03 Sigma: server, na ktorom beží tvoja stránka03 Sigma: the server your page runs on

Sigma (sigma.tuke.sk) is the university Linux server with Apache, PHP 8.1 and the MariaDB database. Every student has a home folder there with public_html inside. Whatever you put there is visible at

https://sigma.tuke.sk/student/name.surname/

(if your university e-mail contains a number, e.g. jan.novak.2@student.tuke.sk, it is in the address too: …/student/jan.novak.2/).

Code is not written on sigma. It is written in Kubeflow and copied to sigma automatically on every save (the SFTP extension). Sigma is only the place where the page runs and where you test it.

Access from your own computer (browser, WinSCP, PuTTY) needs the VPN off campus (guide 00). From Kubeflow no VPN is needed.

The user name is your TUKE login (e.g. jn123ab), the password is your TUKE password. Three ways:

a) From Kubeflow (the terminal in VS Code), used in the lab:

ssh jn123ab@sigma.tuke.sk

If you did guide 02 part 5, it logs you in without a password. The prompt changes to jn123ab@sigma:~$, you are on sigma. Back to Kubeflow: exit.

b) PuTTY (Windows, from your own computer): download from putty.org, Download PuTTY, putty.exe (64-bit x86). Run it, Host Name sigma.tuke.sk, Port 22, Open. On the first connection confirm the fingerprint (Accept). login as: TUKE login, password: TUKE password (nothing is shown).

c) Windows terminal: Start, "Terminal", ssh jn123ab@sigma.tuke.sk. The same as a).

WinSCP copies files between your computer and sigma (the SFTP protocol) and lets you work with folders by clicking. You use it for the first setup and then occasionally (uploading Adminer, an image, a fallback when something fails).

1. Download and install from winscp.net (Installation package).
2. Run it, the Login window, New Site: File protocol SFTP, Host name sigma.tuke.sk, Port number 22, User name your TUKE login. Leave the password empty.
3. Save, name sigma, OK. Next time you pick the session from the list on the left.
4. Login, enter the password (it asks at every connection). The first time confirm the fingerprint (Yes).

5. Your computer is on the left, sigma on the right (your home folder). You move files by dragging.

Creating the folders (once)

In the right panel (sigma):

1. If you do not see public_html: right click an empty spot, New, Directory, public_html, OK.
2. Open public_html (double click).
3. Create the course folder as your teacher says (e.g. ti or it): right click, New, Directory.

Result:

/home/jn123ab/
└── public_html/       →  https://sigma.tuke.sk/student/jan.novak/
    ├── ti/            →  https://sigma.tuke.sk/student/jan.novak/ti/
    └── it/            →  https://sigma.tuke.sk/student/jan.novak/it/

You do not create the folders for individual labs (cv01, cv02…) by hand; they appear by themselves when copying from Kubeflow.

The same can be done in the terminal (after ssh jn123ab@sigma.tuke.sk):

mkdir -p ~/public_html/ti ~/public_html/it
chmod 755 ~ ~/public_html

The second line sets the permissions so that the server may look into the folders.

This is the most important part. After the setup, every file you save in Kubeflow inside the web folder is copied automatically to the same place in public_html on sigma.

1. In Kubeflow, VS Code has the WEB folder open (guide 02 part 6). If Explorer shows JOVYAN, open /home/jovyan/web/ first.
2. Press Ctrl + Shift + P, type sftp config and click SFTP: Config. (The field must start with >. Without it you are searching files, not commands.)
3. The file sftp.json opens with sample content. Select all of it (Ctrl + A) and replace it with this; change only the login jn123ab (twice):

{
    "name": "sigma",
    "host": "sigma.tuke.sk",
    "protocol": "sftp",
    "port": 22,
    "username": "jn123ab",
    "privateKeyPath": "/home/jovyan/.ssh/id_ed25519",
    "remotePath": "/home/jn123ab/public_html",
    "uploadOnSave": true,
    "useTempFile": false,
    "openSsh": false,
    "ignore": [".vscode", ".git", "**/.git/**", ".DS_Store"]
}

What it means: privateKeyPath is the key you put on sigma in guide 02, which is why no password is needed; remotePath is the place on sigma to copy to; uploadOnSave means on every save; ignore is what is not copied (Git and VS Code settings do not belong on sigma).

4. The file saves itself. .vscode/sftp.json appeared in Explorer.

Test:

5. In Explorer: right click WEB, New Folder…, ti (or as your course says). Inside it right click, New File…, index.html. Type ! and Tab, and put <h1>Funguje</h1> into <body>.
6. Stop typing and wait 2 seconds. The purple status bar at the bottom briefly shows done index.html: the file is on sigma.

7. Open https://sigma.tuke.sk/student/name.surname/ti/. "Funguje" appears. If you see an old version, refresh the page (F5).

Useful commands of the extension (right click a folder or file in Explorer, at the very bottom of the menu; newer versions show them without “SFTP:” in front):

• Upload Folder: uploads a whole folder at once (e.g. after git clone of a new assignment, or after composer install).
• Download / Sync Remote → Local: downloads a file from sigma into Kubeflow (if you changed it there by mistake).
• Reveal in Remote Explorer: lists the files on sigma.

Adminer is a single PHP file that you upload into your public_html; in the browser you then work with your database (tables, data, SQL). Nothing gets installed.

1. Download from adminer.org, Adminer for MySQL (English).
2. Rename the downloaded file to adminer.php.
3. Upload it into public_html on sigma: through WinSCP (dragging), or save it in Kubeflow as web/adminer.php and SFTP uploads it by itself.
4. Open https://sigma.tuke.sk/student/name.surname/adminer.php (off campus with the VPN).
5. Login: System MySQL, Server localhost, Username your database login (name_surname, lowercase, no accents, with an underscore), Password you get in the lab, Database leave empty.
6. After logging in you see your database (the same name as the login). You can switch the language at the top right.

The database is yours alone: you can create and drop tables, insert data, run SQL. You do not see other databases and cannot create a new one.

Tab completes file names, the up arrow brings back the previous command.

• PHP on sigma is 8.1, in Kubeflow 8.3. What runs in Kubeflow need not run on sigma if you use features new in PHP 8.2/8.3. Test on sigma.
• PHP error messages are switched off on sigma. During development put ini_set('display_errors', '1'); error_reporting(E_ALL); at the top of the script to see what is wrong.
• Upload limit for files sent through a PHP form: 2 MB.

You need nothing from this part for the labs. It is here in case you want to set up your work differently or are curious how it works under the hood.

Git over SSH instead of HTTPS

In guide 04 you clone over HTTPS and sign in the first time with a code at github.com/login/device. The other option is to give GitHub your public SSH key from Kubeflow (the same one sigma has). Kubeflow then proves itself with the key and there is no sign-in at all.

1. In Kubeflow, in the terminal, print the public key (if you do not have one, create it as in guide 02, part 5):

cat ~/.ssh/id_ed25519.pub

It prints one line starting with ssh-ed25519 AAAA… and ending with kubeflow. Select the whole line with the mouse and copy it (Ctrl + C, or right click, Copy). This line is public. The file without .pub is private; never print or copy it.

2. On GitHub: the profile icon at the top right, Settings, on the left SSH and GPG keys, the green New SSH key.
3. Title: kubeflow. Key type: Authentication Key. Paste the copied line into the Key field (Ctrl + V). Add SSH key. GitHub may ask for your password or a code from the authenticator app.

4. Test in the Kubeflow terminal:

ssh -T git@github.com

The first time it asks "Are you sure you want to continue connecting?", type yes, Enter. It should print "Hi jan-novak! You've successfully authenticated, but GitHub does not provide shell access." The second half of the sentence is not an error; it is the correct answer.

5. When cloning, choose the SSH tab instead of HTTPS in the Code button on GitHub. The address starts with git@github.com:. The rest of the command is the same, including cv01 at the end:

git clone git@github.com:tuke-fberg-stehlikova/technologie-internetu-5k-cv01-jan-novak.git cv01

A repository you already cloned over HTTPS is switched to SSH inside its folder:

git remote set-url origin git@github.com:tuke-fberg-stehlikova/technologie-internetu-5k-cv01-jan-novak.git

If ssh -T says "Permission denied (publickey)", the key is not on GitHub or was copied incompletely. Repeat steps 1 to 3 and copy the whole line including ssh-ed25519.

Working directly on sigma in the terminal

After ssh jn123ab@sigma.tuke.sk you can look at the files (ls, cat) or fix them in vi. Remember, though, that the next save from Kubeflow overwrites such a fix. Whatever should stay, fix in Kubeflow.