COVID-19 Tracker Philippines

This serves as a supplementary tracker for the COVID-19 Tracker maintained by the Department of Health. The data set used in this tracker are pulled from DOH's data drop.

This project started as a report generator initially to track the dalays between testing and confirmation/reporting but evolved into a tracking and reports page where I've experimented with Python tools, frontend frameworks, and CI/CD workflows.

In its current form, it is a static report generator using the DOH Data Drop as a data source.

Disclaimer: I am not affiliated with the DOH or any government agency. This is my own personal project.

Requirements

NOTE This project runs best in Linux and MacOS. You might run into problems that are not documented here if you try running it in Windows. It is recommended to use WSL instead if you're on a Windows machine since it is my current development setup.

install-dependencies script

Run the setup make target to install the needed Ruby and NPM packages for building the site.

make setup

In its current form, it runs the install-dependencies.sh script which installs the dependency packages. However, this is written for Ubuntu which uses the apt package manager. If you're on a different platform, please consider updating the the script to accomodate your specific environment. I'll be happy to merge your pull request if you submit one.

Python

Python can be installed from python.org. If you're setting up your project on a then most probably it already has Python installed.

There are also several ways to setup a Python development environment but I have created a script for it for my typical development environment setup which is pyenv + Poetry. For those who are using Ubuntu (or WSL Ubuntu), you can run the setup-python make target.

make setup-python

This target executes the setup-python.sh script which installs pyenv and Poetry. If you prefer a different method of creating your virtual environments then you may do so. The required packages are listed in the pyproject.toml file.

Hardware Requirements

Due to the amount of data that's available in the Data Drop, you will need around 10GB of RAM to run the update-tracker.py script on an 8-core machine. If you only have ~8GB of physical RAM, consider increasing your swap partition (if in Linux).

If you're on WSL, you can set your memory through the .wslconfig or wsl.config files. The configuration settings are documented here.

[wsl2]
memory=12GB
swap=10GB

Overview

The update-tracker.py script downloads the data from the DOH Data Drop and generates the charts used in the COVID-19 Tracker PH page.

Go to tracker

How to Run

Create a Client Secret

Create and download a OAth 2.0 client secret from the Google APIs site. Follow the Quickstart Guide to understand how the API works and follow the Enable the Google Drive API Guide to create your client secret file.

Copy the client secret file to your project directory and rename the file as client_secret.json.

Open the Files in the DOH Data Drop Google Drive Folder

Open README file in the DOH folder. This link is also available at the DOH Covid19 Tracker.

The README file will have a link to the latest Data Drop folder at the last page. Click on that link to open the latest Data Drop folder.

Open all of the files in the Data Drop Folder.

You need to do this step due to a limitation in the Google Drive API. See Limitations below.

Running the Script

Navigate to your project directory then run the updatetracker script.

NOTE Make sure that the covid19trackerph project package has been installed in your virtual environment before running the script.

updatetracker

Errors

Sometimes, the link in the PDF file is not annotated - meaning it is only a text and not a link - so PyPDF2 will not be able to find it. To get around that, you can use the --folder-id option of the script.

updatetracker --folder-id=<folder-id-of-latest-datadrop>

# example
updatetracker --folder-id=12l_bfB_wuQ8wrauCbesKURswRJFl-ih_

TODOs

Plots

• Testing ang Confirmation Gap
• Death and Recovery Reporting
• Recovery Time
• Period from Infection to Death (what's the proper term for this?)
• R0 and projection
• Per region and city/municipality pages
• Hospital daily report - occupancy
• Hospital weekly report - PPE inventory
• Quarantine facility reports

Theme

• Organize post tags.
• Create own icon.
• Change about image.
• Migrate to Next.js.

Limitations

You need to open each of the new files in the DOH datadrop before the script can download the Google Drive files for you. This is because the files need to be either explicitly shared to your account or need to be opened first in order for them to be listed in your Drive. See this Stackoverflow question.

Other Useful Trackers

• covid19stats.ph
• covid19ph
• Baguio Covid19 Tracker
• Our World in Data