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from pathlib import Path
import numpy as np
import pytest
from numpy.testing import assert_array_equal
import tiledb
def test_schema_evolution(tmp_path):
ctx = tiledb.default_ctx()
se = tiledb.ArraySchemaEvolution(ctx)
uri = str(tmp_path)
attrs = [
tiledb.Attr(name="a1", dtype=np.float64),
tiledb.Attr(name="a2", dtype=np.int32),
]
dims = [tiledb.Dim(domain=(0, 3), dtype=np.uint64)]
domain = tiledb.Domain(*dims)
schema = tiledb.ArraySchema(domain=domain, attrs=attrs, sparse=False)
tiledb.Array.create(uri, schema)
data1 = {
"a1": np.arange(5, 9),
"a2": np.random.randint(0, 1e7, size=4).astype(np.int32),
}
with tiledb.open(uri, "w") as A:
A[:] = data1
with tiledb.open(uri) as A:
res = A[:]
assert_array_equal(res["a1"], data1["a1"])
assert_array_equal(res["a2"], data1["a2"])
assert "a3" not in res.keys()
newattr = tiledb.Attr("a3", dtype=np.int8)
se.add_attribute(newattr)
with pytest.raises(tiledb.TileDBError) as excinfo:
se.add_attribute(newattr)
assert "Input attribute name is already there" in str(excinfo.value)
assert str(Path("tiledb") / "schema_evolution.cc") in str(excinfo.value)
se.array_evolve(uri)
data2 = {
"a1": np.arange(5, 9),
"a2": np.random.randint(0, 1e7, size=4).astype(np.int32),
"a3": np.random.randint(0, 255, size=4).astype(np.int8),
}
with tiledb.open(uri, "w") as A:
A[:] = data2
def test_it():
with tiledb.open(uri) as A:
res = A[:]
assert_array_equal(res["a1"], data2["a1"])
assert_array_equal(res["a2"], data2["a2"])
assert_array_equal(res["a3"], data2["a3"])
test_it()
tiledb.consolidate(uri)
test_it()
se = tiledb.ArraySchemaEvolution(ctx)
se.drop_attribute("a1")
se.array_evolve(uri)
data3 = {
"a2": np.random.randint(0, 1e7, size=4).astype(np.int32),
"a3": np.random.randint(0, 255, size=4).astype(np.int8),
}
def test_it2():
with tiledb.open(uri) as A:
res = A[:]
assert "a1" not in res.keys()
assert_array_equal(res["a2"], data3["a2"])
assert_array_equal(res["a3"], data3["a3"])
with tiledb.open(uri, "w") as A:
A[:] = data3
test_it2()
tiledb.consolidate(uri)
test_it2()
def test_schema_evolution_timestamp(tmp_path):
ctx = tiledb.default_ctx()
se = tiledb.ArraySchemaEvolution(ctx)
vfs = tiledb.VFS()
uri = str(tmp_path)
schema_uri = os.path.join(uri, "__schema")
attrs = [tiledb.Attr(name="a1", dtype=np.float64)]
domain = tiledb.Domain(tiledb.Dim(domain=(0, 3), dtype=np.uint64))
schema = tiledb.ArraySchema(domain=domain, attrs=attrs, sparse=False)
tiledb.Array.create(uri, schema)
def get_schema_timestamps(schema_uri):
schema_files = filter(lambda x: "__enumerations" not in x, vfs.ls(schema_uri))
return [int(os.path.basename(file).split("_")[2]) for file in schema_files]
assert 123456789 not in get_schema_timestamps(schema_uri)
newattr = tiledb.Attr("a2", dtype=np.int8)
se.timestamp(123456789)
se.add_attribute(newattr)
se.array_evolve(uri)
assert 123456789 in get_schema_timestamps(schema_uri)
def test_schema_evolution_with_enmr(tmp_path):
ctx = tiledb.default_ctx()
se = tiledb.ArraySchemaEvolution(ctx)
uri = str(tmp_path)
attrs = [
tiledb.Attr(name="a1", dtype=np.float64),
tiledb.Attr(name="a2", dtype=np.int32),
]
dims = [tiledb.Dim(domain=(0, 3), dtype=np.uint64)]
domain = tiledb.Domain(*dims)
schema = tiledb.ArraySchema(domain=domain, attrs=attrs, sparse=False)
tiledb.Array.create(uri, schema)
data1 = {
"a1": np.arange(5, 9),
"a2": np.random.randint(0, 1e7, size=4).astype(np.int32),
}
with tiledb.open(uri, "w") as A:
A[:] = data1
with tiledb.open(uri) as A:
assert not A.schema.has_attr("a3")
newattr = tiledb.Attr("a3", dtype=np.int8, enum_label="e3")
se.add_attribute(newattr)
with pytest.raises(tiledb.TileDBError) as excinfo:
se.array_evolve(uri)
assert " Attribute refers to an unknown enumeration" in str(excinfo.value)
se.add_enumeration(tiledb.Enumeration("e3", True, np.arange(0, 8)))
se.array_evolve(uri)
se = tiledb.ArraySchemaEvolution(ctx)
with tiledb.open(uri) as A:
assert A.schema.has_attr("a3")
assert A.attr("a3").enum_label == "e3"
se.drop_enumeration("e3")
with pytest.raises(tiledb.TileDBError) as excinfo:
se.array_evolve(uri)
assert "Unable to drop enumeration" in str(excinfo.value)
se.drop_attribute("a3")
se.array_evolve(uri)
with tiledb.open(uri) as A:
assert not A.schema.has_attr("a3")
@pytest.mark.parametrize(
"type,data",
(
("int", [0]),
("bool", [True, False]),
("str", ["abc", "defghi", "jk"]),
("bytes", [b"abc", b"defghi", b"jk"]),
),
)
def test_schema_evolution_extend_enmr(tmp_path, type, data):
uri = str(tmp_path)
enmr = tiledb.Enumeration("e", True, dtype=type)
attrs = [tiledb.Attr(name="a", dtype=int, enum_label="e")]
domain = tiledb.Domain(tiledb.Dim(domain=(0, 3), dtype=np.uint64))
schema = tiledb.ArraySchema(domain=domain, attrs=attrs, enums=[enmr])
tiledb.Array.create(uri, schema)
with tiledb.open(uri) as A:
assert A.schema.has_attr("a")
assert A.attr("a").enum_label == "e"
assert A.enum("e") == enmr
se = tiledb.ArraySchemaEvolution()
updated_enmr = enmr.extend(data)
se.extend_enumeration(updated_enmr)
se.array_evolve(uri)
with tiledb.open(uri) as A:
assert A.schema.has_attr("a")
assert A.attr("a").enum_label == "e"
assert A.enum("e") == updated_enmr
def test_schema_evolution_extend_check_bad_type():
enmr = tiledb.Enumeration("e", True, dtype=str)
with pytest.raises(tiledb.TileDBError):
enmr.extend([1, 2, 3])
with pytest.raises(tiledb.TileDBError):
enmr.extend([True, False])
enmr.extend(["a", "b"])
enmr = tiledb.Enumeration("e", True, dtype=int)
with pytest.raises(tiledb.TileDBError):
enmr.extend(["a", "b"])
with pytest.raises(tiledb.TileDBError):
enmr.extend([True, False])
enmr.extend([1, 2, 3])
enmr = tiledb.Enumeration("e", True, dtype=bool)
with pytest.raises(tiledb.TileDBError):
enmr.extend(["a", "b"])
with pytest.raises(tiledb.TileDBError):
enmr.extend([1, 2, 3])
enmr.extend([True, False])
@pytest.mark.skipif(
tiledb.libtiledb.version() < (2, 27),
reason="Dropping a fixed-sized attribute and adding it back"
"as a var-sized attribute is not supported in TileDB < 2.27",
)
def test_schema_evolution_drop_fixed_attribute_and_add_back_as_var_sized(tmp_path):
ctx = tiledb.default_ctx()
uri = str(tmp_path)
attrs = [
tiledb.Attr(name="a", dtype=np.int32),
tiledb.Attr(name="b", dtype=np.int32),
]
dims = [tiledb.Dim(domain=(1, 10), dtype=np.int32)]
domain = tiledb.Domain(*dims)
schema = tiledb.ArraySchema(domain=domain, attrs=attrs, sparse=False)
tiledb.Array.create(uri, schema)
original_data = np.arange(1, 11)
with tiledb.open(uri, "w") as A:
A[:] = {"a": original_data, "b": original_data}
se = tiledb.ArraySchemaEvolution(ctx)
se.drop_attribute("a")
se.array_evolve(uri)
# check schema after dropping attribute
with tiledb.open(uri) as A:
assert not A.schema.has_attr("a")
assert A.schema.attr("b").dtype == np.int32
se = tiledb.ArraySchemaEvolution(ctx)
newattr = tiledb.Attr("a", dtype="S", var=True)
se.add_attribute(newattr)
se.array_evolve(uri)
# check schema and data after adding attribute back as a var-sized attribute
with tiledb.open(uri) as A:
assert A.schema.has_attr("a")
assert A.schema.attr("a").dtype == "S"
assert A.schema.attr("b").dtype == np.int32
# check that each value == b'\x80' (empty byte)
assert_array_equal(A[:]["a"], np.array([b"\x80" for _ in range(10)]))
# add new data to the array
new_data = np.array(
["tiledb-string-n.{}".format(i) for i in range(1, 11)], dtype="S"
)
with tiledb.open(uri, "w") as A:
A[:] = {"a": new_data, "b": original_data}
# check data for both attributes
with tiledb.open(uri) as A:
res = A[:]
assert_array_equal(res["a"], new_data)
assert_array_equal(res["b"], original_data)
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