(jsalarm.timer)
                                countdowntimer()
                        }
                }

Heres the code. The website that is on the SD card can be accessed through this website:www.itcup.skuttcatholic.com. So you can just inspect the source on this website to see the code of it.

Here is the code on the arduino. It simply reads the SD Card:

#include <SPI.h>
#include <Ethernet.h>
#include <SD.h>

// MAC address from Ethernet shield sticker under board
byte mac[] = { 0x90, 0xA2, 0xDA, 0x0F, 0x01, 0xE8 };
IPAddress ip(192,168,0,38);// IP address, may need to change depending on network
EthernetServer server(80);  // create a server at port 80

File webFile;

void setup()
{
    Ethernet.begin(mac, ip);  // initialize Ethernet device
    server.begin();           // start to listen for clients
    Serial.begin(9600);       // for debugging
    pinMode(9,OUTPUT);
    
    // initialize SD card
    Serial.println("Initializing SD card...");
    if (!SD.begin(4)) {
        Serial.println("ERROR - SD card initialization failed!");
        return;    // init failed
    }
    Serial.println("SUCCESS - SD card initialized.");
    // check for index.htm file
    if (!SD.exists("index.htm")) {
        Serial.println("ERROR - Can't find index.htm file!");
        return;  // can't find index file
    }
    Serial.println("SUCCESS - Found index.htm file.");
}

void loop()
{
    EthernetClient client = server.available();  // try to get client

    if (client) {  // got client?
        boolean currentLineIsBlank = true;
        while (client.connected()) {
            if (client.available()) {   // client data available to read
                char c = client.read(); // read 1 byte (character) from client
                // last line of client request is blank and ends with \n
                // respond to client only after last line received
                if (c == '\n' && currentLineIsBlank) {
                    // send a standard http response header
                    client.println("HTTP/1.1 200 OK");
                    client.println("Content-Type: text/html");
                    client.println("Connection: close");
                    client.println();
                    // send web page
                    webFile = SD.open("index.htm");        // open web page file
                    if (webFile) {
                        while(webFile.available()) {
                            client.write(webFile.read()); // send web page to client
                        }
                        webFile.close();
                    }
                    break;
                }
                // every line of text received from the client ends with \r\n
                if (c == '\n') {
                    // last character on line of received text
                    // starting new line with next character read
                    currentLineIsBlank = true;
                } 
                else if (c != '\r') {
                    // a text character was received from client
                    currentLineIsBlank = false;
                }
            } // end if (client.available())
        } // end while (client.connected())
        delay(1);      // give the web browser time to receive the data
        client.stop(); // close the connection
    } // end if (client)
}

The simplest approach is to have the web app open the Arduino's serial port and send messages to the Arduino, and have the Arduino respond via the serial port. There is a whole section of the forum dedicated to interfacing the Arduino with software on the PC and I'm sure you'll find examples in the playground showing how to do it in various types of web server.