From 764a46e791eb94965d6fb4befacd9a4b67c2ea3d Mon Sep 17 00:00:00 2001
From: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com>
Date: Wed, 10 Mar 2021 13:36:38 +0100
Subject: [PATCH 1/2] Sanitise species names with partial matches of invalid
 terms correctly

---
 R/bd_retrieve_data.R                 | 2 +-
 tests/testthat/test-sanitise_input.R | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/R/bd_retrieve_data.R b/R/bd_retrieve_data.R
index 7f2b7e4..8743a02 100644
--- a/R/bd_retrieve_data.R
+++ b/R/bd_retrieve_data.R
@@ -63,7 +63,7 @@ sanitise_term <- function(searchTerm, searchType) {
     x = searchTerm,
     ignore.case = TRUE
   ) |
-    grepl("(true|false|nil)", searchTerm, ignore.case = TRUE)) {
+    grepl("\\b(true|false|nil)\\b", searchTerm, ignore.case = TRUE)) {
     stop(
       "Illegal character detected! My apologies, but your search can only contain letters, numbers and white-space. Abbreviating genus names (e.g. 'B. subtilis') is not supported. Please spell out your searchTerm ('Bacillus subtilis'), don't use any 'special' characters and try again."
     )
diff --git a/tests/testthat/test-sanitise_input.R b/tests/testthat/test-sanitise_input.R
index 9bb716f..85c2c3e 100644
--- a/tests/testthat/test-sanitise_input.R
+++ b/tests/testthat/test-sanitise_input.R
@@ -10,4 +10,5 @@ test_that("Taxon species is escaped to taxon/species", {
 
 test_that("Normal searchTerm is return without sanitation", {
   expect_identical(sanitise_term("Bacillus", "taxon"), "Bacillus")
+  expect_identical(sanitise_term("Cellulomonas xylanilytica", "taxon"), "Cellulomonas/xylanilytica")
 })

From fcfd2410182eb5823bed260b7e98f44b000ad037 Mon Sep 17 00:00:00 2001
From: Katrin Leinweber <9948149+katrinleinweber@users.noreply.github.com>
Date: Wed, 10 Mar 2021 13:36:38 +0100
Subject: [PATCH 2/2] Separate & test invalid test cases

---
 R/bd_retrieve_data.R                 | 7 +++++--
 tests/testthat/test-sanitise_input.R | 6 ++++++
 2 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/R/bd_retrieve_data.R b/R/bd_retrieve_data.R
index 8743a02..6155c68 100644
--- a/R/bd_retrieve_data.R
+++ b/R/bd_retrieve_data.R
@@ -62,11 +62,14 @@ sanitise_term <- function(searchTerm, searchType) {
     pattern = "[^[:alnum:] ]",
     x = searchTerm,
     ignore.case = TRUE
-  ) |
-    grepl("\\b(true|false|nil)\\b", searchTerm, ignore.case = TRUE)) {
+  )) {
     stop(
       "Illegal character detected! My apologies, but your search can only contain letters, numbers and white-space. Abbreviating genus names (e.g. 'B. subtilis') is not supported. Please spell out your searchTerm ('Bacillus subtilis'), don't use any 'special' characters and try again."
     )
+  } else if (grepl("\\b(true|false|nil)\\b", searchTerm, ignore.case = TRUE)) {
+    stop(
+      "Invalid search term! My apologies, but your search can not contain only 'true', 'false' or 'nil."
+    )
   } else if (identical(searchType, "taxon") & grepl("\\s", searchTerm)) {
     gsub(pattern = "\\s", replacement = "/", searchTerm)
     # expand "Taxon species" to "taxon/species"
diff --git a/tests/testthat/test-sanitise_input.R b/tests/testthat/test-sanitise_input.R
index 85c2c3e..50c855f 100644
--- a/tests/testthat/test-sanitise_input.R
+++ b/tests/testthat/test-sanitise_input.R
@@ -12,3 +12,9 @@ test_that("Normal searchTerm is return without sanitation", {
   expect_identical(sanitise_term("Bacillus", "taxon"), "Bacillus")
   expect_identical(sanitise_term("Cellulomonas xylanilytica", "taxon"), "Cellulomonas/xylanilytica")
 })
+
+test_that("Invalid search terms cause errors", {
+  expect_error(sanitise_term("true", "taxon"))
+  expect_error(sanitise_term("false", "taxon"))
+  expect_error(sanitise_term("nil", "taxon"))
+})