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Sanitise species names with partial matches of invalid terms correctly #117

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Sanitise species names with partial matches of invalid terms correctly #117

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764a46e
Sanitise species names with partial matches of invalid terms correctly
katrinleinweber Mar 10, 2021
fcfd241
Separate & test invalid test cases
katrinleinweber Mar 10, 2021
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7 changes: 5 additions & 2 deletions R/bd_retrieve_data.R
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Original file line number Diff line number Diff line change
Expand Up @@ -62,11 +62,14 @@ sanitise_term <- function(searchTerm, searchType) {
pattern = "[^[:alnum:] ]",
x = searchTerm,
ignore.case = TRUE
) |
grepl("(true|false|nil)", 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"
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7 changes: 7 additions & 0 deletions tests/testthat/test-sanitise_input.R
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Expand Up @@ -10,4 +10,11 @@ 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")
})

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"))
})