update_time_series_links.yaml

name: Update time series links
on:
  workflow_dispatch:
    inputs:
      name:
        description: 'Update time series data links'
        required: false
  schedule:
    - cron: "0 0 * * *"
    - cron: "0 17 * * *"

jobs:
  update_time_series_links:
    runs-on: macOS-latest
    steps:
      - name: Checkout covidData repo
        uses: actions/checkout@v3
        with: 
          fetch-depth: 0
      
      - name: Setup R 
        uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true
      
      - name: Install dependencies
        run: |
          install.packages(c("tidyverse", "dplyr", "httr", "readr", "here", "RSocrata"))
        shell: Rscript {0}

      - name: Update time series
        run: |
          library(httr)
          library(RSocrata)
          library(dplyr)
          library(here)
          setwd(here())
          source("R/get_time_series_data_link.R")
          # get US data links
          jhu_us_deaths_data_links <- get_time_series_data_link(measure = "deaths", 
                                                                geography = "US",
                                                                download_files = FALSE,
                                                                download_recent = FALSE)
          write.csv(jhu_us_deaths_data_links, file = "data/jhu_us_deaths_data_links.csv", row.names = FALSE) 
          jhu_us_cases_data_links <- get_time_series_data_link(measure = "cases",
                                                               geography = "US",
                                                               download_files = FALSE,
                                                               download_recent = FALSE)
          write.csv(jhu_us_cases_data_links, file = "data/jhu_us_cases_data_links.csv", row.names = FALSE)
          # get global data links
          jhu_global_deaths_data_links <- get_time_series_data_link(measure = "deaths", 
                                                                    geography = "global",
                                                                    download_files = FALSE,
                                                                    download_recent = FALSE)
          write.csv(jhu_global_deaths_data_links, file = "data/jhu_global_deaths_data_links.csv", row.names = FALSE) 
          jhu_global_cases_data_links <- get_time_series_data_link(measure = "cases",
                                                                   geography =  "global",
                                                                   download_files = FALSE,
                                                                   download_recent = FALSE)
          write.csv(jhu_global_cases_data_links, file = "data/jhu_global_cases_data_links.csv", row.names = FALSE)
        shell: Rscript {0}

      - name: Commit changes
        uses: EndBug/add-and-commit@v7
        with: 
          add: '["data/jhu_us_cases_data_links.csv", "data/jhu_us_deaths_data_links.csv", "data/jhu_global_cases_data_links.csv", "data/jhu_global_deaths_data_links.csv"]'
          message: "Update time series data links"
          default_author: github_actions
          push: true