Merge pull request #87 from phylotastic/ott-names

Ott names, woo!
phylotastic · Dec 16, 2023 · 52005cd · 52005cd
2 parents 9a24cff + 40d87d4
commit 52005cd
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Showing 2 changed files with 7 additions and 3 deletions.
diff --git a/R/datelife_query.R b/R/datelife_query.R
@@ -125,7 +125,7 @@ make_datelife_query <- function(input = c("Rhea americana", "Pterocnemia pennata
       species_list <- get_opentree_species(taxon_name = cleaned_names_tnrs$unique_name,
                                            ott_id = cleaned_names_tnrs$ott_id,
                                            synth_tree_only = TRUE)
-      cleaned_names <- species_list$species_names
+      cleaned_names <- unname(species_list$tnrs_names)
       ott_ids <- species_list$ott_ids
     } else {
       # example: df <- get_ott_children(ott_ids = 698424, ott_rank = "species")
@@ -169,7 +169,11 @@ make_datelife_query <- function(input = c("Rhea americana", "Pterocnemia pennata
           ifelse(length(cleaned_names) <= 10,
                  ".",
                  paste("... omitted ", length(cleaned_names) - 10, "taxon names.")))
-  message("DateLife query done!\n")
+  if(length(cleaned_names) < 1) {
+    message("ERROR: No names retained for search\n")
+  } else{
+    message("DateLife query made!\n")
+  } 
   return(structure(datelife_query_return, class = "datelifeQuery"))
 }
 #' Process a phylo object or a character string to determine if it's correct newick

diff --git a/R/opentree_taxonomy.R b/R/opentree_taxonomy.R
@@ -90,7 +90,7 @@ check_ott_input <- function(input = NULL, ott_ids = NULL, ...) {
       message(input)
       stop("OTT ids are NULL.")
     }
-    if (is.numeric(input$ott_id) & !is.na(input$ott_id)) {
+    if (all(is.numeric(input$ott_id) & !is.na(input$ott_id))) {
       ott_ids <- input$ott_ids
       names(ott_ids) <- input$cleaned_names
     } else {