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##' @importFrom httr content
## Summary information about the OpenTree Taxonomy (OTT)
.taxonomy_about <- function(...) {
res <- otl_POST(path = "/taxonomy/about", body = list(), ...)
res
}
##' @importFrom jsonlite unbox
##' @importFrom httr content
## Information about an OpenTree Taxonomy (OTT) taxon
.taxonomy_taxon_info <- function(ott_id = NULL,
include_children = FALSE,
include_lineage = FALSE,
include_terminal_descendants = FALSE,
...) {
ott_id <- check_ott_ids(ott_id)
if (length(ott_id) > 1) {
stop("Must only supply one ", sQuote("ott_id"), " argument")
}
check_is_flag(include_children)
check_is_flag(include_lineage)
check_is_flag(include_terminal_descendants)
q <- list(
ott_id = jsonlite::unbox(ott_id),
include_children = jsonlite::unbox(include_children),
include_lineage = jsonlite::unbox(include_lineage),
include_terminal_descendants = jsonlite::unbox(include_terminal_descendants)
)
res <- otl_POST(path = "/taxonomy/taxon_info", body = q, ...)
res
}
##' @importFrom jsonlite unbox
##' @importFrom httr content
## Get a subtree from the OpenTree Taxonomy (OTT) taxonomic tree
.taxonomy_subtree <- function(ott_id = NULL, label_format = NULL, ...) {
ott_id <- check_ott_ids(ott_id)
if (length(ott_id) > 1) {
stop("Must only supply one ", sQuote("ott_id"), " argument")
}
q <- list(ott_id = jsonlite::unbox(ott_id))
if (!is.null(label_format)) {
if (!check_label_format(label_format)) {
stop(
sQuote("label_format"), " must be one of: ", sQuote("name"), ", ",
sQuote("id"), ", or ", sQuote("name_and_id")
)
}
q$label_format <- jsonlite::unbox(label_format)
}
res <- otl_POST(path = "/taxonomy/subtree", body = q, ...)
res
}
##' @importFrom httr content
## Get the most recent common ancestor (MRCA) from nodes in the OpenTree Taxonomy (OTT)
.taxonomy_mrca <- function(ott_ids = NULL, ...) {
ott_ids <- check_ott_ids(ott_ids)
q <- list(ott_ids = ott_ids)
res <- otl_POST(path = "/taxonomy/mrca", body = q, ...)
res
}
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