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fix various urls - make coral fxns defunct fix #124
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,111 +1,45 @@ | ||
| #' Search for coral data on coraltraits.org | ||
| #' | ||
| #' @name coral | ||
| #' @param taxon A taxon id | ||
| #' @param trait A trait id | ||
| #' @param location A location id | ||
| #' @param methodology A methodology id | ||
| #' @param resource A resource id | ||
| #' @param taxonomy logical; Include contextual data. Default: `FALSE` | ||
| #' @param contextual logical; Include contextual data. Default: `TRUE` | ||
| #' @param global logical; Include contextual data. Default: `FALSE` | ||
| #' @param ... Curl options passed on to [crul::verb-GET] | ||
| #' | ||
| #' DEFUNCT: As far as we can tell the coraltraits.org API is down | ||
| #' for good | ||
| #' | ||
| #' @name coral-defunct | ||
| #' @keywords internal | ||
| #' @param ... ignored | ||
| #' @references https://coraltraits.org/ | ||
| #' @author Scott Chamberlain \email{myrmecocystus@@gmail.com} | ||
| #' @examples \dontrun{ | ||
| #' # Get the species and their Ids | ||
| #' head( coral_species() ) | ||
| #' | ||
| #' # Get data by taxon | ||
| #' coral_taxa(8) | ||
| #' | ||
| #' # Get data by trait | ||
| #' coral_traits(3) | ||
| #' | ||
| #' # Get data by methodology | ||
| #' coral_methodologies(2) | ||
| #' | ||
| #' # Get data by location | ||
| #' coral_locations(132) | ||
| #' | ||
| #' # Get data by resource | ||
| #' coral_resources(9) | ||
| #' | ||
| #' # curl options | ||
| #' coral_taxa(8, verbose=TRUE) | ||
| #' } | ||
|
|
||
| #' @export | ||
| #' @rdname coral | ||
| coral_taxa <- function(taxon, taxonomy = FALSE, contextual = TRUE, | ||
| global = FALSE, ...) { | ||
| args <- list(taxonomy = lsw(taxonomy), contextual = lsw(contextual), | ||
| global = lsw(global)) | ||
| coral_GET(coral_url("species", taxon), args, ...) | ||
| #' @rdname coral-defunct | ||
| coral_taxa <- function(...) { | ||
| .Defunct(msg = "the coraltraits.org API is down for good") | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname coral | ||
| coral_traits <- function(trait, taxonomy = FALSE, contextual = TRUE, | ||
| global = FALSE, ...) { | ||
| args <- list(taxonomy = lsw(taxonomy), contextual = lsw(contextual), | ||
| global = lsw(global)) | ||
| coral_GET(coral_url("traits", trait), args, ...) | ||
| #' @rdname coral-defunct | ||
| coral_traits <- function(...) { | ||
| .Defunct(msg = "the coraltraits.org API is down for good") | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname coral | ||
| coral_locations <- function(location, taxonomy = FALSE, contextual = TRUE, | ||
| global = FALSE, ...) { | ||
| args <- list(taxonomy = lsw(taxonomy), contextual = lsw(contextual), | ||
| global = lsw(global)) | ||
| coral_GET(coral_url("locations", location), args, ...) | ||
| #' @rdname coral-defunct | ||
| coral_locations <- function(...) { | ||
| .Defunct(msg = "the coraltraits.org API is down for good") | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname coral | ||
| coral_methodologies <- function(methodology, taxonomy = FALSE, | ||
| contextual = TRUE, global = FALSE, ...) { | ||
| args <- list(taxonomy = lsw(taxonomy), contextual = lsw(contextual), | ||
| global = lsw(global)) | ||
| coral_GET(coral_url("methodologies", methodology), args, ...) | ||
| #' @rdname coral-defunct | ||
| coral_methodologies <- function(...) { | ||
| .Defunct(msg = "the coraltraits.org API is down for good") | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname coral | ||
| coral_resources <- function(resource, taxonomy = FALSE, contextual = TRUE, | ||
| global = FALSE, ...) { | ||
| args <- list(taxonomy = lsw(taxonomy), contextual = lsw(contextual), | ||
| global = lsw(global)) | ||
| coral_GET(coral_url("resources", resource), args, ...) | ||
| #' @rdname coral-defunct | ||
| coral_resources <- function(...) { | ||
| .Defunct(msg = "the coraltraits.org API is down for good") | ||
| } | ||
|
|
||
| #' @export | ||
| #' @rdname coral | ||
| #' @rdname coral-defunct | ||
| coral_species <- function(...) { | ||
| con <- crul::HttpClient$new("https://coraltraits.org/species", | ||
| opts = list(...)) | ||
| res <- con$get(query = list(all="true")) | ||
| res$raise_for_status() | ||
| html <- xml2::read_html(res$parse("UTF-8")) | ||
| ids <- gsub("\n+|\t+|\\s+", "", | ||
| xml2::xml_text(xml2::xml_find_all(html, | ||
| '//li[@class="list-group-item"]//div[@style="color: lightgrey;"]'))) | ||
| nms <- xml2::xml_text( | ||
| xml2::xml_find_all(html, | ||
| '//li[@class="list-group-item"]//div[@class="col-sm-5"]//a')) | ||
| tibble::as_tibble(data.frame(name = nms, id = ids, stringsAsFactors = FALSE)) | ||
| .Defunct(msg = "the coraltraits.org API is down for good") | ||
| } | ||
|
|
||
| coral_GET <- function(url, args, ...) { | ||
| con <- crul::HttpClient$new(url, opts = list(...)) | ||
| res <- con$get(query = args) | ||
| res$raise_for_status() | ||
| txt <- res$parse("UTF-8") | ||
| tibble::as_tibble( | ||
| utils::read.csv(text = txt, header = TRUE, stringsAsFactors = FALSE)) | ||
| } | ||
|
|
||
| coralbase <- function() 'https://coraltraits.org' | ||
| coral_url <- function(var, id) paste0(file.path(coralbase(), var, id), ".csv") | ||
| lsw <- function(x) if (x) "on" else "off" |
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