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#' Download table data
#'
#' This retrieves rows in chunks of `page_size`. It is most suitable for results
#' of smaller queries (<100 MB, say). For larger queries, it is better to
#' export the results to a CSV file stored on google cloud and use the
#' bq command line tool to download locally.
#'
#' @section Complex data:
#' bigrquery will retrieve nested and repeated columns in to list-columns
#' as follows:
#'
#' * Repeated values (arrays) will become a list-column of vectors.
#' * Records will become list-columns of named lists.
#' * Repeated records will become list-columns of data frames.
#'
#' @section Larger datasets:
#' In my timings, this code takes around 1 minute per 100 MB of data.
#' If you need to download considerably more than this, I recommend:
#'
#' * Export a `.csv` file to Cloud Storage using [bq_table_save()].
#' * Use the `gsutil` command line utility to download it.
#' * Read the csv file into R with `readr::read_csv()` or `data.table::fread()`.
#'
#' Unfortunately you can not export nested or repeated formats into CSV, and
#' the formats that BigQuery supports (arvn and ndjson) that allow for
#' nested/repeated values, are not well supported in R.
#'
#' @return Because data retrieval may generate list-columns and the `data.frame`
#' print method can have problems with list-columns, this method returns
#' a tibble. If you need a `data.frame`, coerce the results with
#' [as.data.frame()].
#' @param x A [bq_table]
#' @param n_max Maximum number of results to retrieve. Use `Inf` to retrieve all
#' rows.
#' @param page_size The number of rows requested per chunk. It is recommended to
#' leave this unspecified until you have evidence that the `page_size`
#' selected automatically by `bq_table_download()` is problematic.
#'
#' When `page_size = NULL` bigrquery determines a conservative, natural chunk
#' size empirically. If you specify the `page_size`, it is important that each
#' chunk fits on one page, i.e. that the requested row limit is low enough to
#' prevent the API from paginating based on response size.
#' @param start_index Starting row index (zero-based).
#' @param max_connections Number of maximum simultaneous connections to
#' BigQuery servers.
#' @inheritParams api-job
#' @param bigint The R type that BigQuery's 64-bit integer types should be
#' mapped to. The default is `"integer"`, which returns R's `integer` type,
#' but results in `NA` for values above/below +/- 2147483647. `"integer64"`
#' returns a [bit64::integer64], which allows the full range of 64 bit
#' integers.
#' @param max_results `r lifecycle::badge("deprecated")` Deprecated. Please use
#' `n_max` instead.
#' @section Google BigQuery API documentation:
#' * [list](https://cloud.google.com/bigquery/docs/reference/rest/v2/tabledata/list)
#' @export
#' @examples
#' if (bq_testable()) {
#' df <- bq_table_download("publicdata.samples.natality", n_max = 35000)
#' }
bq_table_download <-
function(x,
n_max = Inf,
page_size = NULL,
start_index = 0L,
max_connections = 6L,
quiet = NA,
bigint = c("integer", "integer64", "numeric", "character"),
max_results = deprecated()) {
x <- as_bq_table(x)
bigint <- match.arg(bigint)
if (lifecycle::is_present(max_results)) {
lifecycle::deprecate_warn(
"1.4.0", "bq_table_download(max_results)", "bq_table_download(n_max)"
)
n_max <- max_results
}
params <- set_row_params(
nrow = bq_table_nrow(x),
n_max = n_max,
start_index = start_index
)
n_max <- params$n_max
start_index <- params$start_index
schema_path <- bq_download_schema(x, tempfile())
withr::defer(file.remove(schema_path))
if (n_max == 0) {
table_data <- bq_parse_files(
schema_path,
file_paths = character(),
n = 0,
quiet = bq_quiet(quiet)
)
return(table_data)
}
pool <- curl::new_pool()
# get first chunk ----
if (!bq_quiet(quiet)) {
message("Downloading first chunk of data.")
}
if (is.null(page_size)) {
chunk_size_from_user <- FALSE
} else {
assert_that(
is.numeric(page_size),
length(page_size) == 1,
page_size > 0
)
chunk_size_from_user <- TRUE
}
chunk_size <- page_size
chunk_plan <- bq_download_plan(
n_max,
chunk_size = chunk_size,
n_chunks = 1,
start_index = start_index
)
handle <- bq_download_chunk_handle(
x,
begin = chunk_plan$dat$chunk_begin[1],
max_results = chunk_plan$dat$chunk_rows[1]
)
curl::multi_add(
handle,
done = bq_download_callback(chunk_plan$dat$path[1]),
pool = pool
)
curl::multi_run(pool = pool)
path_first_chunk <- chunk_plan$dat$path[1]
withr::defer(file.remove(path_first_chunk))
chunk_data <- bq_parse_file(schema_path, path_first_chunk)
n_got <- nrow(chunk_data)
if (n_got >= n_max) {
if (!bq_quiet(quiet)) {
message("First chunk includes all requested rows.")
}
return(convert_bigint(chunk_data, bigint))
}
if (chunk_size_from_user && n_got < chunk_size) {
abort(c(
"First chunk is incomplete:",
x = glue("{big_mark(chunk_size)} rows were requested, but only \\
{big_mark(n_got)} rows were received."),
i = "Leave `page_size` unspecified or use an even smaller value."
))
}
# break rest of work into natural chunks ----
if (!chunk_size_from_user) {
if (!bq_quiet(quiet)) {
message(glue("Received {big_mark(n_got)} rows in the first chunk."))
}
chunk_size <- trunc(0.75 * n_got)
}
n_max_new <- n_max - n_got
start_index_new <- n_got
chunk_plan <- bq_download_plan(
n_max_new,
chunk_size = chunk_size,
start_index = start_index_new
)
progress <- bq_progress(
"Downloading data [:bar] :percent ETA: :eta",
total = chunk_plan$n_chunks,
quiet = quiet
)
if (!bq_quiet(quiet)) {
message(glue_data(
chunk_plan,
"Downloading the remaining {big_mark(n_max)} rows in {n_chunks} \\
chunks of (up to) {big_mark(chunk_size)} rows."
))
}
for (i in seq_len(chunk_plan$n_chunks)) {
handle <- bq_download_chunk_handle(
x,
begin = chunk_plan$dat$chunk_begin[i],
max_results = chunk_plan$dat$chunk_rows[i]
)
curl::multi_add(
handle,
done = bq_download_callback(chunk_plan$dat$path[i], progress),
pool = pool
)
}
curl::multi_run(pool = pool)
withr::defer(file.remove(chunk_plan$dat$path))
table_data <- bq_parse_files(
schema_path,
c(path_first_chunk, chunk_plan$dat$path),
n = n_max,
quiet = bq_quiet(quiet)
)
convert_bigint(table_data, bigint)
}
# This function is a modified version of
# https://github.com/r-dbi/RPostgres/blob/master/R/PqResult.R
convert_bigint <- function(df, bigint) {
if (bigint == "integer64") {
return(df)
}
as_bigint <- switch(bigint,
integer = as.integer,
numeric = as.numeric,
character = as.character
)
rapply_int64(df, f = as_bigint)
}
rapply_int64 <- function(x, f) {
if (is.list(x)) {
x[] <- lapply(x, rapply_int64, f = f)
x
} else if (bit64::is.integer64(x)) {
f(x)
} else {
x
}
}
set_row_params <- function(nrow, n_max = Inf, start_index = 0L) {
assert_that(is.numeric(n_max), length(n_max) == 1, n_max >= 0)
assert_that(is.numeric(start_index), length(start_index) == 1, start_index >= 0)
n_max <- max(min(n_max, nrow - start_index), 0)
list(n_max = n_max, start_index = start_index)
}
bq_download_plan <- function(n_max,
chunk_size = NULL,
n_chunks = NULL,
start_index = 0) {
params <- set_chunk_params(n_max, chunk_size, n_chunks)
list(
n_max = n_max,
chunk_size = params$chunk_size,
n_chunks = params$n_chunks,
dat = set_chunk_plan(
n_max,
params$chunk_size,
params$n_chunks,
start_index
)
)
}
set_chunk_params <- function(n_max, chunk_size = NULL, n_chunks = NULL) {
if (is.null(chunk_size) && is.null(n_chunks)) {
n_chunks <- 1
}
n_chunks <- n_chunks %||% Inf
chunk_size <- pmin(chunk_size %||% ceiling(n_max / n_chunks), n_max)
n_chunks <- pmin(n_chunks, ceiling(n_max / chunk_size))
list(chunk_size = chunk_size, n_chunks = n_chunks)
}
set_chunk_plan <- function(n_max, chunk_size, n_chunks, start_index = 0) {
chunk_begin <- start_index + (seq_len(n_chunks) - 1) * chunk_size
chunk_end <- pmin(chunk_begin + chunk_size, start_index + n_max)
chunk_rows <- chunk_end - chunk_begin
tibble::tibble(
chunk_begin,
chunk_rows,
path = sort(
tempfile(rep_len("bq-download-", length.out = n_chunks), fileext = ".json")
)
)
}
bq_download_chunk_handle <- function(x, begin = 0L, max_results = 1e4) {
x <- as_bq_table(x)
assert_that(is.numeric(begin), length(begin) == 1)
assert_that(is.numeric(max_results), length(max_results) == 1)
# Pre-format query params with forced non-scientific notation, since the BQ
# API doesn't accept numbers like 1e5. See issue #395 for details.
query <- list(
startIndex = format(begin, scientific = FALSE),
maxResults = format(max_results, scientific = FALSE)
)
url <- paste0(base_url, bq_path(x$project, dataset = x$dataset, table = x$table, data = ""))
url <- httr::modify_url(url, query = prepare_bq_query(query))
if (bq_has_token()) {
token <- .auth$get_cred()
signed <- token$sign("GET", url)
url <- signed$url
headers <- signed$headers
} else {
headers <- list()
}
h <- curl::new_handle(url = url)
curl::handle_setopt(h, useragent = bq_ua())
curl::handle_setheaders(h, .list = headers)
h
}
bq_download_callback <- function(path, progress = NULL) {
force(path)
function(result) {
if (!is.null(progress)) progress$tick()
bq_check_response(
result$status_code,
curl::parse_headers_list(result$headers)[["content-type"]],
result$content
)
con <- file(path, open = "wb")
withr::defer(close(con))
writeBin(result$content, con)
}
}
# Helpers for testing -----------------------------------------------------
bq_parse_file <- function(fields, data) {
fields <- brio::read_file(fields)
data <- brio::read_file(data)
bq_parse(fields, data)
}
bq_download_schema <- function(x, path) {
x <- as_bq_table(x)
url <- bq_path(x$project, x$dataset, x$table)
query <- list(fields = "schema")
json <- bq_get(url, query = query, raw = TRUE)
writeBin(json, path)
path
}
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