R/api-tol.R

In rotl: Interface to the 'Open Tree of Life' API

##' @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
}