feat: add notification helpers

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gDRutils
 Type: Package
 Title: A package with helper functions for processing drug response data
-Version: 1.5.1
+Version: 1.5.2
 Date: 2024-11-05
 Authors@R: c(person("Bartosz", "Czech", role=c("aut"),
                    comment = c(ORCID = "0000-0002-9908-3007")),

NAMESPACE

@@ -55,6 +55,7 @@ export(get_default_identifiers)
 export(get_duplicated_rows)
 export(get_env_assay_names)
 export(get_env_identifiers)
+export(get_env_var)
 export(get_expect_one_identifiers)
 export(get_experiment_groups)
 export(get_header)

NEWS.md

@@ -1,3 +1,6 @@
+## gDRutils 1.5.2 - 2024-11-05
+* add `get_env_var` helper
+
 ## gDRutils 1.5.1 - 2024-11-05
 * synchronize Bioconductor and GitHub versioning
 

R/duplicates.R

@@ -185,3 +185,4 @@ throw_msg_if_duplicates <- function(dt, assay_name = "unknown", msg_f = stop, pr
      msg_f(paste0(msg, msg2, msg3))
   }
 }
+

R/utils.R

@@ -761,3 +761,23 @@ calc_sd <- function(x) {
   }
 }
 
+
+
+#' safe wrapper of Sys.getenv()
+#' 
+#' So far the helper is needed to handle env vars containing `:` 
+#' for which the backslash  is automatically added in some contexts
+#' and R could not get the original value for these env vars.
+#' 
+#' @param x string with the name of the environemntal variable
+#' @param ... additional params for Sys.getenev
+#' @keywords package_utils
+#' 
+#' @examples 
+#' get_env_var("HOME")
+#
+#' @export 
+#' @return sanitized value of the env variable
+get_env_var <- function(x, ...) {
+  gsub("\\\\", "", Sys.getenv(x, ...))
+}