[r] Metadata read/write support via libtiledbsoma

[eddelbuettel]

Issue and/or context:

This PR adds support for metadata reading and writing via libtiledbsoma. It does not yet add support for timestamp'ed create / write / read which will follow in subsequent PR building on this.

Changes:

The write-path for object creation and write is now fully utilizing the libtiledbsoma facilities (though the additional timestamp feature is yet to come, work in progress).

Notes for Reviewer:

SC 51949

#2698

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.16%. Comparing base (edabcb6) to head (61dc560).
Report is 9 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2819      +/-   ##
==========================================
+ Coverage   90.06%   90.16%   +0.10%     
==========================================
  Files          37       37              
  Lines        3945     3957      +12     
==========================================
+ Hits         3553     3568      +15     
+ Misses        392      389       -3     

Flag	Coverage Δ
python	90.16% <ø> (+0.10%)	⬆️

Flags with carried forward coverage won't be shown. Click here to find out more.

Components	Coverage Δ
python_api	90.16% <ø> (+0.10%)	⬆️
libtiledbsoma	∅ <ø> (∅)

[nguyenv]

Why are the metadata accessors implemented as static methods? You should be able to use SOMAArray::open to open the array and then use the member functions SOMAArray::get_metadata, etc. (and same for SOMAGroup).

[eddelbuettel]

Can you point to line and file? In src/metadata.cpp I use a (common) helper to return the unique pointer, and utilise that across a half-dozen functions i.e. this to access the bool check for existence

std::unique_ptr<tdbs::SOMAObject> getObjectUniquePointer(bool is_array, OpenMode mode,
                                                         std::string& uri,
                                                         std::shared_ptr<tdbs::SOMAContext> ctx) {
    if (is_array) {
        return tdbs::SOMAArray::open(mode, uri, ctx);
    } else {
        return tdbs::SOMAGroup::open(mode, uri, ctx);
    }
}

// .... more lines omitted ...

// [[Rcpp::export]]
bool has_metadata(std::string& uri, std::string& key, bool is_array,
                  Rcpp::XPtr<somactx_wrap_t> ctxxp) {
    // 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::read, uri, sctx);
    return soup->has_metadata(key);
}

I don't think I add static methods. Am I overlooking something?