Fix couple of issues with summarizing queried taxon presence in datel…

…ife result: when cleaned names have spaces instead of underscores and when datelife_result is empty (no matches).
phylotastic · Jan 8, 2024 · 7088c13 · 7088c13
1 parent e09cbeb
commit 7088c13
Show file tree

Hide file tree

Showing 3 changed files with 35 additions and 18 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -10,6 +10,7 @@ DONE:
 - faster and more accurate way to get study ids and tree ids from opentree API on `get_opentree_chronograms()` that have branch lengths in Myrs, no relative time.
 - update to chronogram database, now with 292 chronograms.
 - `get_taxon_summary()` now manages case when `datelife_result` is empty; throws warning instead of criptic error.
+- better `testthat` suite for `datelife_search()` inner functions.
 
 
 # datelife v0.6.8

diff --git a/R/datelife_summary.R b/R/datelife_summary.R
@@ -32,7 +32,7 @@ get_taxon_summary <- function(datelife_result = NULL,
     message("Taxon summary can not be generated.")
     return(NA)
   }
-  if (length(datelife_result == 0)) {
+  if (length(datelife_result) == 0) {
     warning("'datelife_result' is empty (length == 0).")
     message("Taxon summary can not be generated.")
     return(NA)
@@ -42,7 +42,8 @@ get_taxon_summary <- function(datelife_result = NULL,
       cleaned_names <- gsub(" ", "_", datelife_query$cleaned_names)
     } else {
       input <- attributes(datelife_result)$datelife_query
-      cleaned_names <- gsub(" ", "_", input$cleaned_names)
+      input$cleaned_names <- gsub(" ", "_", input$cleaned_names)
+      cleaned_names <- input$cleaned_names
     }
   } else {
     message("'datelife_query' argument was not provided.")

diff --git a/tests/testthat/test_main.R b/tests/testthat/test_main.R
@@ -1,35 +1,48 @@
 
 test_that("a known datelife_search run works as it should", {
-  datelife_query <- make_datelife_query(input = c("Delphinus_delphis",
-                                               "Gallus gallus",
-                                               "elephas Maximus",
-                                               "felis_catus",
-                                               "homo-sapiens"))
+  expect_no_error(
+    datelife_query <- make_datelife_query(
+      input = c("Delphinus_delphis", 
+                "Gallus gallus", 
+                "elephas Maximus", 
+                "felis_catus", 
+                "homo-sapiens"))
+  )
 
-  datelifeSearch <- datelife_search(datelife_query, 
-                                    summary_format = "phylo_median")
-
-  datelife_result <- get_datelife_result_datelifequery(
-    datelife_query = datelife_query,
-    partial = TRUE,
-    cache = "opentree_chronograms")
+  expect_no_error(
+    datelife_result <- get_datelife_result_datelifequery(
+      datelife_query = datelife_query,
+      partial = TRUE,
+      cache = "opentree_chronograms")
+    )
 
   expect_true(length(datelife_result) > 0)
 
-  res <- summarize_datelife_result(
+  expect_no_error(
+    res <- summarize_datelife_result(
               datelife_result = datelife_result,
               datelife_query = datelife_query,
               summary_format = "phylo_median",
               na_rm = FALSE,
               summary_print = c("citations", "taxa"),
               taxon_summary = c("none", "summary", "matrix"),
               criterion = "taxa")
+    )
 
-  taxon_summ <- get_taxon_summary(
+  expect_no_error(
+    taxon_summ <- get_taxon_summary(
       datelife_result = datelife_result,
       datelife_query = datelife_query)
+  )
+
+  expect_no_error(
+    datelifeSearch <- datelife_search(
+      datelife_query, 
+      summary_format = "phylo_median")
+  )
 }) 
 
+##########################################
 test_that("datelife_use workflows work", {
   du <- datelife_use(
     input = "Rhea americana, Struthio camelus, Gallus gallus",
@@ -78,6 +91,7 @@ test_that("datelife_use workflows work", {
   input_process(input = du0)
 })
 
+#############################################################################
 test_that("input processing a newick string and multiPhylo workflows work", {
   newick <- "(Gallus_gallus,(Rhea_americana,Struthio_camelus)Palaeognathae)Aves;"
   phylo <- input_process(newick)
@@ -94,16 +108,17 @@ test_that("input processing a newick string and multiPhylo workflows work", {
   expect_warning(match_all_calibrations(phy = phylo, calibrations = calibs))
 })
 
+#################################
 test_that("object checks work", {
   expect_warning(match_all_calibrations(phy = NULL))
   expect_error(use_calibrations(phy = NULL))
   expect_error(get_calibrations_datelifequery(datelife_query = NULL))
 })
 
-
+###############################################
 test_that("you can load opentree_chronograms",{
   data(opentree_chronograms, package = "datelife")
-  expect_equal(ls(opentree_chronograms), c("authors","curators","dois","studies","trees"))
+  expect_true(all(c("authors","curators","dois","studies","trees") %in% ls(opentree_chronograms)))
 })