Allow single quotes in get_gbifid

relates to #928

DESCRIPTION

@@ -5,7 +5,7 @@ Description: Interacts with a suite of web 'APIs' for taxonomic tasks,
     species names, getting taxonomic hierarchies, fetching downstream and
     upstream taxonomic names, getting taxonomic synonyms, converting
     scientific to common names and vice versa, and more.
-Version: 0.9.102
+Version: 0.10.0
 License: MIT + file LICENSE
 URL: https://docs.ropensci.org/taxize/ (website),
     https://github.com/ropensci/taxize (devel),

R/class2tree.R

@@ -66,10 +66,12 @@
 #' }
 #' 
 class2tree <- function(input, varstep = TRUE, check = TRUE, remove_shared = FALSE, ...) {
+
   if (any(is.na(input))) {
     message('Removed species without classification')
     input <- input[!is.na(input)]
   }
+
 
   # Check that there is more than 2 taxon
   if (length(input) < 3)
@@ -78,6 +80,9 @@ class2tree <- function(input, varstep = TRUE, check = TRUE, remove_shared = FALS
   if (length(unique(names(input))) < length(names(input)))
     stop("Input list of classifications contains duplicates")
 
+  # Convert tibbles to data.frames
+  input <- lapply(input, as.data.frame)
+
   # Get rank and ID list
   message('Get all ranks and their taxIDs')
   rankList <- dt2df(lapply(input, get_rank), idcol = FALSE)

R/gbif_helpers.R

@@ -3,6 +3,7 @@ gbif_name_backbone <- function(name, rank = NULL, kingdom = NULL, phylum = NULL,
   class = NULL, order = NULL, family = NULL, genus = NULL, strict = FALSE,
   start = NULL, limit = 500, ...) {
 
+
   url = 'https://api.gbif.org/v1/species/match'
   args <- tc(list(name = name, rank = rank, kingdom = kingdom,
                   phylum = phylum, class = class, order = order, family = family,
@@ -13,7 +14,7 @@ gbif_name_backbone <- function(name, rank = NULL, kingdom = NULL, phylum = NULL,
   temp$raise_for_status()
   tt <- jsonlite::fromJSON(temp$parse("UTF-8"), FALSE)
 
-  if (all(names(tt) %in% c('confidence', 'synonym', 'matchType'))) {
+  if (all(names(tt) %in% c('confidence', 'synonym', 'matchType', "note"))) {
     data.frame(NULL)
   } else {
     dd <- data.table::setDF(

R/get_gbifid.R

@@ -140,6 +140,10 @@ get_gbifid <- function(sci, ask = TRUE, messages = TRUE, rows = NA,
   assert(rank, "character")
   assert(method, "character")
   assert_rows(rows)
+
+  # Escape problematic characters
+  sci <- gsub(sci, pattern = "[^\\]?'", replacement = "\\\\'")
+
   if (!is.null(sciname)) {
     lifecycle::deprecate_warn(when = "v0.9.97", what = "get_gbifid(sciname)", with = "get_gbifid(sci)")
     sci <- sciname