Added contents for "Connect with the input database"

docs/source/setup.md

@@ -3,6 +3,7 @@
 - [Get permissions](#get-permissions)
 - [Local setup](#local-setup)
   - [Get the codes](#get-the-codes)
+  - [Connect with the input database](#connect-with-the-input-database)
   - [Prepare software & license](#prepare-software-license)
 - [Euler setup](#euler-setup)
 
@@ -16,7 +17,6 @@ Before setting up, you need permissions to access the codes and the input databa
 - Xuejiao Han (xuhan@eeh.ee.ethz.ch): 
   - permission for the **DistIv** repository 
   - access to the **PSL server** for the database (server name: itet-psl-s02)
-
 - Jared Garrison (garrison@fen.ethz.ch): 
   - permissions for the **eMark** repository
   - permissions for the **Shared** repository,
@@ -49,13 +49,41 @@ The instructions here use **command lines**. If you have a GUI tool for git, you
 
   You will be asked for your username and password for the repository and its submodules. Input your ETH username and password.
 
-In the end, the folder will look like this:
+In the end, the folder will look like the following screenshot. Note: You might not see the hidden files whose names start with a dot. The `UserDBInfo.txt` file will be added in the sction [Connect with the input database](#connect-with-the-input-database).
 
 ![](images/nexus-e-folder.png)
 
 
 ##### 2. Connect with the input database
 
+- Get access to the database  
+Follow the section [Get permissions](#get-permissions) to get access to the database server (PSL server: itet-psl-s02) and your username & password for the database.
+
+- Create a `UserDBInfo.txt` file in the folder where you put the codes as shown in [Get the codes](#get-the-codes). The file should contain four lines:
+```
+itet-psl-s02
+3306
+YOUR_DATABASE_USERNAME
+YOUR_DATABASE_PASSWORD
+```
+An example can be found in `Shared/connectionInfoPSL.txt`.
+
+- View the database
+  - Install MySQL and MySQL Workbench
+  - Connect to ETH VPN
+  - Connect to the database with MySQL Workbench
+    - Add a new MySQL connection  
+    ![](images/mysql-workbench-1.png)
+    - Input connection information  
+    ![](images/mysql-workbench-2.png)
+    - Click the button `Test Connection`. You will be asked to input your database password. Then you will see a seccess message:  
+    ![](images/mysql-workbench-3.png)  
+    ```eval_rst
+    |:warning:| By default, everyone has write permission to the database. 
+    ```  
+    Therefore, to be safe, always make a local copy of the database before playing with it - i.e., first “Dump” it to a local folder, then import it to your personal MySQL account. These can be done in this window:  
+    ![](images/mysql-workbench-4.png)
+
 
 ##### 3. Prepare software & license