test_H5A.R

library(rhdf5)

h5File <- withr::local_tempfile(pattern = "ex_H5A_", fileext = ".h5")
h5createFile(h5File)
h5write(1:15, h5File, "A")

expect_null(h5errorHandling(type = "suppress"))

test_that("writing attributes is silent", {
  expect_silent(fid <- H5Fopen(h5File))
  expect_silent(did <- H5Dopen(fid, "A"))
  expect_silent(sid <- H5Screate_simple(1))
  expect_silent(sid2 <- H5Screate_simple(10))
  expect_silent(tid <- H5Tcopy("H5T_C_S1"))

  ## fixed length strings
  expect_silent(H5Tset_size(tid, 10L))
  expect_silent(aid <- H5Acreate(did, "volume", tid, sid))
  expect_silent(H5Awrite(aid, "liter"))
  expect_silent(H5Aclose(aid))
  expect_silent(aid <- H5Acreate(did, "time", tid, sid))
  expect_silent(H5Awrite(aid, "seconds"))
  expect_silent(H5Aclose(aid))

  ## 64-bit integers
  expect_silent(aid <- H5Acreate(did, "int64", "H5T_NATIVE_INT64", sid))
  expect_silent(H5Awrite(aid, 2^32))
  expect_silent(H5Aclose(aid))

  ## unsigned 32-bit integers
  expect_silent(aid <- H5Acreate(did, "uint32", "H5T_NATIVE_UINT32", sid2))
  expect_silent(H5Awrite(aid, c(1:9, 2^31)))
  expect_silent(H5Aclose(aid))

  expect_silent(H5Sclose(sid))
  expect_silent(H5Sclose(sid2))
  expect_silent(H5Dclose(did))
  expect_silent(H5Fclose(fid))
  expect_silent(H5Tclose(tid))
})


test_that("attributes exist", {
  expect_silent(fid <- H5Fopen(h5File))
  expect_silent(did <- H5Dopen(fid, "A"))

  expect_true(H5Aexists(did, "volume"))
  expect_true(H5Aexists(did, "time"))
  expect_false(H5Aexists(did, "foo"))

  expect_silent(H5Dclose(did))
  expect_silent(H5Fclose(fid))
})

test_that("attributes can be opened and closed", {
  expect_silent(fid <- H5Fopen(h5File))

  expect_silent(aid <- H5Aopen_by_name(fid, objname = "A", name = "volume"))
  expect_output(print(aid), regexp = "volume")
  expect_silent(H5Aclose(aid))
  expect_silent(aid <- H5Aopen_by_name(fid, objname = "A", name = "time"))
  expect_output(print(aid), regexp = "time")
  expect_silent(H5Aclose(aid))

  expect_silent(aid <- H5Aopen_by_idx(fid, n = 2, objname = "A"))
  expect_identical(H5Aget_name(aid), "time")
  expect_silent(H5Aclose(aid))
  expect_silent(aid <- H5Aopen_by_idx(fid, n = 4, objname = "A"))
  expect_identical(H5Aget_name(aid), "volume")
  expect_silent(H5Aclose(aid))

  expect_silent(H5Fclose(fid))

  ## doesn't cope well when a missing attribute is named
  ## H5Aopen_by_name(fid, objname = "A", name = "foobaa")
})

test_that("64-bit integer attributes are read correctly", {
  fid <- H5Fopen(h5File)
  did <- H5Dopen(fid, name = "A")
  aid <- H5Aopen(did, name = "int64")

  expect_warning(H5Aread(aid, bit64conversion = "int")) %>%
    is.na() %>%
    expect_true()

  expect_silent(H5Aread(aid, bit64conversion = "double")) %>%
    expect_equivalent(2^32)

  expect_silent(H5Aread(aid, bit64conversion = "bit64")) %>%
    expect_equivalent(bit64::as.integer64(2^32))

  H5Aclose(aid)
  H5Dclose(did)
  H5Fclose(fid)
})

test_that("unsigned 32-bit integer attributes are read correctly", {
  fid <- H5Fopen(h5File)
  did <- H5Dopen(fid, name = "A")
  aid <- H5Aopen(did, name = "uint32")

  expect_warning(H5Aread(aid, bit64conversion = "int")) |>
    is.na() |>
    any() |>
    expect_true()

  expect_silent(H5Aread(aid, bit64conversion = "double")) |>
    expect_equivalent(c(1:9, 2^31))

  expect_silent(x3 <- H5Aread(aid, bit64conversion = "bit64"))
  expect_equivalent(x3, bit64::as.integer64(c(1:9, 2^31)))
  expect_is(x3, "integer64")

  H5Aclose(aid)
  H5Dclose(did)
  H5Fclose(fid)
})

test_that("attributes can be deleted", {
  expect_silent(fid <- H5Fopen(h5File))
  expect_silent(did <- H5Dopen(fid, "A"))

  ## deleting existing attribute
  expect_true(H5Aexists(did, "volume"))
  expect_identical(H5Adelete(did, "volume"), 0L)
  expect_false(H5Aexists(did, "volume"))

  ## trying to delete non-existant attribute
  expect_identical(H5Adelete(did, "foobaa"), -1L)

  expect_silent(H5Dclose(did))
  expect_silent(H5Fclose(fid))
})

test_that("Missing values in bit64conversion can be passed down", {
  fid <- H5Fopen(h5File)
  did <- H5Dopen(fid, name = "A")
  aid <- H5Aopen(did, name = "uint32")

  f <- function(attribute, bit64conversion) {
    H5Aread(attribute, bit64conversion = bit64conversion)
  }
  expect_warning(f(aid), "To rely on the `bit64conversion` argument default")

  H5Aclose(aid)
  H5Dclose(did)
  H5Fclose(fid)
})

test_that("fixed length string attributes are correct", {
  attr_value <- "Testing"
  attr_name <- "name"

  # create a string datatype with size of 7 bytes
  tid <- H5Tcopy("H5T_C_S1")
  H5Tset_strpad(tid, strpad = "NULLPAD")
  H5Tset_size(tid, nchar(attr_value))

  fid <- H5Fopen(h5File)
  sid <- H5Screate("H5S_SCALAR")
  aid <- H5Acreate(fid, name = attr_name, dtype_id = tid, h5space = sid)

  H5Awrite(aid, attr_value) # string of length 7

  h5closeAll(aid, sid, fid, tid)

  attr <- h5readAttributes(h5File, "/")
  expect_is(attr, class = "list")
  expect_identical(names(attr), attr_name)
  expect_identical(attr$name, attr_value)
})