doc: update env vars

gdrplatform · Apr 23, 2024 · cdb5220 · cdb5220
1 parent 4d4b29b
commit cdb5220
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Showing 4 changed files with 12 additions and 12 deletions.
diff --git a/R/add_annotation.R b/R/add_annotation.R
@@ -11,7 +11,7 @@
 #' @param fill string indicating how unknown cell lines should be filled in the DB
 #' @param annotationPackage string indication name of the package containing cellline annotation
 #' @param externalSource string with path to external file with annotation data; by default it checks 
-#' 'gDR_cellline_annotation' env var. This file should contain columns such as gnumber, drug_name and drug_moa
+#' 'GDR_CELLLINE_ANNOTATION' env var. This file should contain columns such as gnumber, drug_name and drug_moa
 #' @keywords annotation
 #' @details
 #' The logic of adding celline annotation for dt_metadata based on 
@@ -47,7 +47,7 @@ add_CellLine_annotation <- function(
     } else {
       "gDRtestData"
     },
-    externalSource = Sys.getenv("gDR_cellline_annotation")
+    externalSource = Sys.getenv("GDR_CELLLINE_ANNOTATION")
 ) {
 
     # Assertions:
@@ -126,7 +126,7 @@ add_CellLine_annotation <- function(
 #' @param fill string indicating how unknown cell lines should be filled in the DB
 #' @param annotationPackage string indication name of the package containing drug annotation
 #' @param externalSource string with path to external file with annotation data; by default it checks 
-#' 'gDR_drug_annotation' env var. This file should contain columns such as cell_line_identifier,
+#' 'GDR_DRUG_ANNOTATION' env var. This file should contain columns such as cell_line_identifier,
 #' cell_line_name, primary_tissue, doubling_time, parental_identifier, and subtype
 #' @keywords annotation
 #' @details The logic of adding drug annotation for dt_metadata 
@@ -149,7 +149,7 @@ add_Drug_annotation <- function(
     } else {
       "gDRtestData"
     },
-    externalSource = Sys.getenv("gDR_drug_annotation")
+    externalSource = Sys.getenv("GDR_DRUG_ANNOTATION")
 ) {
 
   # Assertions:

diff --git a/man/add_CellLine_annotation.Rd b/man/add_CellLine_annotation.Rd
diff --git a/man/add_Drug_annotation.Rd b/man/add_Drug_annotation.Rd
diff --git a/tests/testthat/test-add_annotation.R b/tests/testthat/test-add_annotation.R
@@ -31,7 +31,7 @@ test_that("add_CellLine_annotation works with custom annotation in external file
                                               subtype = "random")
   data.table::fwrite(custom_annotation,
                      temp_path)
-  Sys.setenv(gDR_cellline_annotation = temp_path)
+  Sys.setenv(GDR_CELLLINE_ANNOTATION = temp_path)
   dt_unknown_annotated <- purrr::quietly(add_CellLine_annotation)(dt_unknown)$result
   expect_equal(unname(dt_unknown_annotated), unname(custom_annotation))
 
@@ -40,7 +40,7 @@ test_that("add_CellLine_annotation works with custom annotation in external file
                    dt_unknown_annotated)
 
   # restore default
-  Sys.setenv(gDR_cellline_annotation = "")
+  Sys.setenv(GDR_CELLLINE_ANNOTATION = "")
   dt_unknown_annotated <- purrr::quietly(add_CellLine_annotation)(dt_unknown)$result
   expect_equal(dt_unknown_annotated$clid, custom_annotation$cell_line_identifier)
 
@@ -84,7 +84,7 @@ test_that("add_Drug_annotation works with custom annotation in external file", {
                                               drug_moa = "custom_moa")
   data.table::fwrite(custom_annotation,
                      temp_path)
-  Sys.setenv(gDR_drug_annotation = temp_path)
+  Sys.setenv(GDR_DRUG_ANNOTATION = temp_path)
   dt_unknown_annotated <- purrr::quietly(add_Drug_annotation)(dt_unknown)$result
   expect_equal(unname(dt_unknown_annotated), unname(custom_annotation))
 
@@ -93,7 +93,7 @@ test_that("add_Drug_annotation works with custom annotation in external file", {
                    dt_unknown_annotated)
 
   # restore default
-  Sys.setenv(gDR_drug_annotation = "")
+  Sys.setenv(GDR_DRUG_ANNOTATION = "")
   dt_unknown_annotated <- purrr::quietly(add_Drug_annotation)(dt_unknown)$result
   expect_equal(dt_unknown_annotated$DrugName, custom_annotation$gnumber)