[r,c++] Use SOMA Context object throughout

[eddelbuettel]

Issue and/or context:

SOMA Context objects are used throughout the C++ library part of SOMA. Where we previously serialized context and configuration to vector, maps or lists of key-value pairs, we now hold on to an allocated object for longer.

Changes:

This PR changes how we provide such a context from the R package by allocating one as a shared pointer and passing it around as an external pointer throuch which the SOMA context object can be accessed. Where needed, the SOMA context also contains a (core) TileDB context object.

We currently cache the most-recently created object at the package level and provide it if no new one is demanded. This scheme is exactly what tiledb-r does, and acts reliably and robust via a single access point soma_context(). One unit test show how to create a different configuration without caching, using it and then reverting to the default.

SOMA classes can obtain their initial default object via the instantiating factory methods. Access is then provided via a member function, allowing both for simple re-use as well variations (object by object) as needed. How to split the core object values off the platform_config object is left for a subsequent PR that will refine the interface.

All tests pass.

Notes for Reviewer:

SC 55146 #2899

[johnkerl]

This is awesome! Just a few minor notes at this point.

[mojaveazure]

I thought we had agreed on not exposing soma_context() via $new() at this point in time #2988 (comment)

[eddelbuettel]

Yes. This gives the object the option to also set one here but it is not a requirement. Having the entry point is good for testing, methinks. See the comment a few lines futher down as well as the need to rework / let go of tiledbsoma_ctx. I think this is all best addressed in a next PR.

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

Lines 34 to 51 in 091e109

	# Set context
	tiledbsoma_ctx <- tiledbsoma_ctx %||% SOMATileDBContext$new()
	if (!inherits(x = tiledbsoma_ctx, what = 'SOMATileDBContext')) {
	stop("'tiledbsoma_ctx' must be a SOMATileDBContext object", call. = FALSE)
	}
	private$.tiledbsoma_ctx <- tiledbsoma_ctx
	private$.tiledb_ctx <- self$tiledbsoma_ctx$context()
	# TODO: re-enable once new UX is worked out
	# soma_context <- soma_context %||% soma_context()
	# stopifnot(
	# "'soma_context' must be a pointer" = inherits(x = soma_context, what = 'externalptr')
	# )
	if (is.null(soma_context)) {
	private$.soma_context <- soma_context() # FIXME via factory and paramater_config
	} else {
	private$.soma_context <- soma_context
	}

[mojaveazure]

Note for future work: this should be replaced with fetching the context from x; currently available with

Suggested change

	soma_context(),
	x$.__enclos_env__$private$.soma_context

[eddelbuettel]

Fair point but not urgent and on the fence as whether we should use opaque internals. "Future work", as you say.