#include // for enums #include // C++ #include "common.h" #include #include #include #include namespace libtiledbcpp { using namespace tiledb; namespace py = pybind11; void init_array(py::module &m) { py::class_(m, "Array") //.def(py::init()) .def( py::init(), py::keep_alive<1, 2>() /* Array keeps Context alive */) // Temporary initializer while Array is converted from Cython to PyBind. .def(py::init([](const Context &ctx, py::object array) { tiledb_array_t *c_array = (py::capsule)array.attr("__capsule__")(); return std::make_unique(ctx, c_array, false); }), py::keep_alive<1, 2>(), py::keep_alive<1, 3>()) // TODO capsule Array(const Context& ctx, tiledb_array_t* carray, // tiledb_config_t* config) .def("is_open", &Array::is_open) .def("uri", &Array::uri) .def("schema", &Array::schema) //.def("ptr", [](Array& arr){ return py::capsule(arr.ptr()); } ) .def("open", (void(Array::*)(tiledb_query_type_t)) & Array::open) .def("reopen", &Array::reopen) .def("set_open_timestamp_start", &Array::set_open_timestamp_start) .def("set_open_timestamp_end", &Array::set_open_timestamp_end) .def_property_readonly("open_timestamp_start", &Array::open_timestamp_start) .def_property_readonly("open_timestamp_end", &Array::open_timestamp_end) .def("set_config", &Array::set_config) .def("config", &Array::config) .def("close", &Array::close) .def("consolidate", [](Array &self, const Context &ctx, Config *config) { if (self.query_type() == TILEDB_READ) { throw TileDBError("cannot consolidate array opened in readonly " "mode (mode='r')"); } Array::consolidate(ctx, self.uri(), config); }) .def("consolidate", [](Array &self, const Context &ctx, const std::vector &fragment_uris, Config *config) { if (self.query_type() == TILEDB_READ) { throw TileDBError("cannot consolidate array opened in readonly " "mode (mode='r')"); } std::vector c_strings; c_strings.reserve(fragment_uris.size()); for (const auto &str : fragment_uris) { c_strings.push_back(str.c_str()); } Array::consolidate(ctx, self.uri(), c_strings.data(), fragment_uris.size(), config); }) .def("consolidate", [](Array &self, const Context &ctx, const std::tuple ×tamp, Config *config) { if (self.query_type() == TILEDB_READ) { throw TileDBError("cannot consolidate array opened in readonly " "mode (mode='r')"); } int start, end; std::tie(start, end) = timestamp; config->set("sm.consolidation.timestamp_start", std::to_string(start)); config->set("sm.consolidation.timestamp_end", std::to_string(end)); Array::consolidate(ctx, self.uri(), config); }) .def("vacuum", &Array::vacuum) .def("create", py::overload_cast( &Array::create)) .def("load_schema", py::overload_cast( &Array::load_schema)) .def("encryption_type", &Array::encryption_type) // TODO non_empty_domain // TODO non_empty_domain_var .def("query_type", &Array::query_type) .def("consolidate_fragments", [](Array &self, const Context &ctx, const std::vector &fragment_uris, Config *config) { std::vector c_strings; c_strings.reserve(fragment_uris.size()); for (const auto &str : fragment_uris) { c_strings.push_back(str.c_str()); } ctx.handle_error(tiledb_array_consolidate_fragments( ctx.ptr().get(), self.uri().c_str(), c_strings.data(), fragment_uris.size(), config->ptr().get())); }) .def("consolidate_metadata", py::overload_cast(&Array::consolidate_metadata)) .def("put_metadata", [](Array &self, std::string &key, tiledb_datatype_t tdb_type, const py::buffer &b) { py::buffer_info info = b.request(); // size_t size = std::reduce(info.shape.begin(), // info.shape.end()); size_t size = 1; for (auto s : info.shape) { size *= s; } // size_t nbytes = size * info.itemsize; self.put_metadata(key, tdb_type, size, info.ptr); /* std::cout << "ndim: " << info.ndim << std::endl; std::cout << "sz: " << size << std::endl; std::cout << "imsz: " << info.itemsize << std::endl; std::cout << "--|" << std::endl; for (auto& s : info.shape) { std::cout << s << std::endl; } */ }) .def("get_metadata", [](Array &self, std::string &key) -> py::buffer { tiledb_datatype_t tdb_type; uint32_t value_num = 0; const void *data_ptr = nullptr; self.get_metadata(key, &tdb_type, &value_num, &data_ptr); if (data_ptr == nullptr && value_num != 1) { throw py::key_error(); } assert(data_ptr != nullptr); return py::memoryview::from_memory( data_ptr, value_num * tiledb_datatype_size(tdb_type)); }) .def("get_metadata_from_index", [](Array &self, uint64_t index) -> py::tuple { tiledb_datatype_t tdb_type; uint32_t value_num = 0; const void *data_ptr = nullptr; std::string key; self.get_metadata_from_index(index, &key, &tdb_type, &value_num, &data_ptr); if (data_ptr == nullptr && value_num != 1) { throw py::key_error(); } // TODO handle empty value case assert(data_ptr != nullptr); auto buf = py::memoryview::from_memory( data_ptr, value_num * tiledb_datatype_size(tdb_type)); return py::make_tuple(tdb_type, buf); }) .def("delete_metadata", &Array::delete_metadata) .def("has_metadata", [](Array &self, std::string &key) -> py::tuple { tiledb_datatype_t has_type; bool has_it = self.has_metadata(key, &has_type); return py::make_tuple(has_it, has_type); }) .def("metadata_num", &Array::metadata_num) .def("delete_array", py::overload_cast( &Array::delete_array)); } } // namespace libtiledbcpp