Currently we're retaining a tiledb-r handle at open:

And we use a temporary open-use-close at every single call to libtiledbsoma -- here is just one of many examples:

On the one hand this might seem lower-pri: the redundant opens are a perf hit but they work.

But as discussed on #3060 we must do this in order to remove the tiledb-r dependency.

See also #3053 which @nguyenv is working on -- this is a case where we do currently require a second open for array reads.

From #3059:

Already done for groups

#2406; [sc-55685].

Steps:

• Status quo is
  • There is a private$.tiledb_array with connection to self$object
    • This is set on construction/open, and closed on close
  • The libtiledbsoma handles are currently ephemeral
    • Every read / write / get_metadata etc which is libtiledbsoma-capable currently takes a uri and a ctx and does open/op/close
• Needing to be done:
  • Remove the last refrences to private$.tiledb_array with connection to self$object
    • [r] Remove last private$.tiledb_array and self$object from R classes [WIP] #3129
  • Glitch: while with 3129 we are removing the last references to self$object within R/*.R, there are hundreds of lines of uses of $object within tests/testthat -- tracked on [r] Remove TileDB-R accesses within tests/testthat #3124
  • Then set a libtiledbsoma handle on construction/open, and close it on close
  • Modify all the methods to not take uri+ctx but rather the open handle

To check:

• Currently the array set_metadata does not error out when the array is opened for read -- this is a bug.
  • This should be auto-fixed by this issue, but, it needs to be tested.