+test-path

Author: HelenaLC

R/path.R

@@ -28,19 +28,29 @@ NULL
 
 #' @export
 #' @rdname path
-setMethod("path", "SpatialDataArray", \(object, ...) 
-    dirname(ZarrArray::path(data(object))))
+#' @importFrom ZarrArray path
+setMethod("path", "SpatialDataArray", \(object, ...) {
+    pa <- tryCatch(path(data(object)), error=\(e) NULL)
+    if (is.null(pa)) return(NA_character_)
+    dirname(pa)
+})
 
 #' @export
 #' @rdname path
-setMethod("path", "SpatialDataFrame", \(object, ...) 
-    attr(data(object), "source_path"))
+setMethod("path", "SpatialDataFrame", \(object, ...) {
+    pa <- attr(data(object), "source_path")
+    if (is.null(pa)) return(NA_character_)
+    pa
+})
 
 #' @export
 #' @rdname path
 #' @importFrom SingleCellExperiment int_metadata
-setMethod("path", "SingleCellExperiment", \(object, ...) 
-    int_metadata(object)$source_path)
+setMethod("path", "SingleCellExperiment", \(object, ...) {
+    pa <- int_metadata(object)$source_path
+    if (is.null(pa)) return(NA_character_)
+    pa
+})
 
 #' @export
 #' @rdname path

tests/testthat/test-path.R

@@ -0,0 +1,105 @@
+zs <- file.path("extdata", "blobs.zarr")
+zs <- system.file(zs, package="spatialdataR")
+sd <- readSpatialData(zs)
+
+test_that("path,image", {
+    x <- path(image(sd))
+    expect_length(x, 1)
+    expect_is(x, "character")
+    expect_true(file.info(x)$isdir)
+    
+    x <- path(SpatialDataImage())
+    expect_length(x, 1)
+    expect_true(is.na(x))
+    expect_is(x, "character")
+})
+
+test_that("path,label", {
+    x <- path(label(sd))
+    expect_length(x, 1)
+    expect_is(x, "character")
+    expect_true(file.info(x)$isdir)
+    
+    x <- path(SpatialDataLabel())
+    expect_length(x, 1)
+    expect_true(is.na(x))
+    expect_is(x, "character")
+})
+
+test_that("path,shape", {
+    x <- path(shape(sd))
+    expect_length(x, 1)
+    expect_is(x, "character")
+    expect_true(file.info(x)$isdir)
+    expect_true(endsWith(x, ".parquet"))
+    
+    x <- path(SpatialDataShape())
+    expect_length(x, 1)
+    expect_true(is.na(x))
+    expect_is(x, "character")
+})
+
+test_that("path,point", {
+    x <- path(point(sd))
+    expect_length(x, 1)
+    expect_is(x, "character")
+    expect_true(file.info(x)$isdir)
+    expect_true(endsWith(x, ".parquet"))
+    
+    x <- path(SpatialDataPoint())
+    expect_length(x, 1)
+    expect_true(is.na(x))
+    expect_is(x, "character")
+})
+
+test_that("path,table", {
+    x <- path(table(sd))
+    expect_length(x, 1)
+    expect_is(x, "character")
+    expect_true(file.info(x)$isdir)
+    
+    x <- path(SpatialDataPoint())
+    expect_length(x, 1)
+    expect_true(is.na(x))
+    expect_is(x, "character")
+})
+
+test_that("path,sdata", {
+    ls <- rownames(sd)
+    es <- unlist(colnames(sd))
+    ne <- length(es)
+    
+    x <- path(sd, simplify=TRUE)
+    expect_is(x, "data.frame")
+    expect_equal(ncol(x), 3)
+    expect_equal(nrow(x), ne)
+    for (. in seq_along(x))
+        expect_is(x[[.]], "character")
+    expect_all_true(x[[1]] %in% ls)
+    expect_all_true(x[[2]] %in% es)
+    expect_all_true(file.exists(x[[3]]))
+    
+    y <- sd
+    label(y, 2) <- SpatialDataLabel()
+    y <- path(y, simplify=TRUE)
+    i <- y[[1]] == "labels" & y[[2]] == labelNames(sd)[2]
+    expect_identical(i, is.na(y[[3]]))
+    y[[3]][i] <- x[[3]][i]
+    expect_identical(x, y)
+    
+    x <- path(sd, simplify=FALSE)
+    expect_is(x, "list")
+    expect_length(unlist(x), ne)
+    expect_equal(names(x), ls)
+    for (l in names(x)) {
+        expect_length(x[[l]], length(sd[[l]]))
+        expect_equal(names(x[[l]]), names(sd[[l]]))
+        for (e in names(x[[l]])) {
+            y <- x[[l]][[e]]
+            expect_length(y, 1)
+            expect_is(y, "character")
+            expect_true(file.exists(y))
+            expect_equal(y, path(sd[[l]][[e]]))
+        }
+    }
+})