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[r] Run clang-format on apis/r/src
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@johnkerl
johnkerl committed Sep 23, 2024
1 parent 0e046b7 commit 0fd2de9
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Showing 8 changed files with 875 additions and 584 deletions.
204 changes: 126 additions & 78 deletions apis/r/src/arrow.cpp
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Original file line number Diff line number Diff line change
@@ -1,43 +1,44 @@
#include <Rcpp/Lighter> // for R interface to C++
#include <nanoarrow/r.h> // for C/C++ interface to Arrow (via header exported from the R package)
#include <nanoarrow/nanoarrow.hpp> // for C/C++ interface to Arrow (vendored)
#include <RcppInt64> // for fromInteger64
#include <nanoarrow/r.h> // for C/C++ interface to Arrow (via header exported from the R package)
#include <Rcpp/Lighter> // for R interface to C++
#include <RcppInt64> // for fromInteger64
#include <nanoarrow/nanoarrow.hpp> // for C/C++ interface to Arrow (vendored)

#include <tiledbsoma/tiledbsoma>
#include <tiledbsoma/reindexer/reindexer.h>
#include <tiledbsoma/tiledbsoma>

#include "rutilities.h" // local declarations
#include "xptr-utils.h" // xptr taggging utilities
#include "rutilities.h" // local declarations
#include "xptr-utils.h" // xptr taggging utilities

namespace tdbs = tiledbsoma;

void _show_content(const nanoarrow::UniqueArray& ap, const nanoarrow::UniqueSchema& sp) {
void _show_content(
const nanoarrow::UniqueArray& ap, const nanoarrow::UniqueSchema& sp) {
int n = sp.get()->n_children;
ArrowError ec;
for (auto i=0; i<n; i++) {
for (auto i = 0; i < n; i++) {
Rcpp::Rcout << " " << sp.get()->children[i]->name << " : ";

nanoarrow::UniqueArrayView col;
ArrowArrayViewInitFromSchema(col.get(), sp.get()->children[i], &ec);
ArrowArrayViewSetArray(col.get(), ap.get()->children[i], &ec);

int m = col.get()->length;
for (auto j=0; j<m; j++)
for (auto j = 0; j < m; j++)
Rcpp::Rcout << ArrowArrayViewGetDoubleUnsafe(col.get(), j) << " ";
Rcpp::Rcout << std::endl;
}
}

// [[Rcpp::export]]
Rcpp::XPtr<somactx_wrap_t> createSOMAContext(Rcpp::Nullable<Rcpp::CharacterVector> config = R_NilValue) {

Rcpp::XPtr<somactx_wrap_t> createSOMAContext(
Rcpp::Nullable<Rcpp::CharacterVector> config = R_NilValue) {
// if we hae a config, use it
std::shared_ptr<tdbs::SOMAContext> somactx;
if (config.isNotNull()) {
std::map<std::string, std::string> smap;
auto config_vec = config.as();
auto config_names = Rcpp::as<Rcpp::CharacterVector>(config_vec.names());
for (auto &name : config_names) {
for (auto& name : config_names) {
std::string param = Rcpp::as<std::string>(name);
std::string value = Rcpp::as<std::string>(config_vec[param]);
smap[param] = value;
Expand All @@ -52,24 +53,30 @@ Rcpp::XPtr<somactx_wrap_t> createSOMAContext(Rcpp::Nullable<Rcpp::CharacterVecto
return xp;
}


// ctx_wrap_t* ctxwrap_p = new ContextWrapper(ctxptr);
// Rcpp::XPtr<ctx_wrap_t> ctx_wrap_xptr = make_xptr<ctx_wrap_t>(ctxwrap_p, false);
// Rcpp::XPtr<ctx_wrap_t> ctx_wrap_xptr = make_xptr<ctx_wrap_t>(ctxwrap_p,
// false);

// [[Rcpp::export]]
void createSchemaFromArrow(const std::string& uri, naxpSchema nasp, naxpArray nadimap, naxpSchema nadimsp,
bool sparse, std::string datatype, Rcpp::List pclst, Rcpp::XPtr<somactx_wrap_t> ctxxp,
Rcpp::Nullable<Rcpp::DatetimeVector> tsvec = R_NilValue) {

//struct ArrowArray* ap = (struct ArrowArray*) R_ExternalPtrAddr(naap);
//struct ArrowSchema* sp = (struct ArrowSchema*) R_ExternalPtrAddr(nasp);
void createSchemaFromArrow(
const std::string& uri,
naxpSchema nasp,
naxpArray nadimap,
naxpSchema nadimsp,
bool sparse,
std::string datatype,
Rcpp::List pclst,
Rcpp::XPtr<somactx_wrap_t> ctxxp,
Rcpp::Nullable<Rcpp::DatetimeVector> tsvec = R_NilValue) {
// struct ArrowArray* ap = (struct ArrowArray*) R_ExternalPtrAddr(naap);
// struct ArrowSchema* sp = (struct ArrowSchema*) R_ExternalPtrAddr(nasp);
//
// or
// auto ap = nanoarrow_array_from_xptr(naap);
// auto sp = nanoarrow_schema_from_xptr(nasp);
// or
// auto ap = nanoarrow_array_from_xptr(naap);
// auto sp = nanoarrow_schema_from_xptr(nasp);
//
// or:
//nanoarrow::UniqueArray ap{nanoarrow_array_from_xptr(naap)};
// or:
// nanoarrow::UniqueArray ap{nanoarrow_array_from_xptr(naap)};
nanoarrow::UniqueSchema sp{nanoarrow_schema_from_xptr(nasp)};
//_show_content(ap, sp);
nanoarrow::UniqueArray apdim{nanoarrow_array_from_xptr(nadimap)};
Expand All @@ -85,19 +92,22 @@ void createSchemaFromArrow(const std::string& uri, naxpSchema nasp, naxpArray na
apdim.move(dimarr.get());

tdbs::PlatformConfig pltcfg;
pltcfg.dataframe_dim_zstd_level = Rcpp::as<int>(pclst["dataframe_dim_zstd_level"]);
pltcfg.sparse_nd_array_dim_zstd_level = Rcpp::as<int>(pclst["sparse_nd_array_dim_zstd_level"]);
pltcfg.dense_nd_array_dim_zstd_level = Rcpp::as<int>(pclst["dense_nd_array_dim_zstd_level"]);
pltcfg.write_X_chunked = Rcpp::as<bool>(pclst["write_X_chunked"]);
pltcfg.goal_chunk_nnz = Rcpp::as<double>(pclst["goal_chunk_nnz"]);
pltcfg.capacity = Rcpp::as<double>(pclst["capacity"]);
pltcfg.offsets_filters = Rcpp::as<std::string>(pclst["offsets_filters"]);
pltcfg.validity_filters = Rcpp::as<std::string>(pclst["validity_filters"]);
pltcfg.allows_duplicates = Rcpp::as<bool>(pclst["allows_duplicates"]);
pltcfg.cell_order = Rcpp::as<std::string>(pclst["cell_order"]);
pltcfg.tile_order = Rcpp::as<std::string>(pclst["tile_order"]);
pltcfg.attrs = Rcpp::as<std::string>(pclst["attrs"]);
pltcfg.dims = Rcpp::as<std::string>(pclst["dims"]);
pltcfg.dataframe_dim_zstd_level = Rcpp::as<int>(
pclst["dataframe_dim_zstd_level"]);
pltcfg.sparse_nd_array_dim_zstd_level = Rcpp::as<int>(
pclst["sparse_nd_array_dim_zstd_level"]);
pltcfg.dense_nd_array_dim_zstd_level = Rcpp::as<int>(
pclst["dense_nd_array_dim_zstd_level"]);
pltcfg.write_X_chunked = Rcpp::as<bool>(pclst["write_X_chunked"]);
pltcfg.goal_chunk_nnz = Rcpp::as<double>(pclst["goal_chunk_nnz"]);
pltcfg.capacity = Rcpp::as<double>(pclst["capacity"]);
pltcfg.offsets_filters = Rcpp::as<std::string>(pclst["offsets_filters"]);
pltcfg.validity_filters = Rcpp::as<std::string>(pclst["validity_filters"]);
pltcfg.allows_duplicates = Rcpp::as<bool>(pclst["allows_duplicates"]);
pltcfg.cell_order = Rcpp::as<std::string>(pclst["cell_order"]);
pltcfg.tile_order = Rcpp::as<std::string>(pclst["tile_order"]);
pltcfg.attrs = Rcpp::as<std::string>(pclst["attrs"]);
pltcfg.dims = Rcpp::as<std::string>(pclst["dims"]);

// shared pointer to SOMAContext from external pointer wrapper
std::shared_ptr<tdbs::SOMAContext> sctx = ctxxp->ctxptr;
Expand All @@ -115,56 +125,72 @@ void createSchemaFromArrow(const std::string& uri, naxpSchema nasp, naxpArray na
} else if (datatype == "SOMADenseNDArray") {
exists = tdbs::SOMADenseNDArray::exists(uri, sctx);
} else {
Rcpp::stop(tfm::format("Error: Invalid SOMA type_argument '%s'", datatype));
Rcpp::stop(
tfm::format("Error: Invalid SOMA type_argument '%s'", datatype));
}

if (exists) {
Rcpp::stop(tfm::format("Error: Array '%s' already exists", uri));
}

if (datatype == "SOMADataFrame") {
tdbs::SOMADataFrame::create(uri, std::move(schema),
std::pair(std::move(dimarr), std::move(dimsch)),
sctx, pltcfg, tsrng);
tdbs::SOMADataFrame::create(
uri,
std::move(schema),
std::pair(std::move(dimarr), std::move(dimsch)),
sctx,
pltcfg,
tsrng);
} else if (datatype == "SOMASparseNDArray") {
// for arrays n_children will be three as we have two dims and a data col
std::string datacoltype = sp->children[sp->n_children-1]->format;
tdbs::SOMASparseNDArray::create(uri, datacoltype,
std::pair(std::move(dimarr), std::move(dimsch)),
sctx, pltcfg, tsrng);
// for arrays n_children will be three as we have two dims and a data
// col
std::string datacoltype = sp->children[sp->n_children - 1]->format;
tdbs::SOMASparseNDArray::create(
uri,
datacoltype,
std::pair(std::move(dimarr), std::move(dimsch)),
sctx,
pltcfg,
tsrng);
} else if (datatype == "SOMADenseNDArray") {
// for arrays n_children will be three as we have two dims and a data col
std::string datacoltype = sp->children[sp->n_children-1]->format;
tdbs::SOMADenseNDArray::create(uri, datacoltype,
std::pair(std::move(dimarr), std::move(dimsch)),
sctx, pltcfg, tsrng);
// for arrays n_children will be three as we have two dims and a data
// col
std::string datacoltype = sp->children[sp->n_children - 1]->format;
tdbs::SOMADenseNDArray::create(
uri,
datacoltype,
std::pair(std::move(dimarr), std::move(dimsch)),
sctx,
pltcfg,
tsrng);
} else {
Rcpp::stop(tfm::format("Error: Invalid SOMA type_argument '%s'", datatype));
Rcpp::stop(
tfm::format("Error: Invalid SOMA type_argument '%s'", datatype));
}

}


// [[Rcpp::export]]
void writeArrayFromArrow(const std::string& uri, naxpArray naap, naxpSchema nasp,
Rcpp::XPtr<somactx_wrap_t> ctxxp,
const std::string arraytype = "",
Rcpp::Nullable<Rcpp::CharacterVector> config = R_NilValue,
Rcpp::Nullable<Rcpp::DatetimeVector> tsvec = R_NilValue) {

//struct ArrowArray* ap = (struct ArrowArray*) R_ExternalPtrAddr(naap);
//struct ArrowSchema* sp = (struct ArrowSchema*) R_ExternalPtrAddr(nasp);
void writeArrayFromArrow(
const std::string& uri,
naxpArray naap,
naxpSchema nasp,
Rcpp::XPtr<somactx_wrap_t> ctxxp,
const std::string arraytype = "",
Rcpp::Nullable<Rcpp::CharacterVector> config = R_NilValue,
Rcpp::Nullable<Rcpp::DatetimeVector> tsvec = R_NilValue) {
// struct ArrowArray* ap = (struct ArrowArray*) R_ExternalPtrAddr(naap);
// struct ArrowSchema* sp = (struct ArrowSchema*) R_ExternalPtrAddr(nasp);
//
// or
// auto ap = nanoarrow_array_from_xptr(naap);
// auto sp = nanoarrow_schema_from_xptr(nasp);
// or
// auto ap = nanoarrow_array_from_xptr(naap);
// auto sp = nanoarrow_schema_from_xptr(nasp);
//
// or:
// or:
nanoarrow::UniqueArray ap{nanoarrow_array_from_xptr(naap)};
nanoarrow::UniqueSchema sp{nanoarrow_schema_from_xptr(nasp)};

// now move nanoarrow unique arrays (created from objects handed from R) into
// proper unique pointers to arrow schema and array
// now move nanoarrow unique arrays (created from objects handed from R)
// into proper unique pointers to arrow schema and array
auto schema = std::make_unique<ArrowSchema>();
sp.move(schema.get());
auto array = std::make_unique<ArrowArray>();
Expand All @@ -180,8 +206,9 @@ void writeArrayFromArrow(const std::string& uri, naxpArray naap, naxpSchema nasp
// if (config.isNotNull()) {
// std::map<std::string, std::string> smap;
// auto config_vec = config.as();
// auto config_names = Rcpp::as<Rcpp::CharacterVector>(config_vec.names());
// for (auto &name : config_names) {
// auto config_names =
// Rcpp::as<Rcpp::CharacterVector>(config_vec.names()); for (auto &name
// : config_names) {
// std::string param = Rcpp::as<std::string>(name);
// std::string value = Rcpp::as<std::string>(config_vec[param]);
// smap[param] = value;
Expand All @@ -196,14 +223,35 @@ void writeArrayFromArrow(const std::string& uri, naxpArray naap, naxpSchema nasp

std::shared_ptr<tdbs::SOMAArray> arrup;
if (arraytype == "SOMADataFrame") {
arrup = tdbs::SOMADataFrame::open(OpenMode::write, uri, somactx, "unnamed", {},
"auto", ResultOrder::automatic, tsrng);
arrup = tdbs::SOMADataFrame::open(
OpenMode::write,
uri,
somactx,
"unnamed",
{},
"auto",
ResultOrder::automatic,
tsrng);
} else if (arraytype == "SOMADenseNDArray") {
arrup = tdbs::SOMADenseNDArray::open(OpenMode::write, uri, somactx, "unnamed", {},
"auto", ResultOrder::colmajor, tsrng);
arrup = tdbs::SOMADenseNDArray::open(
OpenMode::write,
uri,
somactx,
"unnamed",
{},
"auto",
ResultOrder::colmajor,
tsrng);
} else if (arraytype == "SOMASparseNDArray") {
arrup = tdbs::SOMASparseNDArray::open(OpenMode::write, uri, somactx, "unnamed", {},
"auto", ResultOrder::automatic, tsrng);
arrup = tdbs::SOMASparseNDArray::open(
OpenMode::write,
uri,
somactx,
"unnamed",
{},
"auto",
ResultOrder::automatic,
tsrng);
} else { // not reached
Rcpp::stop(tfm::format("Unexpected array type '%s'", arraytype));
}
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