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GSUR Data Automation Tool

Automate the Process of Downloading and Analyzing Patient Data

About

The GSUR Data Automation Tool has two features. An automated downloader tool that runs off of the requests python library or selenium to open your browser and login into the EMMA patient portal website and downloads all necessary files that researchers need access to, and the analysis tool that reads through all the data files and outputs the result into a single .csv file.

Features / Tools

  • Python 3
  • Requests, CustomTkinter, Selenium
  • Browser Automation to Download Data
  • Automation to Analyze Data and Output Results to singular CSV file.

Installation & Setup

The GSUR Automation tool has two main iterations available for you to set up and use. One version utilizes the Python Requests library, while the other uses the Python web automation library Selenium. Setup instructions for both versions are described below. As a general reference, the Requests implementation is the most recently worked-on version, so its support is the most updated.

Note

While this project can function, only people with EMMA accounts to login into the host site can access the full functionality of it.

  • This is optional step you can take before the installation & setup section to help keep the project libraries seperate
  • (OPTIONAL) Create a virtual environment if you choose to do so
    • In the /GSUR folder
    • python -m venv myenv
    • On Windows myenv/Scripts/activate
    • On macOS and Linux source myenv/bin/activate
  • (OPTIONAL) Managing the virtual environment
    • When you want to leave use deactivate
    • Make sure to upgrade pip python -m pip install --upgrade pip

Requests

Using the GUI (Graphical User Interface) and Requests Library

  1. Ensure you have Python3 installed and download the codebase to your local machine.

  2. Download External Python Libraries

    pip install -r requirements.txt

  3. Run the GUI (Graphical User Interface)

    python3 gui_menu.py

  4. The GUI should appear and look like this GSUR GUI

  5. If you need to download files begin with setting up your credentials with the edit login tab, it will not work otherwise.

Selenium

Using the CLI (Command Line Interface) with Selenium

  1. Ensure you have Python3 installed and download the codebase to your local machine.

  2. Download External Python Libraries

    pip install -r requirements.txt

  3. Setup Login Credentials

  • For logging into the EMMA site you have to have your username and password setup in a seperate file for the automation to pull from.
  • Create a new file .env in the same directory as the chrome_automation.py file and have it contain this: 
    USERNAME = "your_username"
PASSWORD = "your_password"
  1. Install Browser Webdrivers
  • Webdrivers are specific for each web browser and must be installed by the user for this software to download files properly. Supported Browsers: Google Chrome

Find out what the version number is for your browser.

  • Open a new tab in Chrome
  • Click the three dot button in the top right
  • Click the "Help" button that is second from the bottom
  • Click "About Google Chrome"
  • The tab will reload and you should be able to see your browser version number listed and the option to update the browser if you have not

Chrome Version Number Image ^^^ Remember your Version Number

Note

Your Browser will most likely have a different number than what is shown above.

Download your specific webdriver version.

Webdrivers for Google Chrome

  • Chrome Webdriver Download Page
  • If the version of your chrome doesn't have stable webdrivers released yet (your version number will be colored red instead of green). You can download previous stable chrome browser versions along with their drivers that are certified to work from the site above. As long as the browser and webdriver version match everything will work.

Move Webdriver to Correct Place.

  • MacOS

    • Once the Chrome webdriver is downloaded, on MacOS extract the folder.
    • You will need to move the chromedriver.exe to your /usr/local/bin folder. You can easily go to this folder by holding CMD+SHIFT+G in Finder and once the /bin dialog box appears press enter.
    • Once in the /bin folder move the chromedriver.exe to this.
    • Need Help? Installing Chrome Driver Web Driver on Mac

  • Windows

    • NA

Verify Webdriver Installation and Permissions

  • MacOS

    • After pasting the chromedriver.exe into the /bin folder if you get this dialog box at any point, here's how you can solve it. Chromedriver Error Image
    • Open a terminal window at /usr/local/bin using the method above and enter
    ls -l
    • If the chromedriver file has an @ symbol at the end of the permissions for example, -rwxr-xr-x@
    • Use this command to remove this file from MacOS quarentine.
    xattr -d com.apple.quarantine chromedriver

  • Windoows

    • NA

To Run the GSUR Web Automation

  • In terminal or code editor navigate to the /GSUR folder. Ensure you have the webdrivers installed, requirements.txt downloaded, and credentials .env created.
    • Use python3 gui_menu.py or python3 chrome-automation.py to run the downloader code with whatever GUI you desire.
    • Use python3 djcbarmaker.py to run the analysis code if you are using the chrome-automation method

Learn More

This software was built by Mitchell Kolb for use in the Psychology Department at WSU GSUR Program.