import os 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)