Tests passing on Windows

R/PNNL_DMS_utils.R

@@ -112,7 +112,7 @@ get_auth <- function(){
    }
 }
 
-
+#' @importFrom RPostgres Postgres
 get_db_connection <- function(
     driver = Postgres,
     driver_args = list(),

R/read_MSstats_from_MSFragger_job.R

@@ -59,22 +59,26 @@ read_MSstats_from_MSFragger_job <- function(data_package_num,
    }
 
    path <- unique(job_records$folder)
-   remote_folder <- gsub("\\\\", "/", path)
-   mount_folder <- local_folder <- .new_tempdir()
-   mount_cmd <- sprintf("mount -t smbfs %s %s", remote_folder, local_folder)
-   system(mount_cmd)
-   on.exit(system(glue("umount {mount_folder}")))
 
    if (length(path) == 0) {
       stop("No jobs found.")
    }
 
+   if (.Platform$OS.type == "unix") {
+      remote_folder <- gsub("\\\\", "/", path)
+      mount_folder <- local_folder <- .new_tempdir()
+      mount_cmd <- sprintf("mount -t smbfs %s %s", remote_folder, local_folder)
+      system(mount_cmd)
+      on.exit(system(glue("umount {mount_folder}")))
+      path <- local_folder
+   }
+
    if (length(path) > 1) {
       stop(paste0("More than one MSFragger search found per data package.\n", 
                   "Please refine the arguments to make sure they uniquely", 
                   " define the MSFragger job."))
    }
-   path_to_file <- file.path(local_folder, "MSstats.csv")
+   path_to_file <- file.path(path, "MSstats.csv")
 
    if (!file.exists(path_to_file)) {
       stop(sprintf("MSstats.csv file not found in %s", path))
@@ -85,9 +89,6 @@ read_MSstats_from_MSFragger_job <- function(data_package_num,
    return(m)
 }
 
-
-
-
 utils::globalVariables(
    c("Parameter_File", "Settings_File", "Organism_DB", "ProteinName",
      "PeptideSequence", "Run", "Intensity", ".", "featureName")

R/read_msfragger_data_from_DMS.R

@@ -60,11 +60,6 @@ read_msfragger_data_from_DMS <- function(data_package_num,
    }
 
    path <- unique(job_records$folder)
-   remote_folder <- gsub("\\\\", "/", path)
-   mount_folder <- local_folder <- .new_tempdir()
-   mount_cmd <- sprintf("mount -t smbfs %s %s", remote_folder, local_folder)
-   system(mount_cmd)
-   on.exit(system(glue("umount {mount_folder}")))
 
    if (length(path) == 0) {
       stop("No jobs found.")
@@ -76,21 +71,29 @@ read_msfragger_data_from_DMS <- function(data_package_num,
                   " define the MSFragger job."))
    }
 
+   if (.Platform$OS.type == "unix") {
+      remote_folder <- gsub("\\\\", "/", path)
+      mount_folder <- local_folder <- .new_tempdir()
+      mount_cmd <- sprintf("mount -t smbfs %s %s", remote_folder, local_folder)
+      system(mount_cmd)
+      on.exit(system(glue("umount {mount_folder}")))
+      path <- local_folder
+   }
    aggregate_zip_file_exists <- file.exists(
-      file.path(local_folder, "Dataset_PSM_tsv.zip"))
+      file.path(path, "Dataset_PSM_tsv.zip"))
 
    if (aggregate_zip_file_exists) {
       # Copy folder to temporary directory and extract psm files
-      aggregate_zip_file <- file.path(local_folder, "Dataset_PSM_tsv.zip")
+      aggregate_zip_file <- file.path(path, "Dataset_PSM_tsv.zip")
       exdir <- .new_tempdir()
       unzip(zipfile = aggregate_zip_file, list = FALSE, exdir = exdir)
-      local_folder <- exdir
+      path <- exdir
    }
 
    fileNamePttrn <- "_psm\\.tsv"
    # 
    # 
-   path_to_files <- list.files(local_folder, pattern = fileNamePttrn, full.names = TRUE)
+   path_to_files <- list.files(path, pattern = fileNamePttrn, full.names = TRUE)
    cn <- colnames(read_tsv(path_to_files[1], n_max = 1))
 
    # last_col <- which(cn == "Quan Usage") - 1

R/read_study_design_from_DMS.R

@@ -43,8 +43,7 @@
 
 #' @export
 #' @rdname read_study_design
-path_to_study_design_from_DMS <- function(data_package_num,
-                                          useHTTP = FALSE) 
+path_to_study_design_from_DMS <- function(data_package_num) 
 {
 
   con <- get_db_connection()
@@ -59,7 +58,7 @@ path_to_study_design_from_DMS <- function(data_package_num,
   dataPkgReport <- dbFetch(qry)
   dbClearResult(qry)
 
-  if(.Platform$OS.type == "unix" | useHTTP){
+  if(.Platform$OS.type == "unix"){
     local_folder <- .new_tempdir()
 
     remote_folder <- gsub("\\\\","/", dataPkgReport$share_path)

tests/tests.R

@@ -2,36 +2,37 @@ library(testthat)
 
 path_check <- function(path) {
     expect_true(grepl("Rtmp", path, ignore.case = FALSE))
-    system(glue::glue("umount {path}"))
+    if (.Platform$OS.type == "unix") {
+        system(glue::glue("umount {path}"))
+    }
 }
-cat("1------\n")
+# cat("1------\n")
 expect_true(is_PNNL_DMS_connection_successful())
-cat("2------\n")
+# cat("2------\n")
 expect_equal(dim(get_dms_job_records(4232)), c(1, 23))
-cat("3------\n")
+# cat("3------\n")
 expect_equal(get_output_folder_for_job_and_tool(2344924, "DiaNN"), "DNN202408121049_Auto2344924")
-cat("4------\n")
+# cat("4------\n")
 expect_equal(dim(get_job_records_by_dataset_package(4232)), c(2, 22))
-cat("5------\n")
+# cat("5------\n")
 expect_equal(dim(get_datasets_by_data_package(4232)), c(1, 13))
-cat("6------\n")
+# cat("6------\n")
 path <- path_to_FASTA_used_by_DMS(4232)
 path_check(path)
-expect_equal(dim(read_AScore_results_from_DMS(4136)), c(916130, 12)) # check args
-cat("7------\n")
+# cat("7------\n")
 path <- path_to_study_design_from_DMS(4232)
-path_check(path)
-cat("8------\n")
-path <- path_to_study_design_from_DMS(4232, T)
-path_check(path)
-cat("9------\n")
+if (.Platform$OS.type == "unix") {
+    path_check(path)
+}
+# cat("8------\n")
 expect_equal(dim(read_masic_data_from_DMS(4232)), c(20938, 22)) # check args
-cat("10------\n")
-expect_equal(dim(read_msfragger_data_from_DMS(
+# cat("9------\n")
+expect_equal(dim(read_msfragger_data_from_DMS( # Fail
     4804,
     "MSFragger_Tryp_ProlineRule_ProtNTermAcet_Stat_CysAlk_TMT_6Plex_20ppmParTol.params",
     "MSFragger_PepFDR_0.99_ProtFDR_0.99_IncludeDecoys.xml",
     "ID_008350_56958B5A.fasta"
 )), c(266203, 11))
-
+# cat("11------\n")
+expect_equal(dim(read_AScore_results_from_DMS(4136)), c(916130, 12)) # check args
 # get_tool_output_files_for_job_number(2344924, fileNamePttrn = ".") -> res