[c++/python] Add soma_type argument for SOMAObject::open

[nguyenv]

Issue and/or context:

SOMAObject::open introduced a performance degradation due to its overzealous usage of tiledb::Object::object, which checks for the type by opening the purpoted TileDB object at the given URI. In some cases, the type of the TileDB object is already known beforehand which makes these operations unnecessary.

The example below takes ~15 seconds to run and yields three 404 errors.

SOMA_URI = "tiledb://TileDB-Inc/soma-exp-tabula-sapiens-immune"
var_columns = ["soma_joinid", "var_id", "ensemblid", "feature_type"]

with tiledbsoma.open(SOMA_URI, context=sctx) as exp:
    var = (
        exp.ms["RNA"]
        .var.read(column_names=var_columns)
        .concat()
        .to_pandas()
        .set_index("soma_joinid")
    )

With the changes in this PR, the example takes ~8 seconds and yields no 404 errors.

Changes:

Bypass the need to use tiledb::Object::object by explcitly passing in a soma_type argument of either SOMAArray or SOMAGroup.

[codecov]

Codecov Report

Merging #2350 (f8a3f47) into main (7eef2c6) will decrease coverage by 3.24%.
Report is 1 commits behind head on main.
The diff coverage is 61.36%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2350      +/-   ##
==========================================
- Coverage   82.17%   78.94%   -3.24%     
==========================================
  Files          89      140      +51     
  Lines        8226    10856    +2630     
  Branches        0      216     +216     
==========================================
+ Hits         6760     8570    +1810     
- Misses       1466     2186     +720     
- Partials        0      100     +100     

Flag	Coverage Δ
libtiledbsoma	67.77% <28.57%> (?)
python	90.59% <91.30%> (+0.02%)	⬆️
r	75.11% <ø> (+0.42%)	⬆️

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

Components	Coverage Δ
python_api	90.59% <91.30%> (+0.02%)	⬆️
libtiledbsoma	49.21% <28.57%> (∅)

[aaronwolen]

[sc-44157]

[shortcut-integration]

This pull request has been linked to Shortcut Story #44157: Notebook cloud-query performance, story 1 of 2.

[johnkerl]

🚢

[johnkerl]

@aaronwolen @nguyenv in order to take full advantage of this PR we should be using

with tiledbsoma.Experiment.open(SOMA_URI, context=sctx) as exp:

at the notebook level -- making tiledbsoma.open more performant will require core mods this PR cannot implement.

Found additional 404 error.

[johnkerl]

There is a missed callsite -- more details in Slack

The root cause is Experiment.open does not have its own impl and neither does CollectionBase.open and so therefore tiledbsoma.Experiment.open's impl is TileDBObject.open (along the inheritance hierarchy) and there is not a soma_type plumbed through to there

[johnkerl]

🚢
Thanks @nguyenv !!!! :)