[r] Replace tiledb-r with `libtiledbsoma` in the R API (parent task) #2406

johnkerl · 2024-04-08T18:03:18Z

This is a sibling of #1632. Its sole job is to link-track, at the GitHub Issues level, smaller issues which will be split out as individual GitHub Issues.

Some sequencings:

[r] Push schema accessor down to libtiledbsoma #3079 is the last spot R/TileDBArray.R needs the .tiledb_array / self$object TileDB-R array handle
That in turn (as narrated on that PR) is blocked by [r] Use libtiledbsoma for schema evolution #3057
Once 3057 and 3079 are merged then we can do [r] Use libtiledbsoma handles for arrays #3059
Then [r] Use libtiledbsoma for the mode accessor #3060
[r] Port QueryCondition from tiledb-r to tiledbsoma-r [WIP] #3083 appears somewhat orthogonal to that list just now
Likewise [r] Use libtiledbsoma for schema/filter specification #3056

Status quo and to-do items as of 2025-02-03:

Many tiledbsoma-r unit-test cases call into tiledb-r and should not.
- Some assertions can be removed as no longer needed (they were needed during initial bring-up but are now redundant).
- Some assertions will need to be ported to use tiledbsoma-r.
- [r] Remove TileDB-R accesses within tests/testthat #3124
The persistent underlying array handle opened at soma open and closed at soma close is a tiledb-r handle. These need to go away.
All the calls into libtiledbsoma pass in URI and context, doing open-use-close.
- These libtiledbsoma handles need to be opened persistently as soma array open and closed at soma array close.
- All the calls into libtiledbsoma need to then be modified to take in an open handle.
- [r] Use libtiledbsoma for array handles #3061
This will require passing around SOMATileDBContext without breaking unit-test cases.
- On discussion with @mojaveazure we need to:
  - Retain the existing under-the-hood SOMATileDBContext
  - For the user-facing API, replace the complex user-facing context object with a simple named list.
- [r] Remove all references to tiledb-r context #3052

The text was updated successfully, but these errors were encountered:

Remove an unused custom class as part of replacing `TileDBObject` with a new SOMA base-object class that is not reliant on tiledb-r [SC-63206](https://app.shortcut.com/tiledb-inc/story/63206) continues work for #2406 Note: this PR is not going into `main`, but into a separate branch to accumulate all of these little PRs before filing the larger one to remove tiledb-r

Remove an unused custom class as part of replacing `TileDBObject` with a new SOMA base-object class that is not reliant on tiledb-r [SC-63206](https://app.shortcut.com/tiledb-inc/story/63206) continues work for #2406

Replace tiledb-r with SOMA for test helper function to create an empty sparse nd-array [SC-64301](https://app.shortcut.com/tiledb-inc/story/64301) continues work for #2406

Replace the various tiledb-r wrapper base classes with new and expanded SOMA base classes: - `TileDBObject` replaced by new `SOMAObject` - `TileDBArray` replaced by expanded `SOMAArrayBase` - `TileDBGroup` replaced by expanded `SOMACollectionBase` [SC-64345](https://app.shortcut.com/tiledb-inc/story/64345) continues work for #2406

Replace `tiledb::is.sparse()` and `tiledb::allows_dups()` with new R/Rcpp functions in tiledbsoma-r - `tiledb::is.sparse()` is replaced by `c_is_sparse()` and exposed as `SOMAArrayBase$is_sparse()` - `tiledb::allows_dups()` is replaced with `c_allows_dups()` and exposed as `SOMAArrayBase$allows_duplicates()` [SC-64424](https://app.shortcut.com/tiledb-inc/story/64424) continues work for #2406

Replace `TileDBArray$attributes()` with new `SOMAArrayBase$attributes()`; this method uses a libtiledbsoma/Rcpp function rather than `tiledb::attrs()` and returns a named list instead of a tiledb-r wrapper around external pointers [SC-64814](https://app.shortcut.com/tiledb-inc/story/64814) continues work for #2406

…3834) Replace `TileDBArray$attributes()` with new `SOMAArrayBase$attributes()`; this method uses a libtiledbsoma/Rcpp function rather than `tiledb::attrs()` and returns a named list instead of a tiledb-r wrapper around external pointers [SC-64814](https://app.shortcut.com/tiledb-inc/story/64814) continues work for #2406

Remove an unused custom class as part of replacing `TileDBObject` with a new SOMA base-object class that is not reliant on tiledb-r [SC-63206](https://app.shortcut.com/tiledb-inc/story/63206) continues work for #2406

Replace `tiledb::is.sparse()` and `tiledb::allows_dups()` with new R/Rcpp functions in tiledbsoma-r - `tiledb::is.sparse()` is replaced by `c_is_sparse()` and exposed as `SOMAArrayBase$is_sparse()` - `tiledb::allows_dups()` is replaced with `c_allows_dups()` and exposed as `SOMAArrayBase$allows_duplicates()` [SC-64424](https://app.shortcut.com/tiledb-inc/story/64424) continues work for #2406

…3834) Replace `TileDBArray$attributes()` with new `SOMAArrayBase$attributes()`; this method uses a libtiledbsoma/Rcpp function rather than `tiledb::attrs()` and returns a named list instead of a tiledb-r wrapper around external pointers [SC-64814](https://app.shortcut.com/tiledb-inc/story/64814) continues work for #2406

Replace schema filter checking with new libtiledbsoma/Rcpp `c_schema_fitlers()` function to return a named list of schema fitlers [SC-64998](https://app.shortcut.com/tiledb-inc/story/64998) continues work for #2406

Replace calls to `tiledb::attrs()` with `$attributes()` accessor [SC-64999](https://app.shortcut.com/tiledb-inc/story/64999) continues work for #2406

Replace calls to `tiledb::domain()` and other domain accessors with libtiledbsom/Rcpp `c_domain()` [SC-65000](https://app.shortcut.com/tiledb-inc/story/65000) continues work for #2406

Replace calls to `tiledb::attrs()` with `$attributes()` accessor [SC-64999](https://app.shortcut.com/tiledb-inc/story/64999) continues work for #2406

Replace tiledb-r enum accessors with new libtiledb/Rcpp accessors [SC-65002](https://app.shortcut.com/tiledb-inc/story/65002) continues work for #2406

Replace schema filter checking with new libtiledbsoma/Rcpp `c_schema_fitlers()` function to return a named list of schema fitlers [SC-64998](https://app.shortcut.com/tiledb-inc/story/64998) continues work for #2406

Replace calls to `tiledb::domain()` and other domain accessors with libtiledbsom/Rcpp `c_domain()` [SC-65000](https://app.shortcut.com/tiledb-inc/story/65000) continues work for #2406

johnkerl added r-api cpp-api parent labels Apr 8, 2024

johnkerl mentioned this issue Apr 17, 2024

[r] Use lower and upper pin bounds on tiledb-r for release-1.9 branch #2374

Merged

johnkerl self-assigned this Sep 24, 2024

This was referenced Sep 24, 2024

[r] Remove the unused fragment_count accessor #3050

Closed

[r] Port the query-condition logic from TileDB-R to TileDB-SOMA-R #3051

Closed

johnkerl changed the title ~~[r] Use new C++ bindings in R API (parent task)~~ [r] Use new C++ bindings in R API, and remove tiledb-r dependency (parent task) Sep 24, 2024

johnkerl changed the title ~~[r] Use new C++ bindings in R API, and remove tiledb-r dependency (parent task)~~ [r] Replace tiledb-r with libtiledbsoma in the R API (parent task) Sep 24, 2024

mojaveazure mentioned this issue Feb 11, 2025

[r] Remove TileDBURI Custom Class #3689

Merged

mojaveazure added a commit that referenced this issue Mar 11, 2025

[r] Replace tiledb-r with SOMA for test helper

bbb2a6c

Replace tiledb-r with SOMA for test helper function to create an empty sparse nd-array [SC-64301](https://app.shortcut.com/tiledb-inc/story/64301) continues work for #2406

mojaveazure mentioned this issue Mar 11, 2025

[r] Replace tiledb-r with SOMA for test helper #3767

Merged

mojaveazure mentioned this issue Mar 13, 2025

[r] [WIP] Replace TileDB* base classes with SOMA* base classes #3771

Draft

mojaveazure mentioned this issue Mar 21, 2025

[r] Repace $attributes() accessor with one that uses libtiledbsoma #3834

Merged

mojaveazure mentioned this issue Mar 26, 2025

[r] Replace calls to tiledb-r schema checkers with libtiledbsoma #3850

Merged

mojaveazure mentioned this issue Mar 26, 2025

[r] Replace calls to tiledb::filter_list() on schemas #3851

Open

mojaveazure added a commit that referenced this issue Mar 26, 2025

[r] Replace tiledb attribute filter checks with $attributes()

88f2d8f

Replace calls to `tiledb::attrs()` with `$attributes()` accessor [SC-64999](https://app.shortcut.com/tiledb-inc/story/64999) continues work for #2406

mojaveazure mentioned this issue Mar 26, 2025

[r] Replace tiledb attribute filter checks with $attributes() #3852

Merged

mojaveazure mentioned this issue Mar 26, 2025

[r] [WIP] Replace tiledb::domain() with Rcpp c_domain() #3854

Draft

mojaveazure added a commit that referenced this issue Mar 26, 2025

[r] Replace tiledb-r enum accessors with libtiledb/Rcpp

61f617a

Replace tiledb-r enum accessors with new libtiledb/Rcpp accessors [SC-65002](https://app.shortcut.com/tiledb-inc/story/65002) continues work for #2406

mojaveazure mentioned this issue Mar 26, 2025

[r] [WIP] Replace tiledb-r enum accessors with libtiledb/Rcpp #3855

Draft

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[r] Replace tiledb-r with `libtiledbsoma` in the R API (parent task) #2406

[r] Replace tiledb-r with `libtiledbsoma` in the R API (parent task) #2406

johnkerl commented Apr 8, 2024 •

edited

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[r] Replace tiledb-r with libtiledbsoma in the R API (parent task) #2406

[r] Replace tiledb-r with libtiledbsoma in the R API (parent task) #2406

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johnkerl commented Apr 8, 2024 • edited Loading

[r] Replace tiledb-r with `libtiledbsoma` in the R API (parent task) #2406

[r] Replace tiledb-r with `libtiledbsoma` in the R API (parent task) #2406

johnkerl commented Apr 8, 2024 •

edited

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