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##' @importFrom jsonlite unbox
##' @importFrom httr content
## Return a list of studies from the OpenTree docstore that match a given properties
.studies_find_studies <- function(property = NULL, value = NULL, verbose = FALSE,
exact = FALSE, ...) {
if (!is.logical(verbose)) stop("Argument \'verbose\' should be logical")
if (!is.logical(exact)) stop("Argument \'exact\' should be logical")
req_body <- list()
if (!is.null(property)) {
if (!is.character(property)) {
stop("Argument \'property\' must be of class \"character\"")
}
req_body$property <- jsonlite::unbox(property)
} else {
stop("Must supply a \'property\' argument")
}
if (!is.null(value)) {
if (!is.character(value)) {
if (check_numeric(value)) {
value <- as.character(value)
} else {
stop("Argument \'value\' must be of class \"character\"")
}
}
req_body$value <- jsonlite::unbox(value)
} else {
stop("Must supply a \'value\' argument")
}
req_body$verbose <- jsonlite::unbox(verbose)
req_body$exact <- jsonlite::unbox(exact)
res <- otl_POST(
path = "studies/find_studies/",
body = req_body,
...
)
res
}
##' @importFrom jsonlite unbox
##' @importFrom httr content
## Return a list of trees from the OpenTree docstore that match a given properties
.studies_find_trees <- function(property = NULL, value = NULL, verbose = FALSE,
exact = FALSE, ...) {
if (!is.logical(verbose)) {
stop("Argument \'verbose\' must be of class \"logical\"")
}
if (!is.logical(exact)) {
stop("Argument \'exact\' must be of class \"logical\"")
}
req_body <- list()
if (!is.null(property)) {
if (!is.character(property)) {
stop("Argument \'property\' must be of class \"character\"")
}
req_body$property <- jsonlite::unbox(property)
} else {
stop("Must supply a \'property\' argument")
}
if (!is.null(value)) {
if (!is.character(value)) {
if (check_numeric(value)) {
value <- as.character(value)
} else {
stop("Argument \'value\' must be of class \"character\"")
}
}
req_body$value <- jsonlite::unbox(value)
} else {
stop("Must supply a \'value\' argument")
}
res <- otl_POST(
path = "studies/find_trees",
body = c(
req_body,
verbose = jsonlite::unbox(verbose),
exact = jsonlite::unbox(exact)
), ...
)
res
}
##' @importFrom httr content
## Return a list of properties that can be used to search studies and trees
.studies_properties <- function() {
res <- otl_POST(path = "studies/properties/", body = list())
res
}
##' @importFrom httr content
## Get a study from the OpenTree docstore
.get_study <- function(study_id = NULL, format = c("", "nexus", "newick", "nexml", "json"),
...) {
if (is.null(study_id)) {
stop("Must supply a \'study_id\' argument")
} else if (!is.character(study_id)) {
if (check_numeric(study_id)) {
study_id <- as.character(study_id)
} else {
stop("Argument \'study_id\' must be of class \"character\"")
}
}
format <- match.arg(format)
res <- otl_GET(
path = paste("study",
paste0(study_id, otl_formats(format)),
sep = "/"
),
...
)
res
}
##' @importFrom httr content
## Get a tree in a study from the OpenTree docstore
.get_study_tree <- function(study_id = NULL, tree_id = NULL, format = c("json", "newick", "nexus"),
tip_label = c("ot:originallabel", "ot:ottid", "ot:otttaxonname"),
...) {
if (is.null(study_id)) {
stop("Must supply a \'study_id\' argument")
} else if (!is.character(study_id)) {
stop("Argument \'study_id\' must be of class \"character\"")
}
if (is.null(tree_id)) {
stop("Must supply a \'tree\' argument")
} else if (!is.character(tree_id)) {
stop("Argument \'tree\' must be of class \"character\"")
}
format <- match.arg(format)
tip_label <- match.arg(tip_label)
tip_label <- paste0("/?tip_label=", tip_label)
tree_file <- paste0(tree_id, otl_formats(format), tip_label)
res <- otl_GET(path = paste("study", study_id, "tree", tree_file, sep = "/"), ...)
res
}
##' @importFrom httr content
.get_study_meta <- function(study_id, ...) {
otl_GET(path = paste("study", study_id, "meta", sep = "/"), ...)
}
##' @importFrom httr content
.get_study_subtree <- function(study_id, tree_id, subtree_id,
format = c("newick", "nexus", "nexml"),
tip_label = c("ot:originallabel", "ot:ottid", "ot:otttaxonname"),
...) {
if (is.null(study_id)) {
stop("Must supply a \'study_id\' argument")
} else if (!is.character(study_id)) {
stop("Argument \'study_id\' must be of class \"character\"")
}
if (is.null(tree_id)) {
stop("Must supply a \'tree\' argument")
} else if (!is.character(tree_id)) {
stop("Argument \'tree\' must be of class \"character\"")
}
if (is.null(subtree_id)) {
stop("Must supply a \'subtree\' argument")
} else if (!is.character(subtree_id)) {
stop("Argument \'subtree\' must be of class \"character\"")
}
format <- match.arg(format)
format <- otl_formats(format)
tip_label <- match.arg(tip_label)
url_stem <- paste("study", study_id, "subtree", paste0(tree_id, format), sep = "/")
res <- otl_GET(path = paste0(url_stem, "?subtree_id=", subtree_id, "&tip_label=", tip_label), ...)
res
}
### Let's not worry about those for now, as their results could be
### obtained using get_study_tree
get_study_otu <- function(study_id, otu = NULL, ...) {
otl_GET(path = paste("study", study_id, "otu", otu, sep = "/"), ...)
}
get_study_otus <- function(study_id, otus, ...) {
otl_GET(path = paste("study", study_id, "otu", otus, sep = "/"), ...)
}
get_study_otumap <- function(study_id, ...) {
otl_GET(path = paste("study", study_id, "otumap", sep = "/"))
}
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