From 7711d87db00a0bb5f029122f324e4ff6dce42340 Mon Sep 17 00:00:00 2001 From: Czech Date: Tue, 27 Jan 2026 14:38:00 +0000 Subject: [PATCH 1/5] refactor: add support for csv envision --- R/utils.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utils.R b/R/utils.R index 2288bf7..4ca8a42 100644 --- a/R/utils.R +++ b/R/utils.R @@ -74,7 +74,7 @@ detect_file_format <- function(results_file) { } else if ("Repeat Barcode" %in% c( do.call(paste, results_data[, 2:3]), paste(names(results_data[, 2:3]), collapse = " ") - )) { + ) | any(grepl("Repeat,Barcode", results_data[, 1]))) { "EnVision" } else { "long_tsv" From 4526b510dcde8679624ff7a8f136f3d6d98f5055 Mon Sep 17 00:00:00 2001 From: Czech Date: Tue, 27 Jan 2026 14:38:17 +0000 Subject: [PATCH 2/5] chore: bump version and update changelog --- DESCRIPTION | 4 ++-- NEWS.md | 3 +++ 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index f7e787f..8f87679 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: gDRimport Type: Package Title: Package for handling the import of dose-response data -Version: 1.9.5 -Date: 2025-12-17 +Version: 1.9.6 +Date: 2026-01-27 Authors@R: c( person("Arkadiusz", "Gladki", role=c("aut", "cre"), email="gladki.arkadiusz@gmail.com", comment = c(ORCID = "0000-0002-7059-6378")), diff --git a/NEWS.md b/NEWS.md index 781ba68..29d1422 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,6 @@ +## gDRimport 1.9.6 - 2025-12-27 +* extend support for csv EnVision format + ## gDRimport 1.9.5 - 2025-12-17 * add support broad_id in PRISM data * add suport for combo data in private prism data From 7bd400f24077b441b39011419bad0318e2bc3015 Mon Sep 17 00:00:00 2001 From: Czech Date: Wed, 28 Jan 2026 05:58:44 -0800 Subject: [PATCH 3/5] refactor: fix reading files --- R/load_files.R | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/R/load_files.R b/R/load_files.R index 5a93d2e..80011c2 100755 --- a/R/load_files.R +++ b/R/load_files.R @@ -1588,9 +1588,10 @@ read_in_EnVision_file <- function(file, nrows, seps) { results.list <- list() current.line <- 1 - while (length(line <- - readLines(con, n = 1, warn = FALSE)) > 0 && current.line < nrows) { - results.list[[current.line]] <- line + + while (length(line <- readLines(con, n = 1, warn = FALSE)) > 0 && current.line < nrows) { + cleaned.line <- gsub('="([^"]*)"', '\\1', line) + results.list[[current.line]] <- cleaned.line current.line <- current.line + 1 } close(con) From a9727a56a6a69c30651eb42ad9a922872f7c6bc0 Mon Sep 17 00:00:00 2001 From: Czech Date: Thu, 29 Jan 2026 10:08:07 +0000 Subject: [PATCH 4/5] chore: appease lintr --- R/utils.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/utils.R b/R/utils.R index 4ca8a42..a10e94d 100644 --- a/R/utils.R +++ b/R/utils.R @@ -74,7 +74,7 @@ detect_file_format <- function(results_file) { } else if ("Repeat Barcode" %in% c( do.call(paste, results_data[, 2:3]), paste(names(results_data[, 2:3]), collapse = " ") - ) | any(grepl("Repeat,Barcode", results_data[, 1]))) { + ) || any(grepl("Repeat,Barcode", results_data[, 1]))) { "EnVision" } else { "long_tsv" From e6b7a6d85899c22f33c416041a1ce2b0313c56bd Mon Sep 17 00:00:00 2001 From: Bartek Czech Date: Mon, 2 Feb 2026 17:08:56 +0100 Subject: [PATCH 5/5] refactor: appease lintr --- R/load_files.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/load_files.R b/R/load_files.R index 80011c2..1ae83b3 100755 --- a/R/load_files.R +++ b/R/load_files.R @@ -1590,7 +1590,7 @@ read_in_EnVision_file <- function(file, nrows, seps) { current.line <- 1 while (length(line <- readLines(con, n = 1, warn = FALSE)) > 0 && current.line < nrows) { - cleaned.line <- gsub('="([^"]*)"', '\\1', line) + cleaned.line <- gsub("=\"([^\"]*)\"", "\\1", line) results.list[[current.line]] <- cleaned.line current.line <- current.line + 1 }