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Ott names #87

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merged 4 commits into from
Dec 16, 2023
Merged

Ott names #87

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40fe9e9
update ott species name code
snacktavish Dec 15, 2023
8e2aea3
Error if no names
snacktavish Dec 15, 2023
10d8764
fix ifelse bug
snacktavish Dec 15, 2023
40d87d4
fix bug in https://github.com/phylotastic/datelife/issues/81
snacktavish Dec 15, 2023
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8 changes: 6 additions & 2 deletions R/datelife_query.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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$ott_ids
} else {
# example: df <- get_ott_children(ott_ids = 698424, ott_rank = "species")
Expand Down Expand Up @@ -169,7 +169,11 @@ make_datelife_query <- function(input = c("Rhea americana", "Pterocnemia pennata
ifelse(length(cleaned_names) <= 10,
".",
paste("... omitted ", length(cleaned_names) - 10, "taxon names.")))
message("DateLife query done!\n")
if(length(cleaned_names) < 1) {
message("ERROR: No names retained for search\n")
} else{
message("DateLife query made!\n")
}
return(structure(datelife_query_return, class = "datelifeQuery"))
}
#' Process a phylo object or a character string to determine if it's correct newick
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2 changes: 1 addition & 1 deletion R/opentree_taxonomy.R
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Expand Up @@ -90,7 +90,7 @@ check_ott_input <- function(input = NULL, ott_ids = NULL, ...) {
message(input)
stop("OTT ids are NULL.")
}
if (is.numeric(input$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 {
Expand Down