Merge pull request #74 from PixelgenTechnologies/exe-2108-read-edgeli…

…st-bug-fix

Minor bug fixes

R/read_edgelist.R

@@ -46,21 +46,28 @@ ReadMPX_arrow_edgelist <- function(
   }
 
   # Extract the edgelist parquet file
+  edge_list_dir <- fs::path_temp()
   if (!is.null(edge_list_file)) {
+    # Validate path string
     assert_single_value(edge_list_file, type = "string")
     assert_file_ext(edge_list_file, ext = "parquet")
   } else {
-    edge_list_dir <- fs::path_temp()
-    if (verbose && check_global_verbosity()) {
-      cli_alert_info("Extracting edgelist.parquet file to {col_br_blue(file.path(edge_list_dir, 'edgelist.parquet'))}")
-    }
+    edge_list_file <- fs::path(edge_list_dir, "edgelist.parquet")
+  }
+
+  if (verbose && check_global_verbosity()) {
+    cli_alert_info("Extracting edgelist.parquet file to {.file {edge_list_file}}")
   }
 
   # Extract the edgelist.parquet file
   utils::unzip(pxl_file, files = "edgelist.parquet", exdir = edge_list_dir)
+  if (!is.null(edge_list_file)) {
+    # Move the file to the desired location if edge_list_file is provided
+    fs::file_move(fs::path(edge_list_dir, "edgelist.parquet"), edge_list_file)
+  }
 
   # Read the parquet file
-  ds <- arrow::open_dataset(fs::path(edge_list_dir, "edgelist.parquet"))
+  ds <- arrow::open_dataset(edge_list_file)
 
   # Convert selected columns uint64 to string
   sel_fields <- grep(pattern = "^umi", names(ds), value = TRUE)

R/types_check.R

@@ -255,7 +255,7 @@ assert_file_ext <- function(
   )
   if (fs::path_ext(x) != ext) {
     cli::cli_abort(
-      c("x" = "File {.file {x}} is not a PXL file"),
+      c("x" = "File {.file {x}} is not a {ext} file"),
       call = call
     )
   }

R/utils.R

@@ -484,7 +484,7 @@ abort_if_not <- function(
 .validate_or_set_assay <- function(object, assay = NULL, call = caller_env()) {
   # Use default assay if assay = NULL
   if (!is.null(assay)) {
-    assert_single_value(assay, type = "character", call = call)
+    assert_single_value(assay, type = "string", call = call)
   } else {
     assay <- DefaultAssay(object)
   }

tests/testthat/test-ReadMPX_edgelist.R

@@ -1,15 +1,29 @@
+pxl_file <- system.file("extdata/five_cells", "five_cells.pxl", package = "pixelatorR")
+
 test_that("ReadMPX_arrow_edgelist works as expected", {
-  el <- ReadMPX_arrow_edgelist(system.file("extdata/five_cells", "five_cells.pxl", package = "pixelatorR"))
+  el <- ReadMPX_arrow_edgelist(pxl_file)
   expect_type(el, type = "environment")
   expect_equal(names(el), c(
     "upia", "upib", "marker", "count",
     "component"
   ))
   expect_no_error({
     msg <- capture_messages({
-      el <- ReadMPX_arrow_edgelist(system.file("extdata/five_cells", "five_cells.pxl", package = "pixelatorR"))
+      el <- ReadMPX_arrow_edgelist(pxl_file)
     })
   })
+
+  tmp_f <- fs::path_temp("test.parquet")
+  expect_no_error({
+    el <-
+      ReadMPX_arrow_edgelist(
+        pxl_file,
+        edge_list_file = tmp_f,
+        verbose = FALSE
+      )
+  })
+  expect_true(fs::file_exists(tmp_f))
+  expect_true(basename(tmp_f) == "test.parquet")
 })
 
 
@@ -19,4 +33,8 @@ test_that("ReadMPX_arrow_edgelist fails when invalid input is provided", {
       outdir = tempdir()
     )
   })
+  expect_error({
+    el <- ReadMPX_arrow_edgelist("Invalid file", edge_list_file = fs::path_temp("test.pxl")
+    )
+  })
 })