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The following document, copied below, is a quick guide to using RStudio as the tool to querying the APPROACH Online Reporting platform

Step 1. Connect to AHS

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When you want to access the Approach AHS RStudio location , first connect to AHS VPN . Or or make sure to already be within the AHS network environment.

NOTE: You cannot use AHS’s MyApps via Citrix at present because AHS currently forces you to use Internet Explorer and it is not compatible with that.https://researchcalgary.atlassian.net/browse/ASD-9684

FYI: For a VPN client: Download and install, for example FortiClient VPN client. For setup and usage:

http://vpnextranet.albertahealthservices.ca/vpnfiles/Fortigate_VPN5_Client_Architecture_and_Installation_Document.htm

 

Step 2. Connect to RStudio

Point your browser to RStudio by navigating to https://rstudio.approach.org. Login using your RStudio account credentials.

If you don’t yet have an RStudio account, check in with the Approach Service Desk to check if your account was assigned and set up to have one. One can be requested through the Approach access approval form and registration process.

Tip: Changing your password

You will most likely want to change the auto-generated password provided to you. To do so, follow these steps.

1. Sign into RStudio with your credentials

2. Click on the ‘Terminal’ tab

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   Type passwd and press Enter

   1. Fill out your current password, your new password and confirm your new password

   2. Your password has been changed. Next time you log into RStudio, use your new password.
      

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Step 3. RStudio landing page layout and summary

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I.        Script/Source Editor:
R scripts can be written and tested here. Either create a new script from File -> New File, or you may open and edit an existing script/project saved to your workspace. RStudio provides a set of core features as part of the source editor tool which is explained in detail here - https://support.rstudio.com/hc/en-us/articles/200484448-Editing-and-Executing-Code

II.     Workspace Variables & Console History:

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The Packages tab lists all existing R packages installed and available for use (both system and user level packages). You may view documentation for any package by clicking on the package name within this list. The Packages tab also provides the ability to search for and install new packages; as well as searching and applying updates to existing packages.

 Step 4. Installing and importing the necessary libraries used to query the Approach database

Note: The Approach library and dependencies should already be preinstalled once you have access to your account.

To confirm the APPROACH package has been installed, do the following:

1. Sign into RStudio

2. On the right-hand side of the screen, click on the 'Packages' tab

   1. Confirm that the ‘approach’ library is underneath the ‘User Library’ list
      

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a.     (Ignore this step if you already have the package installed)
Install the Query Utility R Package for APPROACH. This package is not public, and only available on the RStudio server. To install, run the following command in the console

install.packages("/home/cru/approach_0.1.1.tar.gz", source = TRUE, repos = NULL)

If successful, the console should return the following

Installing package into ‘/home/

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<your-username>/R/x86_64-pc-linux-gnu-library/3.6’

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(as ‘lib’ is unspecified)

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*  installing *source* package ‘approach’ ...

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** using staged installation

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** R

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** byte-compile and prepare package for lazy loading

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** help

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**

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 installing help indices

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** building package indices

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** testing if installed package can be loaded from temporary location

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** testing if installed package can be loaded from final location

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** testing if installed package keeps a record of temporary installation path

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*  DONE (approach)

b.      Import the installed APPROACH library, running the following command in console

library(approach)

c.       Create an ApproachAPI instance/object as follows

api = ApproachAPI()

This api variable will be used to authenticate yourself, and send PostgreSQL queries to the database

*You may use any variable name in place of api

Step 5. Using the ApproachAPI class

 a.       Logging In
Before submitting a query, the API must authenticate all subsequent requests. Authenticate yourself first using the ApproachAPI $login() function as below

api$login()

You will be prompted for your APPROACH reporting platform credentials.

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b.      Submitting Queries

Warning - Some tables have 100,000+ records stored. Try to refrain from selecting all from large data sets.

• Ex. Running SELECT * FROM approach.patient; would return 200,000+ records. This would be too much data for the database, RSTudio, as well as your computer to be processing and rendering frequently.

• If you are unsure if a query will return too many rows to process, you can limit the number of rows returned using the LIMIT clause at the end of any query.

  • i.e., SELECT * FROM approach.patient LIMIT 1000

Build your PostgreSQL query and submit it using the ApproachAPI $query(string) function

• The model explorer tool available in the reporting platform can be used to determine tables, field names and relationships used to build your queries.

See here: https://test-front.approach.org/model-explorer  (must be logged in)

e.g.,
api$query("SELECT count(*) as c, bmi FROM approach.patient WHERE bmi IS NOT NULL and bmi > 0 GROUP BY bmi ORDER BY c DESC;")

The query function will render the query’s results into a table

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c.       Logging Out
To close off your session with the API, run the $logout function as below

api$logout()

A confirmation message will be displayed once logged out

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• By default, a session will timeout and close off after 45 minutes of inactivity. However, explicitly logging out is suggested for security purposes.