Context
I received phone call from one person who with his frightened voice said: Dermatologist!. I wanted to say kindly that that person probably has got wrong number because I am not dermatologist and I cannot give any medical advise about skin issues except to suggest to someone to visit dermatologist. But, that person said: I am dermatologist. I have very big problem. I have to transfer a huge number of files from one computer to another. I heard that you can help me. I have got more than fifteen thousands of images, pdf files and I have to transfer them to some server. I have been told that I will receive ssh details. What is that?
We met each other and in our conversation I realized that a huge repository of medical images, scientific texts and program files has to be migrated to new server which will be used by scientists to share scientific research. Dermatologist has got laptop with GNU/Linux and he has no previous experience in working with procedures and software in order to accomplish his task.
It is doable, I said. But, you have to be precise in typing commands and respect order of steps what is needed to do. Focus, concentration and accuracy are keywords, I emphasized. I hope I will be able to do that, he said.
First step – SSH
SSH is a secure communication protocol used to connect to remote GNU/Linux server. SSH stands for Secure SHell. Many people who are not used to work with servers expect that hey will see some complicated graphical interface. There is no complicated graphical interface, there is textual interface without buttons, dropdown menus, various radio and other boxes. Is that even more complicated? No. But, if you are dermatologist or other professional not familiar with IT you can ask someone to help you or just be happy to learn very small number of commands. Just follow and remember this guide and you do not need to learn anything complicate in order to accomplish task of copying a large amount of various files from one server to another that someone gave to you.
Our dermatologist has got those files copied to the laptop which he has to use to transfer files to other server. Since he received information that remote server was set up with SSH enabled he has to learn how to connect to it.
In order to connect to remote server he turned on his laptop and started terminal application that is terminal with text interface that he needs to start SSH session.
Terminal application window usually looks like this:
Terminal application window will prompt you with username and computer name. No buttons, no complicated menus. Only prompt for commands. (Users that use screen readers can easily in textual interface perform all activities required.) However, the most important is that you understand logic what you want to do and to express it in some command. Once you get right commands you can literally copy them to the prompt.
Why Secure Shell? Why not some nice graphical user interface with my password? Security is not only feature. It must be principle. So, how SSH works? Using passwords only can be vulnerable method since many malicious bots and guys with powerful hardware can use various techniques to steel passwords from you. SSH is when security is concerned still better method to be used. Actually, SSH use so called SSH keys which are cryptographic matching pair of keys. One is private key and one is public key. Public key can be shared and exposed to others (do not do that anyway) but private key must not be exposed to anyone. The private key and processes of encryption and decryption during the establishment of connection are essential for security of SSH connection.
Firstly, we have to generate a pair of keys using command:
ssh-keygen
When we issue that command in our prompt the system will ask us to name the file in which key will be saved, and after that we will be asked to enter passphrase. Please type passphrase that you can remember. Your screen will look similar to the screen as on image below:
In the latest versions of GNU/Linux distributions ssh is usually configured by default to generate keys with high level security. In our case default values say that we have got RSA keys with 2048 bits.
After we generated the keys we should transfer public key to remote server by issuing command:
ssh-copy-id username@remote_host
Usually, administrator of that server or hosting company that set it up gave you the username and password while remote_host can be some address: medicaljournal.org or some IP number which looks like 193.243.27.183 or so. (This IP number is unknown to me so please do not use it, I typed just to show people without IT background how it can look like.)
After that you can connect to your serve by issuing command:
ssh -p 2020 username@remote_host
Please note that we use option that SSH is open for connection on port 2020 because sometimes hosting companies use that port instead of default 22. If your hosting company use port 22 you do not need to write “- p 2020”. If they use other port you can use that port and it will be “-p numberofport”. After issuing command we will have on prompt something like:
The authenticity of host '[name or ip number of your host will be here]:numberofport ([name or number of your host]:numberofport)' can't be established.
ECDSA key fingerprint is SHA256:y9aVJtMpIZusjf3bmSEtWg/9RwjTrCbAT0Tli9pvLmM.
Are you sure you want to continue connecting (yes/no)?
When you type “yes” and press Enter it will ask you password of that server. If you are scared you can type “logout” and press Enter and system will log you out. So far so good. Nothing exploded, you are safe and you have done wonderful work which you have to do only once.
Finally copying. But, I have questions!
When I showed that to dermatologist he felt something between happiness due to some new discovery and a sort of stage fright. Should I be able to do that to the end properly?, was visible on his face. But, I have some questions, he said. I have been told that I have to do that with port 2020. Secondly, I will have always on my computer a number of new files how can I copy them on the server? One by one? Should I have some paper evidence of what I copied?
Well, I started, there is easy answer to your questions. We can combine commands rsync and ssh if you have many files. Firstly, you have to keep your file sin some folder on your computer and we should issue this command:
rsync -avz -e "ssh -p $portNumber" source destination
The system will first time copy all files from the computer that in folders contains all files and copy them on remote computer. After copying them firstly it will copy only new files in the second turn. (rsync stands for remote sync)
In the case of our dermatologist he has got folder /research-files which had a lot of subfolders with names of researchers and each has had subfolders /articles /statistics /measurements /photos and /diagrams. He wants that on remote server should be the same principle applied with names of folders and subfolders. On remote server in /home folder administrator created user researcher and the user’s folder named researcher. All files should be copied to that folder using port 2020 in ssh. Sounds complicated, but it is not. on his laptop he has got folder /home and user /dermatology in which all folders and files are copied.
The command will be like this:
rsync -avz -e "ssh -p 2020" /home/dermatology/research-files researcher@remote_host: /home/researcher/
Instead of remote_host type your host name or IP number. After issuing this command the system will ask you to type password of your user. After typing password the process of remote sync will begin. Due to flag v in “avz” which stands for “verbose” you will see on your screen whole process. Duration of the process will depend on your upload speed. You can send mails, open documents, play music on your computer. The first turn can last longer if you have many files. But, the second and other turns will transfer only difference which means files that are added after the first turn. That will probably be considerably shorter. That’s all. Not too hard.
Open Access Admin 