stared eubon methods, #466

DESCRIPTION

@@ -4,7 +4,7 @@ Description: Taxonomic information from around the web. This package
     interacts with a suite of web 'APIs' for taxonomic tasks, such
     as verifying species names, getting taxonomic hierarchies,
     and verifying name spelling.
-Version: 0.6.7.9950
+Version: 0.6.7.9990
 License: MIT + file LICENSE
 URL: https://github.com/ropensci/taxize
 BugReports: https://github.com/ropensci/taxize/issues

NAMESPACE

@@ -119,6 +119,7 @@ export(eol_invasive)
 export(eol_pages)
 export(eol_ping)
 export(eol_search)
+export(eubon)
 export(fg_all_updated_names)
 export(fg_author_search)
 export(fg_deprecated_names)

R/eubon.R

@@ -0,0 +1,44 @@
+#' EU BON taxonomy
+#'
+#' @export
+#' @param query (character) The scientific name to search for. For example: "Bellis perennis",
+#' "Prionus" or "Bolinus brandaris". This is an exact search so wildcard characters
+#' are not supported
+#' @param providers (character) A list of provider id strings concatenated by comma characters.
+#' The default : "pesi,bgbm-cdm-server[col]" will be used if this parameter is not
+#' set. A list of all available provider ids can be obtained from the '/capabilities'
+#' service end point. Providers can be nested, that is a parent provider can have sub
+#' providers. If the id of the parent provider is supplied all subproviders will be
+#' queried. The query can also be restriced to one or more subproviders by using the
+#' following syntax: parent-id[sub-id-1,sub-id2,...]
+#' @param searchMode (character) Specifies the searchMode. Possible search modes are:
+#' scientificNameExact, scientificNameLike (begins with), vernacularNameExact, vernacularNameLike
+#' (contains), findByIdentifier. If the a provider does not support the chosen searchMode it
+#' will be skipped and the status message in the tnrClientStatus will be set to 'unsupported
+#' search mode' in this case.
+#' @param addSynonymy (logical) Indicates whether the synonymy of the accepted taxon should be
+#' included into the response. Turning this option on may cause an increased response time.
+#' @param timeout (numeric) The maximum of milliseconds to wait for responses from any of the
+#' providers. If the timeout is exceeded the service will jut return the resonses that have
+#' been received so far. The default timeout is 0 ms (wait for ever)
+#' @param ... Curl options passed on to \code{\link[httr]{GET}}
+#' @references \url{http://cybertaxonomy.eu/eubon-utis/doc.html}
+#' @examples \dontrun{
+#' eubon("Prionus")
+#' eubon("Salmo", 'worms')
+#' eubon("Salmo", c('pesi', 'worms'))
+#' eubon("Salmo", 'worms', 'scientificNameLike')
+#' }
+eubon <- function(query, providers = 'pesi', searchMode = 'scientificNameExact',
+                  addSynonymy = FALSE, timeout = 0, ...) {
+
+  args <- tc(list(query = query, providers = paste0(providers, collapse = ","),
+                  searchMode = searchMode, addSynonymy = as_l(addSynonymy),
+                  timeout = timeout))
+  res <- GET(eubon_base(), query = args, ...)
+  stop_for_status(res)
+  txt <- content(res, "text")
+  jsonlite::fromJSON(txt, FALSE)
+}
+
+eubon_base <- function() "http://cybertaxonomy.eu/eubon-utis/search"