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[python] Refactor Pybind11 inheritance to reduce repetition
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@nguyenv
nguyenv committed Feb 12, 2024
1 parent 3911930 commit ce950db
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Showing 4 changed files with 154 additions and 422 deletions.
4 changes: 1 addition & 3 deletions apis/python/src/tiledbsoma/_dataframe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -602,9 +602,7 @@ def _set_reader_coord_by_py_seq_or_np_array(

# TODO: bool

raise ValueError(
f"unhandled type {dim.dtype} for index column named {dim.name}"
)
raise ValueError(f"unhandled type {dim.type} for index column named {dim.name}")

def _set_reader_coord_by_numeric_slice(
self, sr: clib.SOMAArray, dim_idx: int, dim: pa.Field, coord: Slice[Any]
Expand Down
150 changes: 143 additions & 7 deletions apis/python/src/tiledbsoma/soma_array.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
*
* The MIT License
*
* @copyright Copyright (c) 2022 TileDB, Inc.
* @copyright Copyright (c) 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
Expand Down Expand Up @@ -86,7 +86,7 @@ bool get_enum_is_ordered(SOMAArray& sr, std::string attr_name){
}

void load_soma_array(py::module &m) {
py::class_<SOMAArray>(m, "SOMAArray")
py::class_<SOMAArray>(m, "SOMAArray", "SOMAObject")
.def(
py::init(
[](std::string_view uri,
Expand Down Expand Up @@ -185,6 +185,23 @@ void load_soma_array(py::module &m) {
"column_names"_a = py::none(),
"batch_size"_a = "auto",
"result_order"_a = ResultOrder::automatic)

.def("reopen", py::overload_cast<OpenMode, std::optional<std::pair<uint64_t, uint64_t>>>(&SOMAArray::open))
.def("close", &SOMAArray::close)
.def_property_readonly("closed", [](SOMAArray& reader) -> bool {
return not reader.is_open();
})
.def_property_readonly("mode", [](SOMAArray& reader){
return reader.mode() == OpenMode::read ? "r" : "w";
})
.def_property_readonly("schema", [](SOMAArray& reader) -> py::object {
auto pa = py::module::import("pyarrow");
auto pa_schema_import = pa.attr("Schema").attr("_import_from_c");
return pa_schema_import(py::capsule(reader.arrow_schema().get()));
})
.def("config", [](SOMAArray& reader) -> py::dict {
return py::cast(reader.config());
})

// After this are short functions expected to be invoked when the coords
// are Python list/tuple, or NumPy arrays. Arrow arrays are in this
Expand Down Expand Up @@ -315,13 +332,13 @@ void load_soma_array(py::module &m) {
&SOMAArray::set_dim_points))

.def(
"set_dim_points_float64",
"set_dim_points_double",
static_cast<void (SOMAArray::*)(
const std::string&, const std::vector<double>&)>(
&SOMAArray::set_dim_points))

.def(
"set_dim_points_float32",
"set_dim_points_float",
static_cast<void (SOMAArray::*)(
const std::string&, const std::vector<float>&)>(
&SOMAArray::set_dim_points))
Expand Down Expand Up @@ -451,14 +468,14 @@ void load_soma_array(py::module &m) {
&SOMAArray::set_dim_ranges))

.def(
"set_dim_ranges_float64",
"set_dim_ranges_double",
static_cast<void (SOMAArray::*)(
const std::string&,
const std::vector<std::pair<double, double>>&)>(
&SOMAArray::set_dim_ranges))

.def(
"set_dim_ranges_float32",
"set_dim_ranges_float",
static_cast<void (SOMAArray::*)(
const std::string&,
const std::vector<std::pair<float, float>>&)>(
Expand Down Expand Up @@ -501,6 +518,125 @@ void load_soma_array(py::module &m) {

.def("get_enum_is_ordered", get_enum_is_ordered)

.def("get_enum_label_on_attr", &SOMAArray::get_enum_label_on_attr);
.def("get_enum_label_on_attr", &SOMAArray::get_enum_label_on_attr)

.def_property_readonly("timestamp", [](SOMAArray& reader) -> py::object {
if(!reader.timestamp().has_value())
return py::none();
return py::cast(reader.timestamp()->second);
})

.def("non_empty_domain", [](SOMAArray& reader, std::string name, py::dtype dtype){
switch (np_to_tdb_dtype(dtype)) {
case TILEDB_UINT64:
return py::cast(reader.non_empty_domain<uint64_t>(name));
case TILEDB_DATETIME_YEAR:
case TILEDB_DATETIME_MONTH:
case TILEDB_DATETIME_WEEK:
case TILEDB_DATETIME_DAY:
case TILEDB_DATETIME_HR:
case TILEDB_DATETIME_MIN:
case TILEDB_DATETIME_SEC:
case TILEDB_DATETIME_MS:
case TILEDB_DATETIME_US:
case TILEDB_DATETIME_NS:
case TILEDB_DATETIME_PS:
case TILEDB_DATETIME_FS:
case TILEDB_DATETIME_AS:
case TILEDB_INT64:
return py::cast(reader.non_empty_domain<int64_t>(name));
case TILEDB_UINT32:
return py::cast(reader.non_empty_domain<uint32_t>(name));
case TILEDB_INT32:
return py::cast(reader.non_empty_domain<int32_t>(name));
case TILEDB_UINT16:
return py::cast(reader.non_empty_domain<uint16_t>(name));
case TILEDB_INT16:
return py::cast(reader.non_empty_domain<int16_t>(name));
case TILEDB_UINT8:
return py::cast(reader.non_empty_domain<uint8_t>(name));
case TILEDB_INT8:
return py::cast(reader.non_empty_domain<int8_t>(name));
case TILEDB_FLOAT64:
return py::cast(reader.non_empty_domain<double>(name));
case TILEDB_FLOAT32:
return py::cast(reader.non_empty_domain<float>(name));
case TILEDB_STRING_UTF8:
case TILEDB_STRING_ASCII:
return py::cast(reader.non_empty_domain_var(name));
default:
throw TileDBSOMAError("Unsupported dtype for nonempty domain.");
}
})
.def("domain", [](SOMAArray& reader, std::string name, py::dtype dtype) {
switch (np_to_tdb_dtype(dtype)) {
case TILEDB_UINT64:
return py::cast(reader.domain<uint64_t>(name));
case TILEDB_DATETIME_YEAR:
case TILEDB_DATETIME_MONTH:
case TILEDB_DATETIME_WEEK:
case TILEDB_DATETIME_DAY:
case TILEDB_DATETIME_HR:
case TILEDB_DATETIME_MIN:
case TILEDB_DATETIME_SEC:
case TILEDB_DATETIME_MS:
case TILEDB_DATETIME_US:
case TILEDB_DATETIME_NS:
case TILEDB_DATETIME_PS:
case TILEDB_DATETIME_FS:
case TILEDB_DATETIME_AS:
case TILEDB_INT64:
return py::cast(reader.domain<int64_t>(name));
case TILEDB_UINT32:
return py::cast(reader.domain<uint32_t>(name));
case TILEDB_INT32:
return py::cast(reader.domain<int32_t>(name));
case TILEDB_UINT16:
return py::cast(reader.domain<uint16_t>(name));
case TILEDB_INT16:
return py::cast(reader.domain<int16_t>(name));
case TILEDB_UINT8:
return py::cast(reader.domain<uint8_t>(name));
case TILEDB_INT8:
return py::cast(reader.domain<int8_t>(name));
case TILEDB_FLOAT64:
return py::cast(reader.domain<double>(name));
case TILEDB_FLOAT32:
return py::cast(reader.domain<float>(name));
case TILEDB_STRING_UTF8:
case TILEDB_STRING_ASCII: {
std::pair<std::string, std::string> str_domain;
return py::cast(std::make_pair("", ""));
}
default:
throw TileDBSOMAError("Unsupported dtype for Dimension's domain");
}
})

.def("set_metadata", &SOMAArray::set_metadata)
.def("delete_metadata", &SOMAArray::delete_metadata)
.def("get_metadata",
py::overload_cast<const std::string&>(&SOMAArray::get_metadata))
.def_property_readonly("meta", [](SOMAArray&soma_dataframe) -> py::dict {
py::dict results;

for (auto const& [key, val] : soma_dataframe.get_metadata()){
tiledb_datatype_t tdb_type = std::get<MetadataInfo::dtype>(val);
uint32_t value_num = std::get<MetadataInfo::num>(val);
const void *value = std::get<MetadataInfo::value>(val);

if(tdb_type == TILEDB_STRING_UTF8){
results[py::str(key)] = py::str(std::string((const char*)value, value_num));
}else if(tdb_type == TILEDB_STRING_ASCII){
results[py::str(key)] = py::bytes(std::string((const char*)value, value_num));
}else{
py::dtype value_type = tdb_to_np_dtype(tdb_type, 1);
results[py::str(key)] = py::array(value_type, value_num, value);
}
}
return results;
})
.def("has_metadata", &SOMAArray::has_metadata)
.def("metadata_num", &SOMAArray::metadata_num);
}
} // namespace tiledbsoma
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