anndataR/tests/testthat/test-roundtrip-uns.R at 0d6341ee6ee6c92585c138114560f2d669d8033b · scverse/anndataR · GitHub

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skip_if_no_anndata()
skip_if_no_dummy_anndata()

library(reticulate)

ad <- reticulate::import("anndata", convert = FALSE)
da <- reticulate::import("dummy_anndata", convert = FALSE)
bi <- reticulate::import_builtins()

known_issues <- read_known_issues()

test_names <- c(
  names(da$matrix_generators),
  names(da$vector_generators),
  names(da$scalar_generators)
)

for (name in test_names) {
  # first generate a python h5ad
  adata_py <- da$generate_dataset(
    x_type = NULL,
    obs_types = list(),
    var_types = list(),
    layer_types = list(),
    obsm_types = list(),
    varm_types = list(),
    obsp_types = list(),
    varp_types = list(),
    uns_types = list(name),
    nested_uns_types = list()
  )

  # create a couple of paths
  file_py <- withr::local_file(
    tempfile(paste0("anndata_py_", name), fileext = ".h5ad")
  )
  file_r <- withr::local_file(
    tempfile(paste0("anndata_r_", name), fileext = ".h5ad")
  )

  # write to file
  adata_py$write_h5ad(file_py)
  # Read it back in to get the version as read from disk
  adata_py <- ad$read_h5ad(file_py)

  test_that(paste0("Reading an AnnData with uns '", name, "' works"), {
    msg <- message_if_known(
      backend = "HDF5AnnData",
      slot = c("uns"),
      dtype = name,
      process = "read",
      known_issues = known_issues
    )
    skip_if(!is.null(msg), message = msg)

    adata_r <- read_h5ad(file_py, as = "HDF5AnnData")

    expect_equal(
      names(adata_r$uns),
      bi$list(adata_py$uns$keys())
    )

    # check that the print output is the same
    str_r <- capture.output(print(adata_r))
    str_py <- capture.output(print(adata_py))
    expect_equal(str_r, str_py)
  })

  test_that(
    paste0("Comparing an anndata with uns '", name, "' with reticulate works"),
    {
      msg <- message_if_known(
        backend = "HDF5AnnData",
        slot = c("uns"),
        dtype = name,
        process = c("read", "reticulate"),
        known_issues = known_issues
      )
      skip_if(!is.null(msg), message = msg)

      adata_r <- read_h5ad(file_py, as = "HDF5AnnData")

      py_value <- convert_py_value(adata_py$uns[[name]], name)

      expect_equal(
        adata_r$uns[[name]],
        py_value
      )
    }
  )

  gc()

  test_that(paste0("Writing an AnnData with uns '", name, "' works"), {
    msg <- message_if_known(
      backend = "HDF5AnnData",
      slot = c("uns"),
      dtype = name,
      process = c("read", "write"),
      known_issues = known_issues
    )
    skip_if(!is.null(msg), message = msg)

    adata_r <- read_h5ad(file_py, as = "InMemoryAnnData")
    write_h5ad(adata_r, file_r)

    # read from file
    adata_py2 <- ad$read_h5ad(file_r)

    # expect name is one of the keys
    expect_contains(
      bi$list(adata_py2$uns$keys()),
      name
    )

    # expect that the objects are the same
    expect_equal_py(
      py_get_item(adata_py2$uns, name),
      py_get_item(adata_py$uns, name)
    )
  })
}