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Merged
darsoo merged 4 commits into from
Feb 16, 2026
Merged

Gdr 3282 #180

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ae3041c
Merge branch 'main' of github.com:gdrplatform/gDRutils
Feb 11, 2026
e180e8d
feat: allow atomic vectors in remove_drug_batch
Feb 12, 2026
dddc3fb
bump version
Feb 12, 2026
7394f92
CI
darsoo Feb 15, 2026
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Package: gDRutils
Type: Package
Title: A package with helper functions for processing drug response data
Version: 1.9.4
Date: 2025-12-02
Version: 1.9.5
Date: 2026-02-12
Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
comment = c(ORCID = "0000-0002-9908-3007")),
person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="gladki.arkadiusz@gmail.com",
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3 changes: 3 additions & 0 deletions NEWS.md
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@@ -1,3 +1,6 @@
## gDRutils 1.9.5 - 2026-02-12
* `remove_drug_batch` supports atomic vectors as input

## gDRutils 1.9.4 - 2025-12-02
* `convert_se_assay_to_dt` supports merging additional variables

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6 changes: 4 additions & 2 deletions R/utils.R
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Expand Up @@ -1003,7 +1003,7 @@ get_env_var <- function(x, ...) {
#' * too long Gnumber
#' * G123456789.1-12
#'
#' @param drug_vec character vector with drug id(s)
#' @param drug_vec atomic vector (e.g., character or integer) with drug id(s)
#' @param drug_p string with regex pattern for drug id. Set to Gnumber format by default: "G\[0-9\]\{8\}".
#' @param sep_p string with regex pattern for separator. Set to any character except for digit and space
#' @param batch_p string with regex pattern for batch substring.
Expand Down Expand Up @@ -1031,11 +1031,13 @@ remove_drug_batch <- function(drug_vec,
drug_p = "^G[0-9]{8}",
sep_p = "[^0-9|^_]",
batch_p = ".+") {
checkmate::assert_character(drug_vec)
checkmate::assert_atomic_vector(drug_vec)
checkmate::assert_string(drug_p)
checkmate::assert_string(sep_p)
checkmate::assert_string(batch_p)

drug_vec <- as.character(drug_vec)

Comment on lines +1039 to +1040
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@gemini-code-assist gemini-code-assist bot Feb 12, 2026

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medium

The sub() function automatically coerces its x argument to a character vector if it's not one already. Therefore, this explicit conversion with as.character() is redundant. You can remove this line and the following empty line for conciseness.

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@darsoo darsoo Feb 12, 2026

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I am aware that sub() performs implicit coercion, but I added the explicit as.character() call intentionally to improve workflow transparency. It makes the type conversion explicit for anyone reading the code, ensuring that the expected data format is clear before it hits the regex logic.

p <- paste0("(", drug_p, ")", sep_p, batch_p, "$")
r <- "\\1"
sub(p, r, drug_vec)
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2 changes: 1 addition & 1 deletion man/remove_drug_batch.Rd
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7 changes: 7 additions & 0 deletions tests/testthat/test-utils.R
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Expand Up @@ -764,6 +764,13 @@ test_that("remove_drug_batch works as expected", {
expect_equal(remove_drug_batch("G00001234.28", batch_p = "[0-9]+"),
"G00001234")

# test drug_vec as non-character input
expect_equal(remove_drug_batch(12345L), "12345")
expect_equal(remove_drug_batch(9876.54), "9876.54")
expect_equal(remove_drug_batch(c("G00060245.1", 112233)), c("G00060245", "112233"))
expect_equal(remove_drug_batch(12345.678, drug_p = "[0-9]{5}", sep_p = "\\."), "12345")

# error tests
expect_error(remove_drug_batch(list(drug = "G00000001")), "Assertion on 'drug_vec' failed")
expect_error(remove_drug_batch("G00000001", drug_p = list(1)),
"Assertion on 'drug_p' failed")
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