From 13302213075c95cb4414d2582e68bc57fe87cbb6 Mon Sep 17 00:00:00 2001
From: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Date: Mon, 11 Dec 2023 08:51:00 +0000
Subject: [PATCH] add case data source

---
 code/auto_download/cases-deaths/get-ecdc.r | 19 ++++++++++++++++---
 1 file changed, 16 insertions(+), 3 deletions(-)

diff --git a/code/auto_download/cases-deaths/get-ecdc.r b/code/auto_download/cases-deaths/get-ecdc.r
index d0c251a13a..184f299980 100644
--- a/code/auto_download/cases-deaths/get-ecdc.r
+++ b/code/auto_download/cases-deaths/get-ecdc.r
@@ -5,6 +5,7 @@ library("purrr")
 library("tidyr")
 library("dplyr")
 library("vroom")
+library("tibble")
 library("ISOweek")
 
 get_ecdc <- function(earliest_date = lubridate::today() - 7,
@@ -61,8 +62,6 @@ get_ecdc <- function(earliest_date = lubridate::today() - 7,
         dplyr::select(
           location_name, location, target_variable, date, value, source
         )
-      file_name <- paste0("covid-cases-deaths_", file_date, ".csv")
-      vroom::vroom_write(df, file.path(local_path, file_name), delim = ",")
       return(df)
     } else {
       return(NULL)
@@ -70,7 +69,21 @@ get_ecdc <- function(earliest_date = lubridate::today() - 7,
   }
 
   ## save snapshots
-  snapshots <- purrr::map(process_files, dl_snapshot)
+  snapshots <- tibble(
+    file_name = process_files,
+    data = purrr::map(process_files, dl_snapshot)
+  ) |>
+    dplyr::mutate(
+      file_date = as.Date(
+        sub("^.*([0-9]{4}-[0-9]{2}-[0-9]{2}).*$", "\\1", file_name)
+      ),
+      file = file.path(
+        local_path, paste0("covid-cases-deaths_", file_date, ".csv")
+      )
+    ) |>
+    dplyr::group_by(file) |>
+    dplyr::summarise(x = list(bind_rows(data)), .groups = "keep") |>
+    purrr::pmap(vroom::vroom_write, delim = ", ")
 
   return(snapshots)
 }