Merge pull request #81 from gdrplatform/GDR-2247

Gdr 2247

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: gDRimport
 Type: Package
 Title: Package for handling the import of dose-response data
-Version: 1.1.7
-Date: 2024-03-07
+Version: 1.1.8
+Date: 2024-03-26
 Authors@R: c(
     person("Arkadiusz", "Gladki", role=c("aut", "cre"), email="[email protected]",
            comment = c(ORCID = "0000-0002-7059-6378")),
@@ -59,7 +59,7 @@ biocViews: Software, Infrastructure, DataImport
 VignetteBuilder: knitr
 ByteCompile: TRUE
 Roxygen: list(markdown = TRUE) 
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1
 SwitchrLibrary: gDRimport
 DeploySubPath: gDRimport
 Encoding: UTF-8

NAMESPACE

@@ -10,6 +10,7 @@ export(get_test_D300_data)
 export(get_test_EnVision_data)
 export(get_test_Tecan_data)
 export(get_test_data)
+export(get_test_tsv_data)
 export(import_D300)
 export(is_readable_v)
 export(load_data)

NEWS.md

@@ -1,3 +1,6 @@
+## gDRimport 1.1.8 - 2024-03-26
+* fix issue with reading tsv files
+
 ## gDRimport 1.1.7 - 2024-03-07
 * clean up the package
 

R/load_files.R

@@ -47,7 +47,7 @@ load_data <-
     treatments <- load_templates(df_template_files)
     data <- load_results(results_file, instrument, headers = headers)
 
-      # check the all template files are available
+    # check the all template files are available
     if (!all(unique(manifest[[headers[["template"]]]][manifest[[headers[["barcode"]]]] %in%
                                                       data[[headers[["barcode"]]]]])
              %in% basename(template_filename))) {
@@ -268,6 +268,7 @@ load_results <-
     stopifnot(any(inherits(df_results_files, "data.table"), checkmate::test_character(df_results_files)))
     checkmate::assert_string(instrument, pattern = "^EnVision$|^long_tsv$|^Tecan$")
     checkmate::assert_list(headers, null.ok = TRUE)
+
     if (data.table::is.data.table(df_results_files)) {
       # for the shiny app
       results_file <- df_results_files$datapath
@@ -277,6 +278,10 @@ load_results <-
       results_filename <- basename(results_file)
     }
     checkmate::assert_file_exists(results_file)
+
+    if (all(endsWith(results_file, ".tsv"))) {
+      instrument <- "long_tsv"
+    }
 
     if (instrument == "EnVision") {
       all_results <-
@@ -345,7 +350,6 @@ load_templates_tsv <-
                        df_type = "template"
                      )})
 
-    metadata_fields <- NULL
     all_templates <- read_in_tsv_template_files(template_file, template_filename, templates)
     futile.logger::flog.info("Templates loaded successfully!")
     all_templates
@@ -358,10 +362,11 @@ load_templates_tsv <-
 #' @param templates list with templates data
 #' @keywords load_files
 #'
-#' @return data.table with templates dataa
+#' @return data.table with templates data
 #'
 read_in_tsv_template_files <- function(template_file, template_filename, templates) {
-    tmpl_l <- lapply(template_file, function(iF) {
+    metadata_fields <- NULL
+    tmpl_l <- lapply(seq_along(template_file), function(iF) {
       futile.logger::flog.info("Loading %s", template_filename[iF])
       # 1) check that the sheet names are ok and 2) identify drug_identifier sheet (case insensitive)
       Gnumber_idx <- grep(paste0(gDRutils::get_env_identifiers("drug"), "$"),
@@ -406,6 +411,7 @@ read_in_tsv_template_files <- function(template_file, template_filename, templat
       df_template$Template <- template_filename[iF]
       colnames(df_template) <-
         check_metadata_names(colnames(df_template), df_name = template_filename[iF])
+      df_template
     })
     do.call(rbind, tmpl_l)
 }
@@ -665,9 +671,12 @@ load_results_tsv <-
     results_filename <- basename(results_file)
 
     all_results <- read_in_result_files(results_file, results_filename, headers)
+
+    cols_subset <- intersect(c(headers[["barcode"]], gDRutils::get_env_identifiers("well_position")),
+                             names(all_results))
 
-    if (dim(unique(all_results[, c(headers[["barcode"]], gDRutils::get_env_identifiers("well_position"))]))[1] !=
-        dim(all_results[, c(headers[["barcode"]], gDRutils::get_env_identifiers("well_position"))])[1]) {
+    if (dim(unique(all_results[, cols_subset, with = FALSE]))[1] !=
+        dim(all_results[, cols_subset, with = FALSE])[1]) {
       futile.logger::flog.error("Multiple rows with the same Barcode and Well across all files")
     }
 
@@ -687,8 +696,8 @@ load_results_tsv <-
 read_in_result_files <- function(results_file, results_filename, headers) {
 
     # read all files
-    res_l <- lapply(results_file, function(iF) {
-      futile.logger::flog.info("Reading file", results_file[iF])
+    res_l <- lapply(seq_along(results_file), function(iF) {
+      futile.logger::flog.info("Reading file %s", results_file[iF])
       tryCatch({
         df <-
         stats::na.omit(data.table::fread(
@@ -716,15 +725,20 @@ read_in_result_files <- function(results_file, results_filename, headers) {
           futile.logger::flog.error("%s needs to be a column of %s", coln, results_filename[iF])
         }
       }
-      if (dim(unique(df[, c(headers[["barcode"]], gDRutils::get_env_identifiers("well_position"))]))[1] !=
-          dim(df[, c(headers[["barcode"]], gDRutils::get_env_identifiers("well_position"))])[1]) {
+
+      cols_subset <- intersect(c(headers[["barcode"]], gDRutils::get_env_identifiers("well_position")),
+                               names(df))
+      if (dim(unique(df[, cols_subset, with = FALSE]))[1] !=
+          dim(df[, cols_subset, with = FALSE])[1]) {
         futile.logger::flog.error("Multiple rows with the same Barcode and Well in %s",
                                   results_filename[iF])
       }
-      if (!("BackgroundValue" %in% colnames(df)))
+      if (!("BackgroundValue" %in% colnames(df))) {
         df$BackgroundValue <- 0
-      futile.logger::flog.info("File %s read; %d wells", results_filename[iF], nrow(df))
-      futile.logger::flog.info("File done")
+        futile.logger::flog.info("File %s read; %d wells", results_filename[iF], nrow(df))
+        futile.logger::flog.info("File done")
+      }
+      df
     })
     all_results <- do.call(rbind, res_l)
 }

R/testdata.R

@@ -121,4 +121,26 @@ get_test_EnVision_data <- function() {
       t_files = grep("\\/Project40.+.xlsx$", fls, value = TRUE),
       ref_l_path = file.path(ddir, "ref_l.qs")
     )
-  }
+}
+
+
+#' get test tsv data
+#'
+#' @examples 
+#' get_test_tsv_data()
+#
+#' @keywords test_data
+#' @export
+#'
+#' @return list with with input data (manifest/template/result paths)
+#' and related reference data (.qs file paths)
+get_test_tsv_data <- function() {
+  ddir <- system.file(package = "gDRimport", "extdata", "data5")
+  fls <- list.files(ddir, full.names = TRUE)
+  list(
+    m_file = grep("\\/Manifest.tsv$", fls, value = TRUE),
+    r_files = grep("\\RawData.tsv$", fls, value = TRUE),
+    t_files = grep("\\Template.+.tsv$", fls, value = TRUE),
+    ref_l_path = file.path(ddir, "ref_l.qs")
+  )
+}

inst/extdata/data5/Manifest.tsv

@@ -0,0 +1,9 @@
+Barcode	Template	Duration	clid
+Plate1	Template_trt.tsv	72	CL_B
+Plate2	Template_trt.tsv	72	CL_B
+Plate3	Template_trt.tsv	72	CL_B
+Plate4	Template_trt.tsv	72	CL_A
+Plate5	Template_trt.tsv	72	CL_A
+Plate6	Template_trt.tsv	72	CL_A
+Plate7	Template_untrt.tsv	0	CL_B
+Plate8	Template_untrt.tsv	0	CL_A