Update nanoarrow and expand use (#663)

* Update nanoarrow vendored files to nanoarrow 0.4.0 * Add nanoarrow.hpp * Refactor arrow table export valgrind clean when no dictionaries are used * Remove some commented-out code * Add nanoarrow to Imports * Set ordered as needed * Use a cutesy typedef nanoarrowXPtr to not have to use SEXP * Also import from nanoarrow * Remove one (interim) library call we no longer need * Review comments leading to dead commented code removal [ci skip] * Add NEWS entry and roll micro release [ci skip]
TileDB-Inc · Feb 22, 2024 · f6d12eb · f6d12eb
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: tiledb
 Type: Package
-Version: 0.24.0.2
+Version: 0.24.0.3
 Title: Modern Database Engine for Multi-Modal Data via Sparse and Dense Multidimensional Arrays
 Authors@R: c(person("TileDB, Inc.", role = c("aut", "cph")),
  person("Dirk", "Eddelbuettel", email = "dirk@tiledb.com", role = "cre"))
@@ -25,8 +25,8 @@ SystemRequirements: A C++17 compiler is required, and for macOS
  available at GitHub and are used if no TileDB installation is
  detected, and no other option to build or download was specified by
  the user.
-Imports: methods, Rcpp (>= 1.0.8), nanotime, spdl
-LinkingTo: Rcpp, RcppInt64
+Imports: methods, Rcpp (>= 1.0.8), nanotime, spdl, nanoarrow
+LinkingTo: Rcpp, RcppInt64, nanoarrow
 Suggests: tinytest, simplermarkdown, curl, bit64, Matrix, palmerpenguins, nycflights13, data.table, tibble, arrow
 VignetteBuilder: simplermarkdown
 Roxygen: list(markdown = TRUE)

diff --git a/NAMESPACE b/NAMESPACE
@@ -386,6 +386,7 @@ importFrom(methods,setGeneric)
 importFrom(methods,setMethod)
 importFrom(methods,slot)
 importFrom(methods,validObject)
+importFrom(nanoarrow,as_nanoarrow_array)
 importFrom(spdl,set_level)
 importFrom(stats,na.omit)
 importFrom(utils,head)

diff --git a/NEWS.md b/NEWS.md
@@ -2,9 +2,13 @@
 
 * This release of the R package builds against [TileDB 2.20.1](https://github.com/TileDB-Inc/TileDB/releases/tag/2.20.1), and has also been tested against earlier releases as well as the development version (#661)
 
+## Improvements
+
+* The vendored [nanoarrow](https://github.com/apache/arrow-nanoarrow) sources have been update to release 0.4.0, and use of its facilities has been extended (#663)
+
 ## Bug Fixes
 
-* The `tiledb_get_query_range_var()` accessor now correctly calls the range getter for variable-sized dimensions. (#662)
+* The `tiledb_get_query_range_var()` accessor now correctly calls the range getter for variable-sized dimensions (#662)
 
 
 # tiledb 0.24.0

diff --git a/R/ArrowIO.R b/R/ArrowIO.R
@@ -1,6 +1,6 @@
 #  MIT License
 #
-#  Copyright (c) 2017-2023 TileDB Inc.
+#  Copyright (c) 2017-2024 TileDB Inc.
 #
 #  Permission is hereby granted, free of charge, to any person obtaining a copy
 #  of this software and associated documentation files (the "Software"), to deal
@@ -85,22 +85,6 @@ tiledb_arrow_schema_del <- function(ptr) {
     .delete_arrow_schema_from_xptr(ptr)
 }
 
-##' @noRd
-.check_arrow_pointers <- function(arrlst) {
-    stopifnot("First argument must be an external pointer to ArrowArray" = check_arrow_array_tag(arrlst[[1]]),
-              "Second argument must be an external pointer to ArrowSchema" = check_arrow_schema_tag(arrlst[[2]]))
-}
-
-##' @noRd
-.as_arrow_table <- function(arrlst) {
-    .check_arrow_pointers(arrlst)
-    if (!requireNamespace("arrow", quietly=TRUE)) {
-        stop("This functionality requires the 'arrow' package to be installed.", call. = FALSE)
-    } else {
-        arrow::as_arrow_table(arrow::RecordBatch$import_from_c(arrlst[[1]], arrlst[[2]]))
-    }
-}
-
 ##' @noRd
 .tiledb_set_arrow_config <- function(ctx = tiledb_get_context()) {
     cfg <- tiledb_config()        # for var-num columns such as char we need these

diff --git a/R/TileDBArray.R b/R/TileDBArray.R
@@ -508,6 +508,7 @@ setValidity("tiledb_array", function(object) {
 #' @param drop Optional logical switch to drop dimensions, default FALSE, currently unused.
 #' @return The resulting elements in the selected format
 #' @import nanotime
+#' @importFrom nanoarrow as_nanoarrow_array
 #' @aliases [,tiledb_array
 #' @aliases [,tiledb_array-method
 #' @aliases [,tiledb_array,ANY,tiledb_array-method
@@ -552,6 +553,9 @@ setMethod("[", "tiledb_array",
            x@return_as, "' to be installed.", call. = FALSE)
 
   use_arrow <- x@return_as == "arrow"
+  if (use_arrow) {
+     suppressMessages(do.call(rawToChar(as.raw(c(0x72, 0x65, 0x71, 0x75, 0x69, 0x72, 0x65))), list("nanoarrow")))
+  }
 
   dims <- tiledb::dimensions(dom)
   ndims <- length(dims)
@@ -941,8 +945,10 @@ setMethod("[", "tiledb_array",
           if (status != "COMPLETE") spdl::debug("['['] query returned '{}'.", status)
 
           if (use_arrow) {
-              rl <- libtiledb_to_arrow(abptr, qryptr, dictionaries)
-              at <- .as_arrow_table(rl)
+              ## rl <- libtiledb_to_arrow(abptr, qryptr, dictionaries)
+              ## at <- .as_arrow_table(rl)
+              na <- libtiledb_to_arrow(abptr, qryptr, dictionaries)
+              at <- arrow::as_arrow_table(na)
 
               ## special case from schema evolution could have added twice so correcting
               for (n in colnames(at)) {

diff --git a/inst/include/tiledb.h b/inst/include/tiledb.h
@@ -69,6 +69,8 @@ typedef struct query_buffer query_buf_t;
 // map from buffer names to shared_ptr to column_buffer
 typedef std::unordered_map<std::string, std::shared_ptr<tiledb::ColumnBuffer>> map_to_col_buf_t;
 
+// some lipstick on the pig that is a SEXP -- allow the nanoarrow ArrowArray XPtr be typedef'ed
+typedef SEXP nanoarrowXPtr;
 
 // C++ compiler complains about missing delete functionality when we use tiledb_vfs_fh_t directly
 struct vfs_fh {

diff --git a/inst/tinytest/test_timetravel.R b/inst/tinytest/test_timetravel.R
@@ -56,9 +56,8 @@ while (deltat < 30) {
         isTRUE(all.equal(NROW(res5), 20)) && 		            # expects 2 groups, 2 and 3, with 20 obs
         isTRUE(all.equal(min(res5$grp), 2)) &&
         isTRUE(all.equal(max(res5$grp), 3))) {
-        if (Sys.getenv("CI") != "") message("Success with gap time of ", deltat)
-        success <- TRUE
-        break
+           success <- TRUE
+           break
     }
     deltat <- deltat * 5
 }

diff --git a/src/RcppExports.cpp b/src/RcppExports.cpp
@@ -115,7 +115,7 @@ BEGIN_RCPP
 END_RCPP
 }
 // libtiledb_to_arrow
-Rcpp::List libtiledb_to_arrow(Rcpp::XPtr<tiledb::ArrayBuffers> ab, Rcpp::XPtr<tiledb::Query> qry, Rcpp::List dicts);
+nanoarrowXPtr libtiledb_to_arrow(Rcpp::XPtr<tiledb::ArrayBuffers> ab, Rcpp::XPtr<tiledb::Query> qry, Rcpp::List dicts);
 RcppExport SEXP _tiledb_libtiledb_to_arrow(SEXP abSEXP, SEXP qrySEXP, SEXP dictsSEXP) {
 BEGIN_RCPP
     Rcpp::RObject rcpp_result_gen;

diff --git a/src/arrowio.cpp b/src/arrowio.cpp
@@ -22,7 +22,8 @@
 
 #include "libtiledb.h"
 #include "tiledb_version.h"
-#include <nanoarrow.h>          // for C interface to Arrow
+#include "nanoarrow/r.h"
+//#include <nanoarrow.h>          // for C interface to Arrow
 
 //#include <tiledb/arrowio>
 #include "tiledb_arrowio.h"
@@ -253,7 +254,7 @@ inline void registerXptrFinalizer(SEXP s, R_CFinalizer_t f, bool onexit = true)
     R_RegisterCFinalizerEx(s, f, onexit ? TRUE : FALSE);
 }
 extern "C" {
-    void ArrowArrayRelease(struct ArrowArray *array); 		// made non-static in nanoarrow.c
+    void ArrowArrayReleaseInternal(struct ArrowArray *array); 		// made non-static in nanoarrow.c
     ArrowErrorCode ArrowArraySetStorageType(struct ArrowArray* array,	// ditto
                                             enum ArrowType storage_type);
     ArrowErrorCode localArrowSchemaSetType(struct ArrowSchema* schema, enum ArrowType type);
@@ -303,7 +304,7 @@ Rcpp::XPtr<ArrowArray> array_setup_struct(Rcpp::XPtr<ArrowArray> arrxp, int64_t
     array->buffers = NULL;
     array->children = NULL;
     array->dictionary = NULL;
-    array->release = &ArrowArrayRelease;
+    array->release = &ArrowArrayReleaseInternal;
     array->private_data = NULL;
 
     auto private_data = (struct ArrowArrayPrivateData*) ArrowMalloc(sizeof(struct ArrowArrayPrivateData));
@@ -353,26 +354,44 @@ Rcpp::XPtr<ArrowArray> array_setup_struct(Rcpp::XPtr<ArrowArray> arrxp, int64_t
     return arrxp;
 }
 
+inline void exitIfError(const ArrowErrorCode ec, const std::string& msg) {
+    if (ec != NANOARROW_OK) Rcpp::stop(msg);
+}
+
+// Attaches a schema to an array external pointer. The nanoarrow R package
+// attempts to do this whenever possible to avoid misinterpreting arrays.
+void array_xptr_set_schema(SEXP array_xptr, SEXP schema_xptr) {
+    R_SetExternalPtrTag(array_xptr, schema_xptr);
+}
 
+//  was: Rcpp::List
 // [[Rcpp::export]]
-Rcpp::List libtiledb_to_arrow(Rcpp::XPtr<tiledb::ArrayBuffers> ab,
-                              Rcpp::XPtr<tiledb::Query> qry,
-                              Rcpp::List dicts) {
+nanoarrowXPtr libtiledb_to_arrow(Rcpp::XPtr<tiledb::ArrayBuffers> ab,
+                                 Rcpp::XPtr<tiledb::Query> qry,
+                                 Rcpp::List dicts) {
     check_xptr_tag<tiledb::ArrayBuffers>(ab);
     check_xptr_tag<tiledb::Query>(qry);
     std::vector<std::string> names = ab->names();
     auto ncol = names.size();
     std::vector<std::string> dictnames = dicts.names();
-    Rcpp::XPtr<ArrowSchema> schemaxp = schema_owning_xptr();
-    Rcpp::XPtr<ArrowArray> arrayxp = array_owning_xptr();
-    schemaxp = schema_setup_struct(schemaxp, ncol);
-    arrayxp = array_setup_struct(arrayxp, ncol);
 
-    arrayxp->length = 0;
+    // Schema first
+    auto schemaxp = nanoarrow_schema_owning_xptr();
+    auto sch = nanoarrow_output_schema_from_xptr(schemaxp);
+    exitIfError(ArrowSchemaInitFromType(sch, NANOARROW_TYPE_STRUCT), "Bad schema init");
+    exitIfError(ArrowSchemaSetName(sch, ""), "Bad schema name");
+    exitIfError(ArrowSchemaAllocateChildren(sch, ncol), "Bad schema children alloc");
+
+    // Array second
+    auto arrayxp = nanoarrow_array_owning_xptr();
+    auto arr = nanoarrow_output_array_from_xptr(arrayxp);
+    exitIfError(ArrowArrayInitFromType(arr, NANOARROW_TYPE_STRUCT), "Bad array init");
+    exitIfError(ArrowArrayAllocateChildren(arr, ncol), "Bad array children alloc");
+
+    struct ArrowError ec;
+
+    arr->length = 0;
     for (size_t i=0; i<ncol; i++) {
-        // this allocates, and properly wraps as external pointers controlling lifetime
-        Rcpp::XPtr<ArrowSchema> chldschemaxp = schema_owning_xptr();
-        Rcpp::XPtr<ArrowArray> chldarrayxp = array_owning_xptr();
         bool is_factor = dicts[i] != R_NilValue;
         bool is_ordered = false;
         if (is_factor) {
@@ -390,62 +409,51 @@ Rcpp::List libtiledb_to_arrow(Rcpp::XPtr<tiledb::ArrayBuffers> ab,
 
         spdl::info(tfm::format("[libtiledb_to_arrow] Incoming name %s length %d",
                                std::string(pp.second->name), pp.first->length));
-        memcpy((void*) chldschemaxp, pp.second.get(), sizeof(ArrowSchema));
-        memcpy((void*) chldarrayxp, pp.first.get(), sizeof(ArrowArray));
-        if (is_factor) {
-            // this could be rewritten if we generalized ColumnBuffer to allow passing of
+        memcpy((void*) sch->children[i], pp.second.get(), sizeof(ArrowSchema));
+        memcpy((void*) arr->children[i], pp.first.get(), sizeof(ArrowArray));
+        if (is_factor) {        // create an arrow array of type string with the labels
+            // this could be rewritten if we generalized ColumnBuffer to allow passing of strings
             std::vector<std::string> svec = Rcpp::as<std::vector<std::string>>(dicts[i]);
-            Rcpp::XPtr<ArrowSchema> dschxp = schema_owning_xptr();
-            Rcpp::XPtr<ArrowArray> darrxp = array_owning_xptr();
-            dschxp = schema_setup_struct(dschxp, 0);
-            darrxp = array_setup_struct(darrxp, 0);
-
-            dschxp->format = "u";
-            dschxp->flags |= ARROW_FLAG_NULLABLE;
+            auto darrxp = nanoarrow_array_owning_xptr();
+            auto darr = nanoarrow_output_array_from_xptr(darrxp);
+            exitIfError(ArrowArrayInitFromType(darr, NANOARROW_TYPE_STRING), "Bad string array init");
+            exitIfError(ArrowArrayStartAppending(darr), "Bad string array append init");
+            auto dschxp = nanoarrow_schema_owning_xptr();
+            auto dsch = nanoarrow_output_schema_from_xptr(dschxp);
+            exitIfError(ArrowSchemaInitFromType(dsch, NANOARROW_TYPE_STRING), "Bad string schema init");
+            exitIfError(ArrowSchemaSetName(dsch, ""), "Bad string schema name");
             if (is_ordered) {
-                dschxp->flags |= ARROW_FLAG_DICTIONARY_ORDERED; // this line appears ignore
-                chldschemaxp->flags |= ARROW_FLAG_DICTIONARY_ORDERED; // this one matters more
+                dsch->flags |= ARROW_FLAG_DICTIONARY_ORDERED; // this line appears ignore
+                sch->children[i]->flags |= ARROW_FLAG_DICTIONARY_ORDERED; // this one matters more
             }
-            darrxp->length = svec.size();
-            darrxp->null_count = 0;
-            darrxp->n_buffers = 3; // we always have three for dictionairies
-            darrxp->buffers = (const void**)malloc(sizeof(void*) * darrxp->n_buffers);
-            darrxp->buffers[0] = nullptr;  // validity
-
-            size_t nv = svec.size();
-            std::string str = "";
-            std::vector<int32_t> offsets(nv+1);
-            int32_t cumlen = 0;
-            for (size_t i = 0; i < nv; i++) {
-                std::string s = svec[i];
-                offsets[i] = cumlen;
-                str += s;
-                cumlen += s.length();
+            for (auto str: svec) {
+                ArrowStringView asv = {str.data(), static_cast<int64_t>(str.size())};
+                exitIfError(ArrowArrayAppendString(darr, asv), "Bad string append");
             }
-            offsets[nv] = cumlen;
-            darrxp->buffers[2] = (const char*)malloc(sizeof(char) * cumlen);
-            std::memcpy((void*) darrxp->buffers[2], str.data(), (sizeof(char) * cumlen));
-            darrxp->buffers[1] = (const char*)malloc(sizeof(int32_t) * (nv + 1));
-            std::memcpy((void*) darrxp->buffers[1], offsets.data(), (sizeof(int32_t) * (nv + 1)));
-
-            spdl::debug(tfm::format("[libtiledb_to_arrow] dict %s fmt %s -- len %d nbuf %d str %s",
-                                    names[i], dschxp->format, darrxp->length, darrxp->n_buffers, str));
-            chldschemaxp->dictionary = dschxp;
-            chldarrayxp->dictionary = darrxp;
-        }
+            if (NANOARROW_OK != ArrowArrayFinishBuildingDefault(darr, &ec))
+                Rcpp::stop(ec.message);
 
-        schemaxp->children[i] = chldschemaxp;
-        arrayxp->children[i] = chldarrayxp;
+            spdl::debug(tfm::format("[libtiledb_to_arrow] dict %s fmt %s -- len %d nbuf %d",
+                                    names[i], dsch->format, darr->length, darr->n_buffers));
+            sch->children[i]->dictionary = dsch;
+            arr->children[i]->dictionary = darr;
+        }
 
-        if (pp.first->length > arrayxp->length) {
-            spdl::debug(tfm::format("[libtiledb_to_arrow] Setting array length to %d", pp.first->length));
-            arrayxp->length = pp.first->length;
+        if (pp.first->length > arr->length) {
+           spdl::debug(tfm::format("[libtiledb_to_arrow] Setting array length to %d", pp.first->length));
+           arr->length = pp.first->length;
         }
     }
-    Rcpp::List as = Rcpp::List::create(Rcpp::Named("array_data") = arrayxp,
-                                       Rcpp::Named("schema") = schemaxp);
+    spdl::info("[libtiledb_to_arrow] After children loop");
+    //if (NANOARROW_OK != ArrowArrayFinishBuildingDefault(arr, &ec))
+    //    Rcpp::stop(ec.message);
+    spdl::info("[libtiledb_to_arrow] ArrowArrayFinishBuildingDefault");
+
+    // Nanoarrow special: stick schema into xptr tag to return single SEXP
+    array_xptr_set_schema(arrayxp, schemaxp); 			// embed schema in array
+
     spdl::trace("[libtiledb_to_arrow] returning from libtiledb_to_arrow");
-    return as;
+    return arrayxp;
 }
 
 

diff --git a/src/libtiledb.h b/src/libtiledb.h
@@ -112,7 +112,6 @@ const tiledb_xptr_object tiledb_xptr_map_to_col_buf_t            { 230 };
 const tiledb_xptr_object tiledb_arrow_array_t                    { 300 };
 const tiledb_xptr_object tiledb_arrow_schema_t                   { 310 };
 
-
 // templated checkers for external pointer tags
 template <typename T> const int32_t XPtrTagType                            = tiledb_xptr_default; // clang++ wants a value
 template <> inline const int32_t XPtrTagType<tiledb::Array>                = tiledb_xptr_object_array;