c-harmonise-data.md

@@ -7,9 +7,51 @@
 # Part C - Harmonising Your Data for the WP7 Demo Project
 
 ## 1. Upload the Harmonisation Dictionary
+The first step in the harmonisation process is to upload the harmonisation dictionary into your repository. You can download the harmonisation dictionary [here](https://gitlab.inesctec.pt/wp4-recap/wp7-demo/-/blob/master/wp7_demo_harmonization_dictionary.xlsx).
+
+1. Log into your Data Repository
+1. Click on `Projects` on the top bar and then select your project
+1. Click on the `Files` tab on the left panel and then click on `Upload`
+1. Browse to the downloaded harmonisation dictionary file, select it and then click `Upload`
 
 ## 2. Create a View over Your Original Table
+The harmonisation process in the Data Repository is based on the concept of `views`.  
+A view is a virtual table in which variables have been derived from some other table.  
+We can pull and transform variables from a table and then save the resulting harmonised variables in a view.  
+
+Just like regular tables, views can be created by using a dictionary. In this case, you need to create a view using the harmonisation dictionary you uploaded in the previous step:
+
+* **2.1.** Click on the `Tables` tab on the left panel and then click on `Add Table` > `Add View`  
+
+  <img src="uploads/create_view_1.png" alt="create_view_1" width="700"/>  
+
+* **2.2.** Type in a name for the view (e.g. epice-pt_data_harmonised)  
+* **2.3.** In the table references, select the table from which the variables will be derived (the table you created in [step 2](b-import-data#2-import-data-into-your-node) of Part B of the tutorial) and click `Add`  
+* **2.4.** Click `Browse` and select the harmonisation dictionary  
+* **2.5.** Click `Save`  
+
+  <img src="uploads/create_view_2.png" alt="create_view_2" width="500"/>  
+
+The view you have created contains the target variables in the harmonisation dictionary and also a reference to the original table. It does not yet contain any data because no data has yet been pulled and transformed from the original table (this will be done in [step 4](#4-harmonise-each-variable)).  
+
+## 3. Grant the Central Node and the Analysis Team Access to the Harmonised View
+Before you actually start harmonising the variables, you should allow both the central node and the analysis team to retrieve the data dictionary and summary statistics from the view you created. This is done by granting the `central_node` and `wp7_demo` accounts (created in [Part A](a-create-accounts) of this tutorial) a specific level of access to your view.
+
+* **3.1.** Click on the view you created in the previous section.  
+* **3.2.** In the `Permissions` tab, click on `Add Permission` > `Add user permission`  
+    ![add_user_perm_1](uploads/add_user_perm_1.png)  
+
+* **3.3.** Type in `central_node` for the name and select `View dictionary and summaries` for the level of access the central node will have to the view.  
+    ![add_user_perm_2](uploads/add_user_perm_2.png)  
+* **3.4.** Click `Save`.  
+* **3.5.** Repeat steps 3.1-3.4, this time using `wp7_demo` as the name.  
+
+The central node and the analysis team will now be able to retrieve the data dictionary and summary statistics from your view.  
+In order to allow the analysis team to also use DataSHIELD to perform analysis, you also need to explicitly grant the `wp7_demo` permission to use DataSHIELD on your node:
 
-## 3. Grant the Central Node and the Analysis Team Access to the Harmonised Table
+* **3.6.** In the top bar, click on `Administration`.  
+* **3.7.** Click on `DataSHIELD` and scroll down to the `Permissions` section.  
+* **3.8.** Click on `Add Permission` > `Add user permission`.  
+* **3.9.** Type in `wp7_demo` and click `Save`.  
 
 ## 4. Harmonise Each Variable