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import xml.etree.ElementTree
import numpy as np
import pytest
from numpy.testing import assert_array_equal
import tiledb
from .common import DiskTestCase, assert_captured, has_pandas
class AttributeTest(DiskTestCase):
def test_minimal_attribute(self):
attr = tiledb.Attr()
self.assertEqual(attr, attr)
self.assertTrue(attr.isanon)
self.assertEqual(attr.name, "")
self.assertEqual(attr.dtype, np.float64)
self.assertFalse(attr.isvar)
self.assertFalse(attr.isnullable)
try:
assert xml.etree.ElementTree.fromstring(attr._repr_html_()) is not None
except:
pytest.fail(f"Could not parse attr._repr_html_(). Saw {attr._repr_html_()}")
def test_attribute_name_only(self, capfd):
attr = tiledb.Attr("foo")
attr.dump()
assert_captured(capfd, "Name: foo")
assert attr == attr
assert attr.name == "foo"
assert attr.dtype == np.float64, "default attribute type is float64"
@pytest.mark.parametrize(
"dtype, fill",
[
(np.dtype(bytes), b"abc"),
(str, "defg"),
(np.float32, np.float32(0.4023573667780681)),
(np.float64, np.float64(0.0560602549760851)),
(np.dtype("M8[ns]"), np.timedelta64(11, "ns")),
(np.dtype([("f0", "<i4"), ("f1", "<i4"), ("f2", "<i4")]), (1, 2, 3)),
],
)
def test_attribute_fill(self, dtype, fill):
attr = tiledb.Attr("", dtype=dtype, fill=fill)
assert attr == attr
assert np.array(attr.fill, dtype=dtype) == np.array(fill, dtype=dtype)
path = self.path()
dom = tiledb.Domain(tiledb.Dim(domain=(0, 0), tile=1, dtype=np.int64))
schema = tiledb.ArraySchema(domain=dom, attrs=(attr,))
tiledb.DenseArray.create(path, schema)
with tiledb.open(path) as R:
assert R.multi_index[0][""] == np.array(fill, dtype=dtype)
assert R[0] == np.array(fill, dtype=dtype)
if has_pandas() and not hasattr(dtype, "fields"):
# record type unsupported for .df
assert R.df[0][""].values == np.array(fill, dtype=dtype)
def test_full_attribute(self, capfd):
filter_list = tiledb.FilterList([tiledb.ZstdFilter(10)])
filter_list = tiledb.FilterList([tiledb.ZstdFilter(10)])
attr = tiledb.Attr("foo", dtype=np.int64, filters=filter_list)
attr.dump()
assert_captured(capfd, "Name: foo")
self.assertEqual(attr, attr)
self.assertEqual(attr.name, "foo")
self.assertEqual(attr.dtype, np.int64)
self.assertIsInstance(attr.filters[0], tiledb.ZstdFilter)
self.assertEqual(attr.filters[0].level, 10)
def test_ncell_attribute(self):
dtype = np.dtype([("", np.int32), ("", np.int32), ("", np.int32)])
attr = tiledb.Attr("foo", dtype=dtype)
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, dtype)
self.assertEqual(attr.ncells, 3)
# dtype subarrays not supported
with self.assertRaises(TypeError):
tiledb.Attr("foo", dtype=np.dtype((np.int32, 2)))
# mixed type record arrays not supported
with self.assertRaises(TypeError):
tiledb.Attr("foo", dtype=np.dtype([("", np.float32), ("", np.int32)]))
def test_complex64_attribute(self):
attr = tiledb.Attr("foo", fill=(0 + 1j), dtype=np.dtype("complex64"))
assert attr == attr
assert attr.fill == attr.fill
assert attr.dtype == np.complex64
assert attr.ncells == 2
def test_complex128_attribute(self):
dtype = np.dtype([("", np.double), ("", np.double)])
attr = tiledb.Attr("foo", fill=(2.0, 2.0), dtype=dtype)
assert attr == attr
assert attr.fill == attr.fill
assert attr.dtype == np.complex128
assert attr.ncells == 2
@pytest.mark.parametrize(
"fill", [(1.0, 1.0), np.array((1.0, 1.0), dtype=np.dtype("f4, f4"))]
)
def test_two_cell_float_attribute(self, fill):
attr = tiledb.Attr("foo", fill=fill, dtype=np.dtype("f4, f4"))
assert attr == attr
assert attr.dtype == np.complex64
assert attr.fill == attr.fill
assert attr.ncells == 2
@pytest.mark.parametrize(
"fill", [(1.0, 1.0), np.array((1.0, 1.0), dtype=np.dtype("f8, f8"))]
)
def test_two_cell_double_attribute(self, fill):
attr = tiledb.Attr("foo", fill=fill, dtype=np.dtype("f8, f8"))
assert attr == attr
assert attr.dtype == np.complex128
assert attr.fill == attr.fill
assert attr.ncells == 2
def test_ncell_double_attribute(self):
dtype = np.dtype([("", np.double), ("", np.double), ("", np.double)])
fill = np.array((0, np.nan, np.inf), dtype=dtype)
attr = tiledb.Attr("foo", dtype=dtype, fill=fill)
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, dtype)
self.assertEqual(attr.ncells, 3)
def test_ncell_not_equal_fill_attribute(self):
dtype = np.dtype([("", np.double), ("", np.double), ("", np.double)])
fill1 = np.array((0, np.nan, np.inf), dtype=dtype)
fill2 = np.array((np.nan, -1, np.inf), dtype=dtype)
attr1 = tiledb.Attr("foo", dtype=dtype, fill=fill1)
attr2 = tiledb.Attr("foo", dtype=dtype, fill=fill2)
assert attr1 != attr2
def test_ncell_bytes_attribute(self):
dtype = np.dtype((np.bytes_, 10))
attr = tiledb.Attr("foo", dtype=dtype)
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, dtype)
self.assertEqual(attr.ncells, 10)
def test_bytes_var_attribute(self):
with pytest.warns(DeprecationWarning, match="Attr given `var=True` but"):
attr = tiledb.Attr("foo", var=True, dtype="S1")
self.assertEqual(attr.dtype, np.dtype("S"))
self.assertTrue(attr.isvar)
with pytest.warns(DeprecationWarning, match="Attr given `var=False` but"):
attr = tiledb.Attr("foo", var=False, dtype="S")
self.assertEqual(attr.dtype, np.dtype("S"))
self.assertTrue(attr.isvar)
attr = tiledb.Attr("foo", var=True, dtype="S")
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, np.dtype("S"))
self.assertTrue(attr.isvar)
attr = tiledb.Attr("foo", var=False, dtype="S1")
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, np.dtype("S1"))
self.assertFalse(attr.isvar)
attr = tiledb.Attr("foo", dtype="S1")
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, np.dtype("S1"))
self.assertFalse(attr.isvar)
attr = tiledb.Attr("foo", dtype="S")
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, np.dtype("S"))
self.assertTrue(attr.isvar)
def test_nullable_attribute(self):
attr = tiledb.Attr("nullable", nullable=True, dtype=np.int32)
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, np.dtype(np.int32))
self.assertTrue(attr.isnullable)
def test_blob_attribute(self):
attr = tiledb.Attr(name="foo", dtype="blob")
self.assertEqual(attr, attr)
self.assertEqual(attr.dtype, np.bytes_)
def test_blob_attribute_dump(self, capfd):
attr = tiledb.Attr(name="foo", dtype="blob")
attr.dump()
assert_captured(capfd, "Type: BLOB")
def test_datetime_attribute(self):
attr = tiledb.Attr("foo", dtype=np.datetime64("", "D"))
self.assertEqual(attr, attr)
assert attr.dtype == np.dtype(np.datetime64("", "D"))
assert attr.dtype != np.dtype(np.datetime64("", "Y"))
assert attr.dtype != np.dtype(np.datetime64)
@pytest.mark.parametrize("sparse", [True, False])
def test_ascii_attribute(self, sparse, capfd):
path = self.path("test_ascii")
dom = tiledb.Domain(
tiledb.Dim(name="d", domain=(1, 4), tile=1, dtype=np.uint32)
)
with pytest.raises(TypeError) as exc_info:
tiledb.Attr(name="A", dtype="ascii", var=False)
assert (
str(exc_info.value) == "dtype is not compatible with var-length attribute"
)
attrs = [tiledb.Attr(name="A", dtype="ascii")]
schema = tiledb.ArraySchema(domain=dom, attrs=attrs, sparse=sparse)
tiledb.Array.create(path, schema)
ascii_data = ["a", "b", "c", "ABC"]
unicode_data = ["±", "×", "÷", "√"]
with tiledb.open(path, "w") as A:
if sparse:
with self.assertRaises(tiledb.TileDBError):
A[np.arange(1, 5)] = unicode_data
A[np.arange(1, 5)] = ascii_data
else:
with self.assertRaises(tiledb.TileDBError):
A[:] = unicode_data
A[:] = ascii_data
with tiledb.open(path, "r") as A:
assert A.schema.nattr == 1
A.schema.dump()
assert_captured(capfd, "Type: STRING_ASCII")
assert A.schema.attr("A").isvar
assert A.schema.attr("A").dtype == np.bytes_
assert A.schema.attr("A").isascii
assert_array_equal(A[:]["A"], np.asarray(ascii_data, dtype=np.bytes_))
def test_modify_attribute_in_schema(self):
path = self.path("test_modify_attribute_in_schema")
tiledb.from_numpy(path, np.random.rand(10))
with tiledb.open(path, "r") as A:
assert A.schema.nattr == 1
assert A.schema.attr(0).name == ""
with pytest.raises(AttributeError) as exc:
A.schema.attr(0).name = "can't change"
if sys.version_info < (3, 11):
assert "can't set attribute" in str(exc.value)
else:
assert "object has no setter" in str(exc.value)
def test_wkt_attribute(self):
A = np.array(
["POINT (30 10)", "POLYGON ((3 1, 4 5, 2 2, 1 2, 3 1))"],
dtype="S",
)
dom = tiledb.Domain(tiledb.Dim(domain=(0, 1), tile=2))
att = tiledb.Attr(dtype="wkt", var=True)
schema = tiledb.ArraySchema(dom, (att,))
tiledb.DenseArray.create(self.path("foo"), schema)
with tiledb.DenseArray(self.path("foo"), mode="w") as T:
T[:] = A
# read back the data
with tiledb.DenseArray(self.path("foo"), mode="r") as T:
for i in range(2):
assert_array_equal(T[i], A[i])
def test_wkb_attribute(self):
A = np.array(
[
# representation of POINT (30 10)
b"\x01\x01\x00\x00\x00\x00\x00\x00\x00\x00\x00>@\x00\x00\x00\x00\x00\x00$@",
# representation of POLYGON ((3 1, 4 5, 2 2, 1 2, 3 1))
(
b"\x01\x03\x00\x00\x00\x01\x00\x00\x00\x05\x00\x00\x00\x00\x00\x00\x00\x00\x00\x08@"
b"\x00\x00\x00\x00\x00\x00\xf0?\x00\x00\x00\x00\x00\x00\x10@\x00\x00\x00\x00\x00\x00\x14@"
b"\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\xf0?"
b"\x00\x00\x00\x00\x00\x00\x00@\x00\x00\x00\x00\x00\x00\x08@\x00\x00\x00\x00\x00\x00\xf0?"
),
],
)
dom = tiledb.Domain(tiledb.Dim(domain=(0, 1), tile=2))
att = tiledb.Attr(dtype="wkb", var=True)
schema = tiledb.ArraySchema(dom, (att,))
tiledb.DenseArray.create(self.path("foo"), schema)
with tiledb.DenseArray(self.path("foo"), mode="w") as T:
T[:] = A
# read back the data
with tiledb.DenseArray(self.path("foo"), mode="r") as T:
for i in range(2):
assert_array_equal(T[:][i].tobytes(), A[i])
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