Startup Instructions

Welcome!

Welcome to The Interventional Services Wiki Project! This page will walk you through the process of creating your very own wiki for your lab.

This startup guide will include all of the information needed to get your wiki running. It will also provide links to further information if you want to dive deeper into the subject matter.

Mini Tutorial

AWS Terminology

• Dashboard - A dashboard is the main page for the different services AWS provides. Just like you email program has a main page where all you emails are listed. When the instructions say to go to your instances, you would go to the EC2 service, and then select Instances. This may also be written like this:

AWS -> EC2 -> Instances

• AMI - Amazon Machine Image. An AMI is a “hard-drive” containing all of the software and data needed to run your wiki. these images are vetted by Amazon and available on the AWS marketplace. A Ubuntu Unix ami was used as a starting point for the wiki. You will go to the AWS marketplace to select the Interventional services wiki AMI.

• Instance - the instance is the “hard-drive“ and the “server“. In this case, it is a virtualized server that mimics the hardware that you choose to run the image. Once you have made all of the configurations to the instance, and launch it, then you will have a running server that you can connect to.

• IAM - Identity and Access Management. AWS includes some very powerful tools for controlling back-end access to your AWS account and instances. For example, the main AWS account that owns the wiki and domain names must include credit card and billing info. It might not be a good idea to have this information available to day-to-day staff. You can create another AWS account that can access the wiki Dashboard without having access to the billing module. This also makes it easy to manage access to any account in case of personnel changes.

• Key Pair - This is a cryptographic tool to keep access to your servers back end, called the command line, secure. You can think of it like a password, but it’s more like a paragraph. One part of the key, called the public key is stored on your server, and isn’t a secret, hence the name. The second part of the pair is the private key. You must keep this protected on your local computer. You will create one as part of the process of launching your first instance.

• Security Group - This is where you define your "firewall" settings. What ports (Channels) your server will communicate on, and whether it will talk to everybody, or only certain people. Like the Key Pair, you will define this before launching your first instance.

Server Terminology

• Command Line - A plain-text interface to the operating system of your computer. All computers have one, most people don't use them. A remote UNIX based server doesn't need one as it takes up a lot of memory and disk space. It is much easier to connect to the command line to control the server. Also referred to as the "Back end" of your server

• Web interface - Your web page. Sometimes known as the "Front end". The program that runs it is called Apache.

• SSH - Secure SHell. The command line program you will use to connect to your servers back-end. It is encrypted using the key pair mentioned above. You open a terminal program on your local computer to do this. There are also apps for your phone or iPad. And, as a last resort, AWS provides a terminal you can access through their website.

• Port - A virtual channel to separate internet communication into categories. Non-encrypted web traffic (http) is on port 80. Https, or encrypted web traffic, is on port 443. SSH connections happen on port 22.

• IP address(IP) - The electronic address of every device connected to a network. Phones, tablets, printers, your smart TV, everything. When you connect through your home WiFi, you have a different IP than when you connect through a cell connection. The IP is assigned to the device when it connects to the network. And the IP that the device has will not be the same IP that the server sees when you connect. It’s complicated…

Create an AWS account (Free)

The first step is to create an Amazon Web Services(AWS) account. If you already have one, that will work, but we encourage you to create an account solely for the wiki. A later tutorial will show you how to access the wiki from your AWS account. AWS requires a unique email address for a new account, so you may need to create one. Gmail works for this, or a dedicated account at your facility. Again, it is good practice to use a dedicated email for this and not a personal email account.

Launch your instance (Free)

After creating the AWS account, you will need to visit the EC2 service. This stands for Elastic Computing Cloud and manages your virtual servers. When it’s time to choose a domain name and link it to your server you will need to visit the Route 53 dashboard.

Once you are in EC2, click on instances. This is where you start, stop, and get info on all running instances. Click on Launch Instance to start your server. The next page will require some info:

1. Give it a name
2. Pick an AMI. Do this by searching for “cath lab”.
3. Instance type: we recommend t2.micro, its free for the first year, and more than enough to run the wiki.
4. Choose or create your key pair
   • If you are creating your key pair here, click create key pair and follow the instructions carefully. The private key should be saved on your computer as you will need it to access the command line interface. You can copy it to other devices should you need to access the command line from other locations or devices.
5. Choose or create your security group
   • To get started, allow SSH from anywhere, and HTTPS as well as HTTP from anywhere. However, we strongly suggest limiting SSH to specific IP addresses as soon as feasible.
6. The storage default should be fine (8Gb)

Click Launch Instance at the bottom of the page, and go get a cup of coffee, as it will take 5-10 minutes for the server to boot up.

Configure your wiki

Connect to your instance

Go to AWS->EC2->Instances dashboard and look in the list of running instances. IF you see one listed with Green Checkmarks by the Running status and 2/2 checks passed, congratulations, you have launched your server.

Now that you have a running server, you must do a few things to install MediaWiki and get it configured. AWS doesn’t allow this to be done for you as it requires choosing usernames and passwords to keep MediaWiki secure.

To do these things, you will connect to your server using a terminal program via SSH and the key-pair you created earlier.

If the policies of your facility don’t allow you to use these programs on work computers, you have a few options:

• Use a home computer
• Use a personal iPad or tablet
• Use the AWS console

Once you decide on a terminal program, familiarize yourself with using it to SSH into a server with a key-pair. They are all a little different and beyond the scope of this tutorial.

Click on the server listing to bring up details for the instance in the bottom panel. You are looking for the “Public IPv4 DNS” it will look something like:

ec2-##-###-##-###.us-west-2.compute.amazonaws.com

Create MySQL user and database

• From the command line launch MySQL with super user privileges.

Sudo MySQL

• Create the database. Pick a database name for your installation.

CREATE DATABASE wikidb;

• Create a user for mediawiki to access the database. Pick a name and good password for this command.

CREATE USER 'wikiuser'@'localhost' IDENTIFIED BY 'strongpassword';

• Give the user rights to the database.

GRANT ALL PRIVILEGES ON wikidb.* TO 'wikiuser'@'localhost' WITH GRANT OPTION;

• Reset the privileges table

Flush privileges;

• Exit MySQL

Exit;

Install MediaWiki

Now you will access the web site directly. In the AWS Instances dashboard, click on your running instance, and look in the bottom part of the page. Here you will find all of the information about your server. One of these items is the AWS supplied domain name for the instance. Click the Open address link under the Public IPv4 heading. This will open your website in a new window. Please note that you may get a warning that the site is not secure, proceed anyway and open the site. We will set up a self-signed https certificate at a later point.

• Follow the instructions on the installer page to install MediaWiki.
  • Under extras, check only Visual Editor. The rest will be installed from the back end.
• When the installer is finished, download the LocalSettings.php file to your local computer.
• Return to the command line and create the LocalSettings.php file using the nano text editor:

sudo nano /var/www/html/wiki/LocalSettings.php

• Open the LocalSettings.php file you downloaded on your computer in the editor of your choice. Copy all the text.
• Switch back to the SSH program and paste this text into the nano editor.
• Make sure you are at the end of the file in nano.
• Use Ctrl-R to read in a file. It will ask for the location of the file. Paste in the following:

/var/www/html/wiki/SettingsExtras.php. 

• Use Ctrl-x to Save the file and exit nano.

Add custom templates to MySQL

• Open MySQL and import theinterwikidata.sql.

sudo MySQL;
use mywikidb; (Your database name)
source /var/www/html/wiki/theinterwikidata.sql;
exit;

This will overwrite all but the admin user with all the template data.

Update the data

• Update the database and Semantic Mediawiki with the data you just imported.

php /var/www/html/wiki/maintenance/update.php  (run this twice)
php /var/www/html/wiki/extensions/SemanticMediaWiki/maintenance/rebuildData.php

Go back to the web interface and reload the page to confirm all is working. Proceed to fill in physicians and procedure data.

Create a domain name ($)

You will need to log-in to the Unix command-line interface(CLI) to make these changes. When you launched your instance from the AMI, you created a key pair. You will reference this key pair when using SSH to connect.

You can find a connection guide by clicking the connect button after selecting your instance from the list on your AWS EC2 dashboard.

Once you are connected to your CLI, you will need to edit the LocalSettings.php file.

First, change directory (cd) to the web server directory:

cd /var/www/html

Now, list all the files:

ls -al

This is your wiki code, the actual information in your pages will be stored in a database, more on that later.

Open a simple text editor and tell it to open the LocalSettings.php file with this command:

sudo nano LocalSettings.php

If you have never used a simple text editor, you may want to read up on it. Just Google "unix nano".

Let's change the name of your wiki first. Look for this section near the top:

$wgSitename = "YourWikiName";
$wgMetaNamespace = "YourWikiName";

Change these to the name of your wiki.

Next, a few lines down is this:

## The protocol and server name to use in fully-qualified URLs
$wgServer = "http://00.00.00.00";

This must be changed to the IP address of your server. You can find this on your Instances page in your AWS console. Click on your instance, and the info will show up below it.

You can save the file at this point by using ctrl-x and entering a "y" for yes. At this point, your wiki should load if you point your web browser to the ip address. Please note you will have to specify a plain http connection, not https. Your browser will probably warn you the connection is unsecure, it's OK we will change this later to be secure.

As long as your wiki page loads, you're good so far! But we're not out of the woods yet, all the passwords and secret stuff needs to be changed as anyone who has this snapshot knows all of your passwords(not secure!)

Securing your server

Here is a list of things to change from the command line via SSH:

• MySQL (or MariaDB):
  • There is no access to the mysql root user, so no need to change it.
  • Create a new user (there isn't one at install)
  • Grant all privileges on database "my_wiki" to new user
• edit LocalSettings "#Database Settings" section to reflect these changes
• Admin user password ("Admin12345" at install)
  • Use the php script ChangePassword.php in the /maintenance directory to change the Admin password so you can log-in to the wiki.
• Change the secret key for the SecureHTML extension at the bottom of LocalSettings.php to a string of your own choosing

Open your Wiki for new users

• Edit LocalSettings.php
  • Change the $wgGroupPermissions to allow account creation

Warning: This shouldn't be left on more than a couple days. Bots will find you!