Check whether a 'HDF5' file can be opened for read/write

Usage

io_h5_valid(file, mode = c("r", "w"), close_all = FALSE)

io_h5_names(file)

Arguments

file: path to file
mode: 'r' for read access and 'w' for write access
close_all: whether to close all connections or just close current connection; default is false. Set this to TRUE if you want to close all other connections to the file. This only applies to the 'hdf5r' backend; 'h5lite' never holds the file open

Value

io_h5_valid returns a logical value indicating whether the file can be opened. io_h5_names returns a character vector of dataset names.

Examples



x <- array(1:27, c(3,3,3))
f <- tempfile()

# No data written to the file, hence invalid
io_h5_valid(f, 'r')
#> [1] FALSE

io_write_h5(x, f, 'dset')
#> /tmp/Rtmpjei90z/file1f6f2ddec920 => dset (Dataset Created)
#> /tmp/Rtmpjei90z/file1f6f2ddec920 => dset (Dataset Removed)
#> /tmp/Rtmpjei90z/file1f6f2ddec920 => dset (Dataset Created)
io_h5_valid(f, 'w')
#> [1] TRUE

# `close_all` applies to the `hdf5r` backend, the only one that holds
# file connections open
if (nzchar(system.file(package = "hdf5r"))) {

  # Open the file and hold a connection
  ptr <- hdf5r::H5File$new(filename = f, mode = 'w')

  # Can read, but cannot write while the connection is held
  print(io_h5_valid(f, 'r'))
  print(io_h5_valid(f, 'w'))

  # However, this can be reset via `close_all=TRUE`
  io_h5_valid(f, 'r', close_all = TRUE)

  # Now the connection is no longer valid
  print(ptr)

  try({ ptr$close_all() }, silent = TRUE)
}
#> [1] TRUE
#> [1] FALSE
#> Class: H5File
#> ID: Object invalid

# clean up
unlink(f)