## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----setup--------------------------------------------------------------------
library(diseasystore)

## ----hidden_options, include = FALSE------------------------------------------
if (rlang::is_installed("withr")) {
  withr::local_options("tibble.print_min" = 5)
  withr::local_options("diseasystore.verbose" = FALSE)
} else {
  opts <- options("tibble.print_min" = 5, "diseasystore.verbose" = FALSE)
}

# We have a "hard" dependency for duckdb to render parts of this vignette
suggests_available <- rlang::is_installed("duckdb")
not_on_cran <- interactive() || identical(Sys.getenv("NOT_CRAN"), "true") || identical(Sys.getenv("CI"), "true")

## ----download_data, eval = FALSE----------------------------------------------
#  # First we set the path we want to use as an option
#  options(
#    "diseasystore.DiseasystoreGoogleCovid19.source_conn" =
#      file.path("local", "path")
#  )
#  
#  # Ensure folder exists
#  source_conn <- diseasyoption("source_conn", "DiseasystoreGoogleCovid19")
#  if (!dir.exists(source_conn)) {
#    dir.create(source_conn, recursive = TRUE, showWarnings = FALSE)
#  }
#  
#  # Define the Google files to download
#  google_files <- c("by-age.csv", "demographics.csv", "index.csv", "weather.csv")
#  
#  # Download each file and compress them to reduce storage
#  purrr::walk(google_files, ~ {
#    url <- paste0(diseasyoption("remote_conn", "DiseasystoreGoogleCovid19"), .)
#  
#    destfile <- file.path(
#      diseasyoption("source_conn", "DiseasystoreGoogleCovid19"),
#      .
#    )
#  
#    if (!file.exists(destfile)) {
#      download.file(url, destfile)
#    }
#  })

## ----download_data_hidden, include = FALSE, eval = not_on_cran----------------
# The files we need are stored remotely in Google's API
google_files <- c("by-age.csv", "demographics.csv", "index.csv", "weather.csv")
remote_conn <- diseasyoption("remote_conn", "DiseasystoreGoogleCovid19")

# In practice, it is best to make a local copy of the data which is stored in the "vignette_data" folder
# This folder can either be in the package folder (preferred, please create the folder) or in the tempdir()
local_conn <- purrr::detect("vignette_data", checkmate::test_directory_exists, .default = tempdir())

if (rlang::is_installed("withr")) {
  withr::local_options("diseasystore.DiseasystoreGoogleCovid19.source_conn" = local_conn)
  withr::local_options("diseasystore.DiseasystoreGoogleCovid19.n_max" = 1000)
} else {
  opts <- c(opts, options("diseasystore.DiseasystoreGoogleCovid19.source_conn" = local_conn,
                          "diseasystore.DiseasystoreGoogleCovid19.n_max" = 1000))
}

# Then we download the first n rows of each data set of interest
try({
  purrr::discard(google_files, ~ checkmate::test_file_exists(file.path(local_conn, .))) |>
    purrr::walk(\(file) {
      paste0(remote_conn, file) |>
        readr::read_csv(n_max = 1000, show_col_types = FALSE, progress = FALSE) |>
        readr::write_csv(file.path(local_conn, file))
    })
})

# Check that the files are available after attempting to download
if (purrr::some(google_files, ~ !checkmate::test_file_exists(file.path(local_conn, .)))) {
  data_available <- FALSE
} else {
  data_available <- TRUE
}

## ----configure_diseasystore, eval = FALSE-------------------------------------
#  # We define target_conn as a function that opens a DBIconnection to the DB
#  target_conn <- \() DBI::dbConnect(duckdb::duckdb())
#  options(
#    "diseasystore.DiseasystoreGoogleCovid19.target_conn" = target_conn
#  )

## ----configure_diseasystore_hidden, include = FALSE, eval = not_on_cran && suggests_available && data_available----
target_conn <- \() DBI::dbConnect(duckdb::duckdb())
if (rlang::is_installed("withr")) {
  withr::local_options("diseasystore.DiseasystoreGoogleCovid19.target_conn" = target_conn)
} else {
  opts <- c(opts, options("diseasystore.DiseasystoreGoogleCovid19.target_conn" = target_conn))
}

## ----initializing_diseasystore, eval = not_on_cran && suggests_available && data_available----
ds <- DiseasystoreGoogleCovid19$new()

## ----using_diseasystore_example_1, eval = not_on_cran && suggests_available && data_available----
# We can see all the available features in the feature store
ds$available_features

## ----using_diseasystore_example_2, eval = not_on_cran && suggests_available && data_available----
# And then retrieve a feature from the feature store
ds$get_feature(feature = "n_hospital",
               start_date = as.Date("2020-01-01"),
               end_date = as.Date("2020-06-01"))

## ----cleanup, include = FALSE-------------------------------------------------
if (exists("ds")) rm(ds)
gc()
if (!rlang::is_installed("withr")) {
  options(opts)
}