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get_sample_sets.R
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get_sample_sets.R
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get_sample_set <- function(resource,
limit = 20L,
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE) {
tbl_json <- get(resource_url = resource,
limit = limit,
verbose = verbose,
warnings = warnings,
progress_bar = progress_bar)
tidy_tbls <- as_tidy_tables_sample_sets(tbl_json)
return(tidy_tbls)
}
get_sample_sets_by_pss_id <- function(pss_id, limit = 20L, verbose = FALSE, warnings = TRUE, progress_bar = TRUE) {
resource <- '/rest/sample_set'
resource_urls <- sprintf("%s/%s", resource, pss_id)
purrr::map(
resource_urls,
get_sample_set,
limit = limit,
warnings = warnings,
verbose = verbose,
progress_bar = progress_bar
) %>%
purrr::pmap(dplyr::bind_rows)
}
get_sample_sets_by_pgs_id <- function(pgs_id, limit = 20L, verbose = FALSE, warnings = TRUE, progress_bar = TRUE) {
resource <- '/rest/sample_set/search'
resource_urls <- sprintf("%s?pgs_id=%s", resource, pgs_id)
purrr::map(
resource_urls,
get_sample_set,
limit = limit,
warnings = warnings,
verbose = verbose,
progress_bar = progress_bar
) %>%
purrr::pmap(dplyr::bind_rows)
}
get_sample_sets_all <- function(limit = 20L, verbose = FALSE, warnings = TRUE, progress_bar = TRUE) {
resource <- '/rest/sample_set/all'
get_sample_set(resource = resource,
limit = limit,
verbose = verbose,
warnings = warnings,
progress_bar = progress_bar)
}
#' Get PGS Catalog Sample Sets
#'
#' Retrieves sample sets via the PGS Catalog REST API. The REST
#' API is queried multiple times with the criteria passed as arguments (see
#' below). By default all sample sets that match the criteria supplied in the
#' arguments are retrieved: this corresponds to the default option
#' \code{set_operation} set to \code{'union'}. If you rather have only the
#' associations that match simultaneously all criteria provided, then set
#' \code{set_operation} to \code{'intersection'}.
#'
#' Please note that all search criteria are vectorised, thus allowing for batch
#' mode search.
#'
#' @param pss_id A character vector of PGS Catalog sample sets accession
#' identifiers.
#' @param pgs_id A \code{character} vector of PGS Catalog score accession
#' identifiers.
#' @param set_operation Either \code{'union'} or \code{'intersection'}. This
#' tells how performance metrics retrieved by different criteria should be combined:
#' \code{'union'} binds together all results removing duplicates and
#' \code{'intersection'} only keeps same sample sets found with different
#' criteria.
#' @param interactive A logical. If all sample sets are requested, whether to ask
#' interactively if we really want to proceed.
#' @param verbose A \code{logical} indicating whether the function should be
#' verbose about the different queries or not.
#' @param warnings A \code{logical} indicating whether to print warnings, if any.
#' @param progress_bar Whether to show a progress bar indicating download
#' progress from the REST API server.
#'
#' @return A \linkS4class{sample_sets} object.
#' @examples
#' \dontrun{
#' # Search by PGS identifier
#' get_sample_sets(pgs_id = 'PGS000013')
#'
#' # Search by the PSS identifier
#' get_sample_sets(pss_id = 'PSS000068')
#' }
#' @export
get_sample_sets <- function(
pss_id = NULL,
pgs_id = NULL,
set_operation = 'union',
interactive = TRUE,
verbose = FALSE,
warnings = TRUE,
progress_bar = TRUE) {
if(!(rlang::is_scalar_character(set_operation) && set_operation %in% c('union', 'intersection')))
stop("set_operation must be either 'union' or 'intersection'")
if(!(rlang::is_scalar_logical(verbose) && verbose %in% c(TRUE, FALSE)))
stop("verbose must be either TRUE or FALSE")
if(!(rlang::is_scalar_logical(warnings) && warnings %in% c(TRUE, FALSE)))
stop("warnings must be either TRUE or FALSE")
list_of_pss <- list()
if (!rlang::is_null(pss_id))
list_of_pss[['get_sample_sets_by_pss_id']] <-
get_sample_sets_by_pss_id(pss_id = pss_id,
verbose = verbose,
warnings = warnings,
progress_bar = progress_bar) %>%
coerce_to_s4_sample_sets()
if (!rlang::is_null(pgs_id))
list_of_pss[['get_sample_sets_by_pgs_id']] <-
get_sample_sets_by_pgs_id(pgs_id = pgs_id,
verbose = verbose,
warnings = warnings,
progress_bar = progress_bar) %>%
coerce_to_s4_sample_sets()
# If no criteria have been passed, i.e. all are NULL then got fetch all
# Sample Sets.
if(rlang::is_empty(list_of_pss)) {
#return(coerce_to_s4_sample_sets(NULL))
msg1 <- "You are about to download all sample sets from the PGS Catalog.\nThis might take a while."
msg2 <- 'Returning an empty sample_sets object!'
msg3 <- 'OK! Getting all sample sets then. This is going to take a while...'
if(interactive)
default_answer = NULL # i.e., use interactive mode.
else
default_answer = 'y'
if (sure(
before_question = msg1,
after_saying_no = msg2,
after_saying_yes = msg3,
default_answer = default_answer
))
return(coerce_to_s4_sample_sets(
get_sample_sets_all(verbose = verbose, warnings = warnings)))
else
return(coerce_to_s4_sample_sets(NULL))
} else {
if (identical(set_operation, "union")) {
return(purrr::reduce(list_of_pss, union))
}
if (identical(set_operation, "intersection")) {
return(purrr::reduce(list_of_pss, intersect))
}
}
}