better input_check function again

phylotastic · Mar 19, 2018 · 38e86e9 · 38e86e9
1 parent e576d2f
commit 38e86e9
Showing 5 changed files with 24 additions and 42 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -2,6 +2,7 @@
 
 export(clean_chronogram)
 export(datelife_authors_tabulate)
+export(datelife_query_check)
 export(datelife_query_length_check)
 export(datelife_result_MRCA)
 export(datelife_result_check)
@@ -13,7 +14,6 @@ export(get_datelife_result)
 export(get_mrbayes_node_calibrations)
 export(get_otol_chronograms)
 export(get_subset_array_dispatch)
-export(input_check)
 export(input_process)
 export(is_good_chronogram)
 export(make_bladj_tree)

diff --git a/R/all_calibrations.R b/R/all_calibrations.R
@@ -96,9 +96,11 @@ get_all_calibrations <- function(input = c("Rhea americana", "Pterocnemia pennat
 #' @export
 make_bold_otol_tree <- function(input = c("Rhea americana",  "Struthio camelus", "Gallus gallus"), use_tnrs = FALSE, approximate_match = TRUE, marker = "COI", otol_version = "v2", chronogram = TRUE, doML = FALSE, get_spp_from_taxon = FALSE, verbose = FALSE) {
 	#otol returns error with missing taxa in v3 of rotl
-	input <- input_check(input = input, use_tnrs = use_tnrs, approximate_match = approximate_match, get_spp_from_taxon = get_spp_from_taxon, verbose = verbose)
+	input <- datelife_query_check(datelife_query = input, use_tnrs = use_tnrs, approximate_match = approximate_match, get_spp_from_taxon = get_spp_from_taxon, verbose = verbose)
 	input <- input$cleaned_names
-	if (verbose) cat("Searching", marker, "sequences for these taxa in BOLD...", "\n")
+	if (verbose) {
+		cat("Searching", marker, "sequences for these taxa in BOLD...", "\n")
+	}
 	xx <- seq(1, length(input), 250)
 	yy <- xx+249
 	yy[length(xx)] <- length(input)

diff --git a/R/datelife.R b/R/datelife.R
@@ -100,7 +100,7 @@ get_datelife_result <- function(input = c("Rhea americana", "Pterocnemia pennata
 	if(update_cache){
 		cache <- update_datelife_cache(save = TRUE, verbose = verbose)
 	}
-	input <- input_check(input = input, use_tnrs = use_tnrs, approximate_match = approximate_match, get_spp_from_taxon = get_spp_from_taxon, verbose = verbose)
+	input <- datelife_query_check(datelife_query = input, use_tnrs = use_tnrs, approximate_match = approximate_match, get_spp_from_taxon = get_spp_from_taxon, verbose = verbose)
 	tree <- input$phy
 	cleaned_names <- input$cleaned_names
 	datelife_query_length_check(cleaned_names = cleaned_names, get_spp_from_taxon = get_spp_from_taxon, verbose = verbose)
@@ -120,24 +120,32 @@ get_datelife_result <- function(input = c("Rhea americana", "Pterocnemia pennata
 }
 
 #' checks if input is a datelifeQuery object, otherwise it uses make_datelife_query to process it
+#' @param datelife_query An object output of make_datelife_query function
 #' @inheritParams datelife_search
 #' @inheritDotParams make_datelife_query
 #' @export
-input_check <- function(input = NULL, ...){
-	if(is.null(input)){
-		input <- NA
-	}
-	if(length(input) == 1 & any(is.na(input))) {
-		stop("input argument is NULL or NA")
-	}
+datelife_query_check <- function(datelife_query = NULL, ...){
+	# if(is.null(input)){
+	# 	input <- NA
+	# }
+	# if(length(input) == 1 & any(is.na(input))) {
+	# 	stop("input argument is NULL or NA")
+	# }
 	badformat <- TRUE
-	if(is.list(input) & "phy" %in% names(input) & "cleaned_names" %in% names(input)) {
+	if(is.list(datelife_query) & "phy" %in% names(datelife_query) & "cleaned_names" %in% names(datelife_query)) {
+		if(!inherits(datelife_query, "datelifeQuery")) {
+			class(datelife_query) <- "datelifeQuery"
+		}
 		badformat <- FALSE
 	}
 	if(badformat){
-		input <- make_datelife_query(input = input, ...)
+		datelife_query <- make_datelife_query(input = datelife_query, ...)
+		badformat <- FALSE
 	}
-	return(input)
+	# if(!badformat){
+	# 	# merge datelife_query_length_check function here
+	# }
+	return(datelife_query)
 }
 #' checks that we have at least two taxon names to perform a search
 #' @inheritParams datelife_search

diff --git a/codecov.yml b/codecov.yml
diff --git a/man/input_check.Rd b/man/input_check.Rd