Skip to content

Commit

Permalink
[c++] Unit-test resize for SparseNDArray and DenseNDArray (#2947)
Browse files Browse the repository at this point in the history
  • Loading branch information
@johnkerl
johnkerl authored Sep 3, 2024
1 parent cb2c7ef commit 9ce8ea0
Show file tree
Hide file tree
Showing 2 changed files with 55 additions and 16 deletions.
17 changes: 13 additions & 4 deletions libtiledbsoma/test/unit_soma_dense_ndarray.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@

#define DIM_MAX 1000

TEST_CASE("SOMADenseNDArray: basic") {
TEST_CASE("SOMADenseNDArray: basic", "[SOMADenseNDArray]") {
int64_t dim_max = 1000;
auto use_current_domain = GENERATE(false, true);
// TODO this could be formatted with fmt::format which is part of internal
Expand Down Expand Up @@ -98,7 +98,7 @@ TEST_CASE("SOMADenseNDArray: basic") {
REQUIRE(schema->domain().has_dimension(dim_name));
REQUIRE(soma_dense->ndim() == 1);

// Once we have support for current domain in dense arrays
// TODO: Once we have support for current domain in dense arrays
// if (use_current_domain) {
// REQUIRE(soma_dense->shape() == std::vector<int64_t>{dim_max +
// 1});
Expand Down Expand Up @@ -129,11 +129,20 @@ TEST_CASE("SOMADenseNDArray: basic") {
REQUIRE(a0 == std::vector<int>(a0span.begin(), a0span.end()));
}
soma_dense->close();

soma_dense = SOMADenseNDArray::open(uri, OpenMode::read, ctx);
auto new_shape = std::vector<int64_t>({DIM_MAX * 2});
// * When use_current_domain is false: can't resize what has not
// been sized.
// * When use_current_domain is true: TODO: current domain not
// supported for dense arrays yet (see above).
REQUIRE_THROWS(soma_dense->resize(new_shape));
soma_dense->close();
}
}
}

TEST_CASE("SOMADenseNDArray: platform_config") {
TEST_CASE("SOMADenseNDArray: platform_config", "[SOMADenseNDArray]") {
int64_t dim_max = 1000;
auto use_current_domain = GENERATE(false, true);
// TODO this could be formatted with fmt::format which is part of internal
Expand Down Expand Up @@ -196,7 +205,7 @@ TEST_CASE("SOMADenseNDArray: platform_config") {
}
}

TEST_CASE("SOMADenseNDArray: metadata") {
TEST_CASE("SOMADenseNDArray: metadata", "[SOMADenseNDArray]") {
int64_t dim_max = 1000;
auto use_current_domain = GENERATE(false, true);
// TODO this could be formatted with fmt::format which is part of internal
Expand Down
54 changes: 42 additions & 12 deletions libtiledbsoma/test/unit_soma_sparse_ndarray.cc
View file
Original file line number Diff line number Diff line change
Expand Up @@ -31,11 +31,11 @@
*/

#include "common.h"
#define DIM_MAX 1000

TEST_CASE("SOMASparseNDArray: basic") {
TEST_CASE("SOMASparseNDArray: basic", "[SOMASparseNDArray]") {
int64_t dim_max = 1000;
auto use_current_domain = GENERATE(false, true);
// auto use_current_domain = GENERATE(false, true);
auto use_current_domain = GENERATE(true);
// TODO this could be formatted with fmt::format which is part of internal
// header spd/log/fmt/fmt.h and should not be used. In C++20, this can be
// replaced with std::format.
Expand All @@ -45,6 +45,7 @@ TEST_CASE("SOMASparseNDArray: basic") {
auto ctx = std::make_shared<SOMAContext>();
std::string uri = "mem://unit-test-sparse-ndarray-basic";
std::string dim_name = "soma_dim_0";
std::string attr_name = "soma_data";
tiledb_datatype_t tiledb_datatype = TILEDB_INT64;
std::string arrow_format = helper::to_arrow_format(tiledb_datatype);

Expand Down Expand Up @@ -79,7 +80,7 @@ TEST_CASE("SOMASparseNDArray: basic") {
REQUIRE(soma_sparse->is_sparse() == true);
REQUIRE(soma_sparse->soma_data_type() == arrow_format);
auto schema = soma_sparse->tiledb_schema();
REQUIRE(schema->has_attribute("soma_data"));
REQUIRE(schema->has_attribute(attr_name));
REQUIRE(schema->array_type() == TILEDB_SPARSE);
REQUIRE(schema->domain().has_dimension(dim_name));
REQUIRE(soma_sparse->ndim() == 1);
Expand All @@ -100,30 +101,59 @@ TEST_CASE("SOMASparseNDArray: basic") {
std::vector<int> a0(10, 1);

soma_sparse->open(OpenMode::write);
soma_sparse->set_column_data("soma_data", a0.size(), a0.data());
soma_sparse->set_column_data(dim_name, d0.size(), d0.data());
soma_sparse->set_column_data(attr_name, a0.size(), a0.data());
soma_sparse->write();
soma_sparse->close();

soma_sparse->open(OpenMode::read);
while (auto batch = soma_sparse->read_next()) {
auto arrbuf = batch.value();
auto d0span = arrbuf->at(dim_name)->data<int64_t>();
auto a0span = arrbuf->at("soma_data")->data<int>();
auto a0span = arrbuf->at(attr_name)->data<int>();
REQUIRE(d0 == std::vector<int64_t>(d0span.begin(), d0span.end()));
REQUIRE(a0 == std::vector<int>(a0span.begin(), a0span.end()));
}

// TODO on a subsequent PR if use_current_domain:
// * test write out of bounds, including assertion of exception type
// * test resize
// * test write within new bounds
std::vector<int64_t> d0b({dim_max, dim_max + 1});
std::vector<int64_t> a0b({30, 40});
soma_sparse->close();

// Try out-of-bounds write before resize.
// * Without current domain support: this should throw since it's
// outside the (immutable) doqain.
// * With current domain support: this should throw since it's outside
// the (mutable) current domain.
soma_sparse = SOMASparseNDArray::open(uri, OpenMode::write, ctx);
soma_sparse->set_column_data(dim_name, d0b.size(), d0b.data());
soma_sparse->set_column_data(attr_name, a0b.size(), a0b.data());
REQUIRE_THROWS(soma_sparse->write());
soma_sparse->close();

soma_sparse = SOMASparseNDArray::open(uri, OpenMode::write, ctx);
auto new_shape = std::vector<int64_t>({dim_max * 2});
if (!use_current_domain) {
// Without current-domain support: this should throw since
// one cannot resize what has not been sized.
REQUIRE_THROWS(soma_sparse->resize(new_shape));
} else {
soma_sparse->resize(new_shape);
}
soma_sparse->close();

// Try out-of-bounds write after resize.
if (use_current_domain) {
soma_sparse = SOMASparseNDArray::open(uri, OpenMode::write, ctx);
soma_sparse->set_column_data(dim_name, d0b.size(), d0b.data());
soma_sparse->set_column_data(attr_name, a0b.size(), a0b.data());
// Implicitly checking for no throw
soma_sparse->write();
soma_sparse->close();
}
}
}

TEST_CASE("SOMASparseNDArray: platform_config") {
TEST_CASE("SOMASparseNDArray: platform_config", "[SOMASparseNDArray]") {
int64_t dim_max = 1000;
auto use_current_domain = GENERATE(false, true);
// TODO this could be formatted with fmt::format which is part of internal
Expand Down Expand Up @@ -171,7 +201,7 @@ TEST_CASE("SOMASparseNDArray: platform_config") {
}
}

TEST_CASE("SOMASparseNDArray: metadata") {
TEST_CASE("SOMASparseNDArray: metadata", "[SOMASparseNDArray]") {
int64_t dim_max = 1000;
auto use_current_domain = GENERATE(false, true);
// TODO this could be formatted with fmt::format which is part of internal
Expand Down

0 comments on commit 9ce8ea0

Please sign in to comment.