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##' @importFrom jsonlite unbox
##' @importFrom httr content
## Summary information about the OpenTree Tree of Life
.tol_about <- function(include_source_list = FALSE, ...) {
check_is_flag(include_source_list)
q <- list(include_source_list = jsonlite::unbox(include_source_list))
res <- otl_POST(path = "tree_of_life/about", body = q, ...)
res
}
##' @importFrom jsonlite unbox
##' @importFrom httr content
## Get summary information about a node in the OpenTree Tree of Life
.tol_node_info <- function(ott_id = NULL, node_id = NULL, include_lineage = FALSE, ...) {
check_is_flag(include_lineage)
if (is.null(ott_id) && is.null(node_id)) {
stop("Must provide either ", sQuote("ott_id"), " or ", sQuote("node_id"))
}
if (!is.null(ott_id) && !is.null(node_id)) {
stop("Must provide either ", sQuote("ott_id"), " or ", sQuote("node_id"), ", not both.")
}
if (!is.null(ott_id)) {
ott_id <- check_ott_ids(ott_id)
if (length(ott_id) != 1) {
stop("Please provide a single ", sQuote("ott_id"), call. = FALSE)
}
q <- list(ott_id = jsonlite::unbox(ott_id), include_lineage = jsonlite::unbox(include_lineage))
} else {
if (!check_valid_node_id(node_id)) {
stop("Argument ", sQuote("node_id"), " must look like \'ott123\' or \'mrcaott123ott456\'.")
}
q <- list(node_id = jsonlite::unbox(node_id), include_lineage = jsonlite::unbox(include_lineage))
}
res <- otl_POST(path = "tree_of_life/node_info", body = q, ...)
res
}
##' @importFrom httr content
## Get the MRCA of a set of nodes
.tol_mrca <- function(ott_ids = NULL, node_ids = NULL, ...) {
if (is.null(ott_ids) && is.null(node_ids)) {
stop("Must provide ", sQuote("ott_ids"), " or ", sQuote("node_ids"), " (or both).")
}
q <- list()
if (!is.null(ott_ids)) {
ott_ids <- check_ott_ids(ott_ids)
q$ott_ids <- ott_ids
}
if (!is.null(node_ids)) {
check_node_ids(node_ids)
q$node_ids <- node_ids
}
res <- otl_POST(path = "tree_of_life/mrca", body = q, ...)
res
}
# ignoring 'include_lineage' for subtree below. arguson only
##' @importFrom jsonlite unbox
##' @importFrom httr content
## Get a subtree from the OpenTree Tree of Life
.tol_subtree <- function(ott_id = NULL, node_id = NULL, label_format = NULL, ...) {
if (is.null(ott_id) && is.null(node_id)) {
stop("Must provide either ", sQuote("ott_id"), " or ", sQuote("node_id"))
}
if (!is.null(ott_id) && !is.null(node_id)) {
stop("Must provide either ", sQuote("ott_id"), " or ", sQuote("node_id"), ", not both.")
}
if (!is.null(ott_id)) {
ott_id <- check_ott_ids(ott_id)
if (length(ott_id) != 1) {
stop("Please provide a single ", sQuote("ott_id"))
}
q <- list(ott_id = jsonlite::unbox(ott_id))
} else {
if (!check_valid_node_id(node_id)) {
stop("Argument ", sQuote("node_id"), " must look like \'ott123\' or \'mrcaott123ott456\'.")
}
q <- list(node_id = jsonlite::unbox(node_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$label_format <- jsonlite::unbox(label_format)
}
res <- otl_POST(path = "tree_of_life/subtree", body = q, ...)
res
}
##' @importFrom httr content
## Get an induced subtree from the OpenTree Tree of Life from a set of nodes
.tol_induced_subtree <- function(ott_ids = NULL, node_ids = NULL, label_format = NULL, ...) {
if (is.null(ott_ids) && is.null(node_ids)) {
stop("Must provide ", sQuote("ott_ids"), " or ", sQuote("node_ids"), " (or both).")
}
q <- list()
if (!is.null(label_format)) {
if (!check_label_format(label_format)) {
stop(
sQuote("label_format"), " must be one of: ", sQuote("name"), ", ",
sQuote("id"), ", or ", sQuote("name_and_id")
)
}
q$label_format <- jsonlite::unbox(label_format)
}
if (!is.null(ott_ids)) {
ott_ids <- check_ott_ids(ott_ids)
q$ott_ids <- ott_ids
}
if (!is.null(node_ids)) {
check_node_ids(node_ids)
q$node_ids <- node_ids
}
if ((length(ott_ids) + length(node_ids)) < 2) {
stop("At least two valid ", sQuote("ott_ids"), " or ", sQuote("node_ids"), " must be provided.")
}
res <- otl_POST("tree_of_life/induced_subtree", body = q, ...)
res
}
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