import os import tempfile import numpy as np import pytest import tiledb import tiledb.cc as lt from tiledb.datatypes import DataType from tiledb.main import PyFragmentInfo def test_config(): cfg = lt.Config() cfg.set("abc", "def") assert cfg.get("abc") == "def" cfg2 = lt.Config({"abc": "def"}) assert cfg == cfg2 assert cfg != lt.Config() cfg["xyz"] = "123" assert cfg["xyz"] == "123" del cfg["xyz"] with pytest.raises(KeyError): cfg["xyz"] with pytest.raises(lt.TileDBError): # TODO should this be KeyError? cfg.get("xyz") cfg2.unset("abc") with pytest.raises(lt.TileDBError): # TODO should this be KeyError? cfg2.get("abc") def test_config_io(tmp_path): cfg = lt.Config({"abc": "def"}) path = tmp_path / "test.cfg" cfg.save_to_file(str(path)) cfg2 = lt.Config(str(path)) assert cfg == cfg2 def test_context(): ctx = lt.Context() cfg = lt.Config() cfg["abc"] = "123" ctx = lt.Context(cfg) assert ctx.config() == cfg @pytest.mark.parametrize( "dtype_str", ["u1", "u2", "u4", "u8", "i1", "i2", "i4", "i8", "f4", "f8"] ) def test_dimension(dtype_str): ctx = lt.Context() dt = DataType.from_numpy(dtype_str) domain = np.array([0, 100.123], dt.np_dtype) lt.Dimension(ctx, "foo", dt.tiledb_type, domain, dt.cast_tile_extent(1)) # test STRING_ASCII lt.Dimension(ctx, "bar", lt.DataType.STRING_ASCII, None, None) def test_enums(): def check_enum(name): """Helper function to iterate over a pybind11 enum and check that the typed value matches name""" enum_type = getattr(lt, name) for name, enum in enum_type.__members__.items(): if name == "NONE": assert lt._enum_string(enum) == "NOOP" elif name == "DICTIONARY": assert lt._enum_string(enum) == "DICTIONARY_ENCODING" else: assert name == lt._enum_string(enum) check_enum("DataType") check_enum("ArrayType") check_enum("FilterType") check_enum("QueryStatus") def test_array(): uri = tempfile.mkdtemp() # TODO BOOTSTRAP tiledb.from_numpy(uri, np.random.rand(4)).close() # lt.from_numpy(uri, np.random.rand(4)).close() ctx = lt.Context() arr = lt.Array(ctx, uri, lt.QueryType.READ) assert arr.is_open() assert os.path.basename(arr.uri()) == os.path.basename(uri) assert arr.schema == arr.schema arr.reopen() arr.set_open_timestamp_start(0) arr.set_open_timestamp_end(1) arr.reopen() assert arr.open_timestamp_start == 0 assert arr.open_timestamp_end == 1 arr.close() assert not arr.is_open() arr = lt.Array(ctx, uri, lt.QueryType.READ) # TODO test # consolidate sig1 # consolidate sig2 # vacuum # load_schema # create lt.Array.encryption_type(ctx, uri) == lt.EncryptionType.NO_ENCRYPTION # TODO assert lt.Array.load_schema(ctx, uri) == arr.schema assert arr.query_type() == lt.QueryType.READ arr.close() #### arr = lt.Array(ctx, uri, lt.QueryType.WRITE) arr.set_open_timestamp_start(1) arr.set_open_timestamp_end(1) arr.close() arr.open(lt.QueryType.WRITE) data = b"abcdef" arr.put_metadata("key", lt.DataType.STRING_ASCII, data) arr.close() arr.set_open_timestamp_start(1) arr.set_open_timestamp_end(1) arr.open(lt.QueryType.READ) assert arr.metadata_num() == 1 assert arr.has_metadata("key") mv = arr.get_metadata("key") assert bytes(mv) == data assert arr.get_metadata_from_index(0)[0] == lt.DataType.STRING_ASCII mv = arr.get_metadata_from_index(0)[1] assert bytes(mv) == data with pytest.raises(lt.TileDBError): arr.get_metadata_from_index(1) arr.close() arr.open(lt.QueryType.WRITE) arr.set_open_timestamp_start(2) arr.set_open_timestamp_end(2) arr.delete_metadata("key") arr.close() arr.set_open_timestamp_start(3) arr.set_open_timestamp_end(3) arr.open(lt.QueryType.READ) with pytest.raises(KeyError): arr.get_metadata("key") assert not arr.has_metadata("key")[0] arr.close() def test_consolidate_fragments(): uri = tempfile.mkdtemp() ctx = lt.Context() config = lt.Config() tiledb.from_numpy(uri, np.random.rand(4)).close() with tiledb.open(uri, "w") as A: A[:] = np.random.rand(4) with tiledb.open(uri, "w") as A: A[:] = np.random.rand(4) schema = tiledb.ArraySchema.load(uri, ctx=ctx) fragment_info = PyFragmentInfo(uri, schema, False, ctx) assert fragment_info.get_num_fragments() == 3 uris = fragment_info.get_uri() # get fragment name form alone, not the full path(s) (the part of each uri after the last /) # https://github.com/TileDB-Inc/TileDB-Py/pull/1946 uris = [uri.split("/")[-1] for uri in uris] arr = lt.Array(ctx, uri, lt.QueryType.WRITE) arr.consolidate_fragments(ctx, uris, config) arr.close() fragment_info = PyFragmentInfo(uri, schema, False, ctx) # Fragmentinfo doesn't see the consolidated range assert fragment_info.get_num_fragments() == 1 def test_array_config(): uri = tempfile.mkdtemp() # TODO BOOTSTRAP tiledb.from_numpy(uri, np.random.rand(4)).close() ctx = lt.Context() arr = lt.Array(ctx, uri, lt.QueryType.READ) arr.close() # TODO update this after SC-26938 config = lt.Config({"foo": "bar"}) arr.set_config(config) assert arr.config()["foo"] == "bar" def test_domain(): ctx = lt.Context() dom = lt.Domain(ctx) dim = lt.Dimension(ctx, "foo", lt.DataType.INT32, np.int32([0, 9]), np.int32([9])) dom._add_dim(dim) assert dom._tiledb_dtype == lt.DataType.INT32 assert dom._ncell == 10 # TODO assert dom.dimension("foo").domain() == ??? np.array? def test_attribute(): ctx = lt.Context() attr = lt.Attribute(ctx, "a1", lt.DataType.FLOAT64) assert attr._name == "a1" assert attr._tiledb_dtype == lt.DataType.FLOAT64 assert attr._cell_size == 8 assert attr._ncell == 1 attr._ncell = 5 assert attr._ncell == 5 assert attr._nullable is False attr._nullable = True assert attr._nullable is True def test_filter(): ctx = lt.Context() fl = lt.FilterList(ctx) fl._add_filter(lt.Filter(ctx, lt.FilterType.ZSTD)) assert fl._filter(0)._type == lt.FilterType.ZSTD assert fl._nfilters() == 1 bzip_filter = lt.Filter(ctx, lt.FilterType.BZIP2) bzip_filter._set_option(ctx, lt.FilterOption.COMPRESSION_LEVEL, 2) assert bzip_filter._get_option(ctx, lt.FilterOption.COMPRESSION_LEVEL) == 2 fl._add_filter(bzip_filter) assert fl._filter(1)._type == lt.FilterType.BZIP2 assert fl._nfilters() == 2 fl._chunksize = 100000 assert fl._chunksize == 100000 def test_schema(): ctx = lt.Context() schema = lt.ArraySchema(ctx, lt.ArrayType.SPARSE) assert schema._array_type == lt.ArrayType.SPARSE schema._capacity = 101 assert schema._capacity == 101 schema._allows_dups = True assert schema._allows_dups with pytest.raises(lt.TileDBError): schema._tile_order = lt.LayoutType.HILBERT if tiledb.libtiledb.version() >= (2, 24, 0): with pytest.raises(lt.TileDBError): schema._tile_order = lt.LayoutType.UNORDERED schema._tile_order = lt.LayoutType.ROW_MAJOR assert schema._tile_order == lt.LayoutType.ROW_MAJOR # TODO schema._set_coords_filter_list(...) # TODO assert schema._coords_filter_list() == lt.FilterListType.NONE # TODO schema._set_offsets_filter_list # TODO assert schema._offsets_filter_list == dom = lt.Domain(ctx) dim = lt.Dimension(ctx, "foo", lt.DataType.INT32, np.int32([0, 9]), np.int32([9])) dom._add_dim(dim) schema._domain = dom # TODO dom and dimension need full equality check assert schema._domain._dim("foo")._name == dim._name def test_query_string(): def create_schema(): schema = lt.ArraySchema(ctx, lt.ArrayType.SPARSE) dom = lt.Domain(ctx) dim = lt.Dimension(ctx, "foo", lt.DataType.STRING_ASCII, None, None) dom._add_dim(dim) schema._domain = dom return schema uri = tempfile.mkdtemp() ctx = lt.Context() schema = create_schema() lt.Array.create(uri, schema) arr = lt.Array(ctx, uri, lt.QueryType.READ) q = lt.Query(ctx, arr, lt.QueryType.READ) assert q.query_type == lt.QueryType.READ subarray = lt.Subarray(ctx, arr) subarray._add_dim_range(0, ("start", "end")) q.set_subarray(subarray) def test_write_sparse(): def create_schema(): ctx = lt.Context() schema = lt.ArraySchema(ctx, lt.ArrayType.SPARSE) dom = lt.Domain(ctx) dim = lt.Dimension( ctx, "x", lt.DataType.INT32, np.int32([0, 9]), np.int32([10]) ) dom._add_dim(dim) attr = lt.Attribute(ctx, "a", lt.DataType.INT32) schema._add_attr(attr) schema._domain = dom return schema coords = np.arange(10).astype(np.int32) data = np.random.randint(0, 10, 10).astype(np.int32) def write(): uri = tempfile.mkdtemp() ctx = lt.Context() schema = create_schema() lt.Array.create(uri, schema) arr = lt.Array(ctx, uri, lt.QueryType.WRITE) q = lt.Query(ctx, arr, lt.QueryType.WRITE) q.layout = lt.LayoutType.UNORDERED assert q.query_type == lt.QueryType.WRITE q.set_data_buffer("a", data) q.set_data_buffer("x", coords) assert q.submit() == lt.QueryStatus.COMPLETE return uri def read(uri): ctx = lt.Context() arr = lt.Array(ctx, uri, lt.QueryType.READ) q = lt.Query(ctx, arr, lt.QueryType.READ) q.layout = lt.LayoutType.ROW_MAJOR assert q.query_type == lt.QueryType.READ rcoords = np.zeros(10).astype(np.int32) rdata = np.zeros(10).astype(np.int32) q.set_data_buffer("a", rdata) q.set_data_buffer("x", rcoords) assert q.submit() == lt.QueryStatus.COMPLETE assert np.all(rcoords == coords) assert np.all(rdata == data) uri = write() read(uri) def test_write_dense(): def create_schema(): ctx = lt.Context() schema = lt.ArraySchema(ctx, lt.ArrayType.DENSE) dom = lt.Domain(ctx) dim = lt.Dimension( ctx, "x", lt.DataType.UINT64, np.uint64([0, 9]), np.uint64([10]) ) dom._add_dim(dim) attr = lt.Attribute(ctx, "a", lt.DataType.FLOAT32) schema._add_attr(attr) schema._domain = dom return schema data = np.random.randint(0, 10, 10).astype(np.float32) def write(): uri = tempfile.mkdtemp() ctx = lt.Context() schema = create_schema() lt.Array.create(uri, schema) arr = lt.Array(ctx, uri, lt.QueryType.WRITE) subarray = lt.Subarray(ctx, arr) subarray._add_dim_range(0, (0, 9)) q = lt.Query(ctx, arr, lt.QueryType.WRITE) q.layout = lt.LayoutType.ROW_MAJOR assert q.query_type == lt.QueryType.WRITE q.set_subarray(subarray) q.set_data_buffer("a", data) # q.set_data_buffer("x", coords) assert q.submit() == lt.QueryStatus.COMPLETE return uri def read(uri): ctx = lt.Context() arr = lt.Array(ctx, uri, lt.QueryType.READ) subarray = lt.Subarray(ctx, arr) subarray._add_dim_range(0, (0, 9)) q = lt.Query(ctx, arr, lt.QueryType.READ) q.layout = lt.LayoutType.ROW_MAJOR assert q.query_type == lt.QueryType.READ q.set_subarray(subarray) rdata = np.zeros(10).astype(np.float32) q.set_data_buffer("a", rdata) assert q.submit() == lt.QueryStatus.COMPLETE assert np.all(rdata == data) uri = write() read(uri)