test_that("load_file with a .csv works", {
skip_if_not_installed("readr")
file <- withr::local_file(tempfile(fileext = ".csv"))
# create a CSV file
df <- data.frame(a = 1L:3L, b = c("a", "b", "c"))
readr::write_csv(df, file)
# load the CSV file
loaded_df <- load_file(file, show_col_types = FALSE)
# ignore class differences
class(loaded_df) <- class(df)
# check that the data frame is the same
expect_equal(loaded_df, df, ignore_attr = TRUE)
})
test_that("load_file with a .tsv works", {
skip_if_not_installed("readr")
file <- withr::local_file(tempfile(fileext = ".tsv"))
# create a TSV file
df <- data.frame(a = 1L:3L, b = c("a", "b", "c"))
readr::write_tsv(df, file)
# load the TSV file
loaded_df <- load_file(file, show_col_types = FALSE)
# ignore class differences
class(loaded_df) <- class(df)
# check that the data frame is the same
expect_equal(loaded_df, df, ignore_attr = TRUE)
})
test_that("load_file with an .h5ad works", {
skip_if_not_installed("anndata")
skip_if_not_installed("reticulate")
skip_if_not(reticulate::py_module_available("anndata"))
file <- withr::local_file(tempfile(fileext = ".h5ad"))
warnings <- reticulate::import("warnings")
warnings$filterwarnings("ignore")
# create an AnnData object
adata <- anndata::AnnData(
X = matrix(1L:6L, nrow = 3),
obs = data.frame(a = 1L:3L),
var = data.frame(b = c("a", "b"))
)
adata$write_h5ad(file)
# load the AnnData object
loaded_adata <- load_file(file)
# check that the AnnData object is the same
expected <- capture_output(print(adata))
actual <- capture_output(print(loaded_adata))
expect_equal(actual, expected)
expect_equal(loaded_adata$obs, adata$obs, ignore_attr = TRUE)
expect_equal(loaded_adata$var, adata$var, ignore_attr = TRUE)
expect_equal(loaded_adata$X, adata$X, ignore_attr = TRUE)
})
###################### TODO: add anndata_zarr tests ######################
test_that("load_file with a .parquet works", {
skip_if_not_installed("nanoparquet")
file <- withr::local_file(tempfile(fileext = ".parquet"))
# create a Parquet file
df <- data.frame(a = 1:3, b = 4:6)
nanoparquet::write_parquet(df, file)
# load the Parquet file
loaded_df <- load_file(file)
# ignore class differences
class(loaded_df) <- class(df)
# check that the data frame is the same
expect_equal(loaded_df, df)
})
###################### TODO: add load_fcs tests ######################
###################### TODO: add load_h5mu tests ######################
test_that("load_file with a .html works", {
skip_if_not_installed("knitr")
file <- withr::local_file(tempfile(fileext = ".html"))
# create an HTML file
html <- "
Hello, world!
"
writeLines(html, file)
# pretend we are in a knitr notebook
knitr::opts_knit$set(out.format = "html")
on.exit(knitr::opts_knit$set(out.format = NULL))
# load the HTML file
loaded_html <- load_file(file)
# check that output is a knit_asis
expect_s3_class(loaded_html, "knit_asis")
# check that the HTML is the same
expected_html <- paste0("\n```{=html}\n", html, "\n```\n")
expect_equal(
unclass(loaded_html),
expected_html,
ignore_attr = TRUE
)
})
test_that("load_file with a .json works", {
skip_if_not_installed("jsonlite")
file <- withr::local_file(tempfile(fileext = ".json"))
data <- list(
a = c(1, 2, 3),
b = c(3, 4, 5)
)
jsonlite::write_json(data, file)
loaded_data <- load_file(file)
expect_equal(loaded_data, data)
})
test_that("load_file with an .svg works", {
skip_if_not_installed("knitr")
file <- withr::local_file(tempfile(fileext = ".svg"))
# create an SVG file
svg <- ""
writeLines(svg, file)
# pretend we are in a knitr notebook
knitr::opts_knit$set(out.format = "html")
on.exit(knitr::opts_knit$set(out.format = NULL))
# load the SVG file
loaded_svg <- load_file(file)
# check that output is a knit_asis
expect_s3_class(loaded_svg, c("knit_image_paths", "knit_asis"))
# check that the SVG is the same
expect_equal(unclass(loaded_svg), file)
})
test_that("load_file with an .rds works", {
file <- withr::local_file(tempfile(fileext = ".rds"))
data <- list(
a = c(1, 2, 3),
b = c(3, 4, 5)
)
saveRDS(data, file)
loaded_data <- load_file(file)
expect_equal(loaded_data, data)
})
test_that("load_file with a .yaml works", {
skip_if_not_installed("yaml")
file <- withr::local_file(tempfile(fileext = ".yaml"))
data <- list(
a = c(1, 2, 3),
b = c(3, 4, 5)
)
yaml::write_yaml(data, file)
loaded_data <- load_file(file)
expect_equal(loaded_data, data)
})