tests/testthat/test-H5File-Subset.R

In h5: Interface to the 'HDF5' Library

context("H5File-Subset")
fname <- "test.h5"

test_that("H5File-Subset-Group",{
  if(file.exists(fname)) file.remove(fname)
  file <- h5file(fname, "a")
  
  f <- function() file[c("1", "2", "3")]
  expect_that(f(), throws_error("Only one path can be specified"))

  group3 <- file["/testgroup3"] 
  expect_that(group3, is_a("H5Group"))
  expect_that(group3@location, is_identical_to("/testgroup3"))
  
  groupnested <- group3["test"]
  expect_that(groupnested, is_a("H5Group"))
  expect_that(groupnested@location, is_identical_to("/testgroup3/test"))
  h5close(groupnested)
  h5close(group3)
  
  group3 <- file["/testgroup3"]
  grouprelative <- group3["/test"]
  expect_that(grouprelative, is_a("H5Group"))
  expect_that(grouprelative@location, is_identical_to("/testgroup3/test"))
  h5close(grouprelative)
  h5close(group3)
  
  # recursive group creation
  group5 <- file["/test1/test2/test3/test4/test5"]
  expect_that(group5, is_a("H5Group"))
  expect_that(group5@location, is_identical_to("/test1/test2/test3/test4/test5"))
  h5close(group5)
  h5close(file)
  expect_that(file.remove(fname), is_true())
})

test_that("H5File-Subset-DataSet",{
  if(file.exists(fname)) file.remove(fname)
  file <- h5file(fname, "a")
  
  file["test/test1/test2/test3/dset1"] <- 1:10
  file["test/test1/test2/test3/dset2"] <- matrix(1:9, nrow = 3)
  file["test/test1/test2/test3/dset3"] <- array(1:6, dim = c(1, 2, 3))    
  file["dset4"] <- matrix(1:10, nrow = 5)

  # TODO: should work without h5close()
  dset <- file["test/test1/test2/test3/dset1"]
  expect_that(dset[], is_identical_to(1:10))
  h5close(dset)

  dset <- file["test/test1/test2/test3/dset2"]
  expect_that(dset[], is_identical_to(matrix(1:9, nrow = 3)))
  h5close(dset)
  
  dset <- file["test/test1/test2/test3/dset3"]
  expect_that(dset[], is_identical_to(array(1:6, dim = c(1, 2, 3))))
  h5close(dset)
  
  dset <- file["dset4"]
  expect_that(dset[], is_identical_to(matrix(1:10, nrow = 5)))
  h5close(dset)
  
  # check subsets
  # TODO: should work without h5close()
  dset <- file["test/test1/test2/test3/dset1"]
  expect_that(dset[1:5], is_identical_to(1:5))
  h5close(dset)
  
  dset <- file["test/test1/test2/test3/dset2"]
  expect_that(dset[1:2,], is_identical_to(matrix(1:9, nrow = 3)[1:2,]))
  h5close(dset)
  
  dset <- file["test/test1/test2/test3/dset3"]
  expect_that(dset[1,1:2,3], 
      is_identical_to(array(1:6, dim = c(1, 2, 3))[1,1:2,3,drop = FALSE]))
  h5close(dset)
  
  # set subsets
  # TODO: include test cases
  h5close(file)
  expect_that(file.remove(fname), is_true())
})