[r] Use libtiledbsoma for array handles

[johnkerl]

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

TileDB-SOMA/apis/r/R/TileDBArray.R

Line 31 in 11d5396

private$.tiledb_array <- tiledb::tiledb_array_open(self$object, type = mode)

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

TileDB-SOMA/apis/r/src/metadata.cpp

Lines 170 to 193 in 11d5396

	void set_metadata(std::string& uri, std::string& key, SEXP valuesxp, std::string& type,
	bool is_array, Rcpp::XPtr<somactx_wrap_t> ctxxp,
	Rcpp::Nullable<Rcpp::DatetimeVector> tsvec = R_NilValue) {
	// shared pointer to SOMAContext from external pointer wrapper
	std::shared_ptr<tdbs::SOMAContext> sctx = ctxxp->ctxptr;
	// SOMA Object unique pointer (aka soup)
	auto soup = getObjectUniquePointer(is_array, OpenMode::write, uri, sctx, tsvec);
	if (type == "character") {
	const tiledb_datatype_t value_type = TILEDB_STRING_UTF8;
	std::string value = Rcpp::as<std::string>(valuesxp);
	spdl::debug("[set_metadata] key {} value {} is_array {} type {}", key, value, is_array, type);
	soup->set_metadata(key, value_type, value.length(), (void*) value.c_str(), true);
	} else if (type == "integer64") {
	const tiledb_datatype_t value_type = TILEDB_INT64;
	double dv = Rcpp::as<double>(valuesxp);
	int64_t value = Rcpp::fromInteger64(dv);
	spdl::debug("[set_metadata] key {} value {} is_array {} type {}", key, value, is_array, type);
	soup->set_metadata(key, value_type, 1, (void*) &value, true);
	} else {
	Rcpp::stop("Unsupported type '%s'", type);
	}
	soup->close();
	}

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.

[johnkerl]

Blocked by #3051 since here
https://github.com/single-cell-data/TileDB-SOMA/blob/1.15.0rc2/apis/r/R/SOMADataFrame.R#L182
the self$object is used. Removing that private$.tiledb_array / self$object from the base class TileDBArray.R causes this query-condition logic to return empty results, in a way that makes unit-test cases fail in non-obvious ways.

We need to move the query-condition logic over from TileDB-R before we can continue here.

[viviannguyen]

I don't believe I'm the correct Vivian to be tagged here. You're probably looking for @nguyenv.

[johnkerl]

Oh no @viviannguyen sorry about that!! Have a nice day though!!