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Gdr 2399 #135

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merged 3 commits into from
Feb 6, 2024
Merged

Gdr 2399 #135

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81be9da
fix: bug with converting standardized mae
bczech Feb 6, 2024
d2f3d39
chore: bump version and update NEWS.md
bczech Feb 6, 2024
c48954a
test: fix unit tests
bczech Feb 6, 2024
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4 changes: 2 additions & 2 deletions DESCRIPTION
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Expand Up @@ -2,8 +2,8 @@ Type: Package
Package: gDRcore
Title: Processing functions and interface to process and analyze drug
dose-response data
Version: 1.1.6
Date: 2024-02-05
Version: 1.1.7
Date: 2024-02-06
Authors@R: c(
person("Bartosz", "Czech", , "[email protected]", role = "aut"),
person("Arkadiusz", "Gladki", role=c("cre", "aut"), email="[email protected]"),
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3 changes: 3 additions & 0 deletions NEWS.md
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@@ -1,3 +1,6 @@
## 1.1.7 (2024-02-06)
- fix bug with converting standardize MAE into raw data

## 1.1.6 (2024-02-05)
- add vignette for a data model

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3 changes: 2 additions & 1 deletion R/runDrugResponseProcessingPipeline.R
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Expand Up @@ -204,7 +204,7 @@ runDrugResponseProcessingPipeline <- function(x,
selected_experiments = NULL) {

checkmate::assert_multi_class(x, c("data.table", "MultiAssayExperiment"))
if (inherits(x, "data.table")) {
if (data.table::is.data.table(x)) {
checkmate::assert_true(any(
gDRutils::get_env_identifiers("untreated_tag") %in%
x[[gDRutils::get_env_identifiers("drug")]]
Expand Down Expand Up @@ -247,6 +247,7 @@ runDrugResponseProcessingPipeline <- function(x,
# when running pipeline with x = MAE the identifiers from MAE's metadata
# should be restored
if (inherits(x, "MultiAssayExperiment")) {
x <- gDRutils::standardize_mae(x, use_default = FALSE)
m_idfs <- S4Vectors::metadata(x[[1]])[["identifiers"]]
for (idx in seq_along(m_idfs)) {
gDRutils::set_env_identifier(names(m_idfs)[idx], m_idfs[[idx]])
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4 changes: 4 additions & 0 deletions tests/testthat/test-runDrugResponseProcessingPipeline.R
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Expand Up @@ -81,6 +81,10 @@ test_that("main pipeline functions works as expected", {
x
})

# Clear internal metadata (sessionInfo) to not break the tests
mae_v3$result$`single-agent`@metadata$.internal <- NULL
mae_v4$result$`single-agent`@metadata$.internal <- NULL

expect_identical(mae_v3$result, mae_v4$result)

testthat::expect_error(
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