#include #include #include #include #include #include #include "common.h" namespace libtiledbcpp { using namespace tiledb; using namespace tiledbpy::common; namespace py = pybind11; void put_metadata_numpy(Group &group, const std::string &key, py::array value) { tiledb_datatype_t value_type; try { value_type = np_to_tdb_dtype(value.dtype()); } catch (const TileDBPyError &e) { throw py::type_error(e.what()); } if (value.ndim() != 1) throw py::type_error("Only 1D Numpy arrays can be stored as metadata"); py::size_t ncells = get_ncells(value.dtype()); // we can't store multi-cell arrays as metadata // e.g. an array of strings containing strings of more than one character if (ncells != 1 && value.size() > 1) throw py::type_error("Unsupported dtype '" + std::string(py::str(value.dtype())) + "' for metadata"); auto value_num = is_tdb_str(value_type) ? value.nbytes() : value.size(); group.put_metadata(key, value_type, value_num, value_num > 0 ? value.data() : nullptr); } void put_metadata(Group &group, const std::string &key, tiledb_datatype_t value_type, uint32_t value_num, py::buffer &value) { py::buffer_info info = value.request(); group.put_metadata(key, value_type, value_num, info.ptr); } bool has_metadata(Group &group, const std::string &key) { tiledb_datatype_t _unused_value_type; return group.has_metadata(key, &_unused_value_type); } std::string get_key_from_index(Group &group, uint64_t index) { std::string key; tiledb_datatype_t tdb_type; uint32_t value_num; const void *value; group.get_metadata_from_index(index, &key, &tdb_type, &value_num, &value); return key; } py::object unpack_metadata_val(tiledb_datatype_t value_type, uint32_t value_num, const char *value_ptr) { if (value_num == 0) throw TileDBError("internal error: unexpected value_num==0"); if (value_type == TILEDB_STRING_UTF8) { return value_ptr == nullptr ? py::str() : py::str(value_ptr, value_num); } if (value_type == TILEDB_BLOB || value_type == TILEDB_CHAR || value_type == TILEDB_STRING_ASCII) { return value_ptr == nullptr ? py::bytes() : py::bytes(value_ptr, value_num); } if (value_ptr == nullptr) return py::tuple(); py::tuple unpacked(value_num); for (uint32_t i = 0; i < value_num; i++) { switch (value_type) { case TILEDB_INT64: unpacked[i] = *((int64_t *)value_ptr); break; case TILEDB_FLOAT64: unpacked[i] = *((double *)value_ptr); break; case TILEDB_FLOAT32: unpacked[i] = *((float *)value_ptr); break; case TILEDB_INT32: unpacked[i] = *((int32_t *)value_ptr); break; case TILEDB_UINT32: unpacked[i] = *((uint32_t *)value_ptr); break; case TILEDB_UINT64: unpacked[i] = *((uint64_t *)value_ptr); break; case TILEDB_INT8: unpacked[i] = *((int8_t *)value_ptr); break; case TILEDB_UINT8: unpacked[i] = *((uint8_t *)value_ptr); break; case TILEDB_INT16: unpacked[i] = *((int16_t *)value_ptr); break; case TILEDB_UINT16: unpacked[i] = *((uint16_t *)value_ptr); break; default: throw TileDBError("TileDB datatype not supported"); } value_ptr += tiledb_datatype_size(value_type); } if (value_num > 1) return unpacked; // for single values, return the value directly return unpacked[0]; } py::array unpack_metadata_ndarray(tiledb_datatype_t value_type, uint32_t value_num, const char *value_ptr) { py::dtype dtype = tdb_to_np_dtype(value_type, 1); if (value_ptr == nullptr) { auto np = py::module::import("numpy"); return np.attr("empty")(py::make_tuple(0), dtype); } // special case for TILEDB_STRING_UTF8: TileDB assumes size=1 if (value_type != TILEDB_STRING_UTF8) { value_num *= tiledb_datatype_size(value_type); } auto buf = py::memoryview::from_memory(value_ptr, value_num); auto np = py::module::import("numpy"); return np.attr("frombuffer")(buf, dtype); } py::tuple get_metadata(Group &group, const py::str &key, bool is_ndarray) { tiledb_datatype_t tdb_type; uint32_t value_num; const char *value_ptr; group.get_metadata(key, &tdb_type, &value_num, (const void **)&value_ptr); if (is_ndarray) { auto arr = unpack_metadata_ndarray(tdb_type, value_num, value_ptr); return py::make_tuple(arr, tdb_type); } else { auto arr = unpack_metadata_val(tdb_type, value_num, value_ptr); return py::make_tuple(arr, tdb_type); } } bool has_member(Group &group, std::string obj) { try { group.member(obj); } catch (const TileDBError &e) { return false; } return true; } void init_group(py::module &m) { py::class_(m, "Group") .def( py::init(), py::keep_alive<1, 2>()) .def(py::init(), py::keep_alive<1, 2>()) .def("_open", &Group::open) .def("_set_config", &Group::set_config) .def("_config", &Group::config) .def("_close", [](Group &self) { self.close(true); }) .def_property_readonly("_isopen", &Group::is_open) .def_property_readonly("_uri", &Group::uri) .def_property_readonly("_query_type", &Group::query_type) .def("_put_metadata", put_metadata_numpy) .def("_put_metadata", put_metadata) .def("_delete_metadata", &Group::delete_metadata) .def("_has_metadata", has_metadata) .def("_metadata_num", &Group::metadata_num) .def("_get_metadata", get_metadata) .def("_get_key_from_index", get_key_from_index) .def("_add", &Group::add_member, py::arg("uri"), py::arg("relative") = false, py::arg("name") = std::nullopt #if TILEDB_VERSION_MAJOR >= 2 && TILEDB_VERSION_MINOR >= 27 , py::arg("type") = std::nullopt #endif ) .def("_remove", &Group::remove_member) .def("_delete_group", &Group::delete_group) .def("_member_count", &Group::member_count) .def("_member", static_cast(&Group::member)) .def("_member", static_cast(&Group::member)) .def("_has_member", has_member) .def("_is_relative", &Group::is_relative) .def("_dump", &Group::dump) /* static methods */ .def_static("_create", &Group::create) .def_static("_consolidate_metadata", &Group::consolidate_metadata, py::arg("ctx"), py::arg("uri"), py::arg("config") = (Config *)nullptr) .def_static("_vacuum_metadata", &Group::vacuum_metadata, py::arg("ctx"), py::arg("uri"), py::arg("config") = (Config *)nullptr); } } // namespace libtiledbcpp