Esacape shell args to allow paths with spaces. (#31)

Author: esiegel

R/cmd.R

@@ -29,8 +29,8 @@ louper_create_cloupe <- function(
   h5path <- normalizePath(path.expand(h5path))
   loupe_path <- suppressWarnings(normalizePath(path.expand(loupe_path)))
 
-  input_flag <- sprintf("--input=%s", h5path)
-  output_flag <- sprintf("--output=%s", loupe_path)
+  input_flag <- sprintf("--input=%s", shQuote(h5path))
+  output_flag <- sprintf("--output=%s", shQuote(loupe_path))
   args <- c("create", input_flag, output_flag)
 
   if (file.exists(loupe_path) && !force) {

tests/testthat/mock_louper

@@ -1,5 +1,59 @@
 #!/usr/bin/env bash
 
 echo "-----------RUNNING MOCK LOUPER EXECUTABLE--------------"
-echo Arguments passed to the script: "$@"
+
+# Default values
+force=false
+
+# Check if the correct number of arguments is provided
+if [ "$#" -lt 3 ] || [ "$#" -gt 4 ]; then
+    echo "Usage: $0 create --input=SOME_PATH --output=SOME_PATH [--force]"
+    exit 1
+fi
+
+# Check if the first argument is "create"
+if [ "$1" != "create" ]; then
+    echo "Error: First argument must be 'create'"
+    exit 1
+fi
+
+# shift args
+shift
+
+# Parse and validate the input and output options
+input=""
+output=""
+
+while [ "$#" -gt 0 ]; do
+    case "$1" in
+        --input=*)
+            input="${1#*=}"
+            ;;
+        --output=*)
+            output="${1#*=}"
+            ;;
+        --force)
+            force=true
+            ;;
+        *)
+            echo "Error: Unknown option '$1'"
+            exit 1
+            ;;
+    esac
+    shift
+done
+
+# Check if input and output paths are provided
+if [ -z "$input" ] || [ -z "$output" ]; then
+    echo "Error: Both --input and --output options must be provided"
+    exit 1
+fi
+
+# Additional processing with the arguments can be added here
+
+echo "Action: create"
+echo "Input path: $input"
+echo "Output path: $output"
+echo "Force: $force"
+
 echo "-------------------------------------------------------"

tests/testthat/mock_louper.bat

@@ -1,5 +1,66 @@
 @echo off
 
 echo "-----------RUNNING MOCK LOUPER.BAT EXECUTABLE--------------"
-echo Arguments passed to the script: %*
+
+setlocal enabledelayedexpansion
+
+set "force=false"
+
+REM Check if the correct number of arguments is provided
+if "%~1" neq "create" (
+    echo Error: First argument must be 'create'
+    goto :eof
+)
+shift
+
+REM Parse and validate the input and output options
+set "input="
+set "output="
+
+:parse_args
+if "%~1" equ "" goto :check_paths
+
+if /i "%~1" equ "--input" (
+    set "input=%~2"
+    shift
+    shift
+    goto :parse_args
+)
+
+if /i "%~1" equ "--output" (
+    set "output=%~2"
+    shift
+    shift
+    goto :parse_args
+)
+
+if /i "%~1" equ "--force" (
+    set "force=true"
+    shift
+    goto :parse_args
+)
+
+echo Error: Unknown option '%1'
+goto :eof
+
+:check_paths
+REM Check if input and output paths are provided
+if not defined input (
+    echo Error: --input option must be provided
+    goto :eof
+)
+
+if not defined output (
+    echo Error: --output option must be provided
+    goto :eof
+)
+
+REM Additional processing with the arguments can be added here
+
+echo Action: create
+echo Input path: !input!
+echo Output path: !output!
+echo Force: !force!
+
+:end
 echo "-----------------------------------------------------------"

tests/testthat/test-lib.R

@@ -1,4 +1,4 @@
-test_that("can run create_loupe_from_seurat", {
+create_default_seurat_obj <- function() {
   barcode_count <- 3
 
   count_mat <- create_count_mat(100, barcode_count, valid_barcodes = TRUE)
@@ -9,23 +9,38 @@ test_that("can run create_loupe_from_seurat", {
   obj[["proj1"]] <- proj
   obj[["cluster1"]] <- cluster
 
+  obj
+}
+
+test_that("can run create_loupe_from_seurat", {
   # create eula lock file to avoid interactive setup
   eula_create()
 
+  obj <- create_default_seurat_obj()
   x <- create_loupe_from_seurat(obj, executable_path = get_executable_path())
   expect(x, "create_loupe_from_seurat returns TRUE")
 })
 
+test_that("can run create_loupe with spaces in output_name", {
+  # create eula lock file to avoid interactive setup
+  eula_create()
+
+  obj <- create_default_seurat_obj()
+  x <- create_loupe_from_seurat(obj, executable_path = get_executable_path(), output_name = "name with spaces")
+  expect(x, "create_loupe_from_seurat returns TRUE")
+})
+
 test_that("can run create_loupe", {
+  # create eula lock file to avoid interactive setup
+  eula_create()
+
   barcode_count <- 5
   count_mat <- create_count_mat(100, barcode_count, valid_barcodes = TRUE)
   proj <- create_dense_mat(barcode_count, 2)
   clusters <- list("f1" = factor(c("a", "c", "b", "a", "b"), levels=c("a", "b", "c"), ordered=TRUE))
   projections <- list("p1" = proj)
 
-  # create eula lock file to avoid interactive setup
-  eula_create()
-
   x <- create_loupe(count_mat, clusters = clusters, projections = projections, executable_path = get_executable_path())
   expect(x, "create_loupe returns TRUE")
 })
+