From 40fe9e9562eccac21b83d622b3e8a1622e364c1e Mon Sep 17 00:00:00 2001
From: Emily Jane McTavish <ejmctavish@gmail.com>
Date: Thu, 14 Dec 2023 16:13:31 -0800
Subject: [PATCH 1/4] update ott species name code

---
 R/datelife_query.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/datelife_query.R b/R/datelife_query.R
index 3e5b3b78..592a65fe 100644
--- 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")

From 8e2aea30dc0fa1d000f85426a64073aad26d3d5d Mon Sep 17 00:00:00 2001
From: Emily Jane McTavish <ejmctavish@gmail.com>
Date: Thu, 14 Dec 2023 16:20:50 -0800
Subject: [PATCH 2/4] Error if no names

---
 R/datelife_query.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/datelife_query.R b/R/datelife_query.R
index 592a65fe..54efd958 100644
--- a/R/datelife_query.R
+++ b/R/datelife_query.R
@@ -169,7 +169,7 @@ 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")
+  ifelse(length(cleaned_names) < 1, message("ERROR: No names retained for search\n"), message("DateLife query done!\n"))
   return(structure(datelife_query_return, class = "datelifeQuery"))
 }
 #' Process a phylo object or a character string to determine if it's correct newick

From 10d876457798d0ac6714753f4ce1fe57a34e611b Mon Sep 17 00:00:00 2001
From: Emily Jane McTavish <ejmctavish@gmail.com>
Date: Fri, 15 Dec 2023 13:49:17 -0800
Subject: [PATCH 3/4] fix ifelse bug

---
 R/datelife_query.R | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/R/datelife_query.R b/R/datelife_query.R
index 54efd958..417731e7 100644
--- a/R/datelife_query.R
+++ b/R/datelife_query.R
@@ -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.")))
-  ifelse(length(cleaned_names) < 1, message("ERROR: No names retained for search\n"), 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

From 40d87d4fbec9a9baaf6ecbf45e21d62837f2c34c Mon Sep 17 00:00:00 2001
From: Emily Jane McTavish <ejmctavish@gmail.com>
Date: Fri, 15 Dec 2023 14:31:53 -0800
Subject: [PATCH 4/4] fix bug in
 https://github.com/phylotastic/datelife/issues/81

---
 R/opentree_taxonomy.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/opentree_taxonomy.R b/R/opentree_taxonomy.R
index 2002a5a0..95fbd189 100644
--- 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 {