# library

skip_on_ci() # dont test on GitHub actions

# file

h5ad_file <- tempfile(fileext = ".h5ad")

zarr_file <- tempfile(fileext = ".zarr")

ometiff_file <- tempfile(fileext = ".ome.tiff")

test_that("as.AnnData", {

  # get data

  data("visium_data")

  data("xenium_data")

  # xenium to anndata

  as.AnnData(xenium_data, file = h5ad_file)

  as.AnnData(xenium_data, file = h5ad_file, assay = "Assay1")

  as.AnnData(xenium_data, file = h5ad_file, flip_coordinates = TRUE)

  # visium to anndata

  as.AnnData(visium_data, file = h5ad_file)

  as.AnnData(visium_data, file = h5ad_file, assay = "Assay1")

  as.AnnData(visium_data, file = h5ad_file, flip_coordinates = TRUE)

  # xenium to anndata

  as.AnnData(xenium_data, file = zarr_file)

  as.AnnData(xenium_data, file = zarr_file, assay = "Assay1")

  as.AnnData(xenium_data, file = zarr_file, flip_coordinates = TRUE)

  # visium to anndata

  as.AnnData(visium_data, file = zarr_file)

  as.AnnData(visium_data, file = zarr_file, assay = "Assay1")

  as.AnnData(visium_data, file = zarr_file, flip_coordinates = TRUE)

  # clean file

  file.remove(h5ad_file)

  unlink(zarr_file, recursive = TRUE)

  expect_equal(1,1L)

})

test_that("as.AnnData, python path", {

  # get data

  data("visium_data")

  data("xenium_data")

  # python.path

  expect_error(as.AnnData(visium_data, file = h5ad_file, python.path = ""))

  # python.path

  python.path <- system("which python", intern = TRUE)

  expect_error(as.AnnData(visium_data, file = zarr_file, python.path = python.path))

  expect_error(as.AnnData(visium_data, file = zarr_file, python.path = ""))

  # options path

  options(voltron.python.path = python.path)

  expect_error(as.AnnData(visium_data, file = zarr_file))

  options(voltron.python.path = NULL)

  expect_true(as.AnnData(visium_data, file = zarr_file))

  # clean file

  expect_equal(1,1L)

})

test_that("as.ometiff", {

  # get image

  data.file <- system.file(file.path('extdata', 'DAPI.tif'), package='VoltRon')

  # save image

  as.OmeTiff(magick::image_read(data.file), out_path = ometiff_file)

  # clean file

  file.remove(ometiff_file)

  expect_equal(1,1L)

})

test_that("as.ometiff, python path", {

  # get image

  data.file <- system.file(file.path('extdata', 'DAPI.tif'), package='VoltRon')

  # save image

  as.OmeTiff(magick::image_read(data.file), out_path = ometiff_file)

  # python.path

  expect_error(as.OmeTiff(magick::image_read(data.file), out_path = ometiff_file, python.path = ""))

  # python.path

  python.path <- system("which python", intern = TRUE)

  expect_error(as.OmeTiff(magick::image_read(data.file), out_path = ometiff_file, python.path = python.path))

  # options path

  options(voltron.python.path = python.path)

  expect_error(as.OmeTiff(magick::image_read(data.file), out_path = ometiff_file))

  options(voltron.python.path = NULL)

  expect_true(as.OmeTiff(magick::image_read(data.file), out_path = ometiff_file))

  # clean file

  file.remove(ometiff_file)

  expect_equal(1,1L)

})

test_that("as.Seurat", {

  # one sample

  test1 <- VoltRon::as.Seurat(xenium_data, cell.assay = "Xenium", type = "image")

  test1_Voltron <- as.VoltRon(test1, assay_name = "Xenium")

  # multiple samples

  xenium_data2 <- xenium_data

  xenium_data2$Sample <- "sample1"

  xenium_data2 <- merge(xenium_data2, xenium_data)

  test1 <- VoltRon::as.Seurat(xenium_data2, cell.assay = "Xenium", type = "image")

  test1_Voltron <- as.VoltRon(test1, assay_name = "Xenium")

  expect_equal(1,1L)

})