def set_tiledb_context(context_params):
"""Set the tiledb context. This should be set before any instances of CxgAdaptor are created"""
try:
CxgAdaptor.tiledb_ctx = tiledb.Ctx(context_params)
tiledb.default_ctx(context_params)
except tiledb.libtiledb.TileDBError as e:
if e.message == "Global context already initialized!":
if tiledb.default_ctx().config().dict() != CxgAdaptor.tiledb_ctx.config().dict():
raise ConfigurationError("Cannot change tiledb configuration once it is set")
else:
raise ConfigurationError(f"Invalid tiledb context: {str(e)}")
def uri(temp_rootdir):
"""
Create a simple dense test array.
"""
path = os.path.abspath(os.path.join(temp_rootdir, "test_array"))
ctx = tiledb.default_ctx()
rows_dim = tiledb.Dim(ctx=ctx, domain=(1, 25), dtype=np.int64)
cols_dim = tiledb.Dim(ctx=ctx, domain=(1, 12), dtype=np.int64)
dom = tiledb.Domain(rows_dim, cols_dim, ctx=ctx)
att1 = tiledb.Attr(name="a", ctx=ctx, dtype=np.float64)
att2 = tiledb.Attr(name="b", ctx=ctx, dtype=np.float64)
schema = tiledb.ArraySchema(ctx=ctx, domain=dom, attrs=(att1, att2))
tiledb.Array.create(path, schema)
data = np.reshape(np.arange(300), (25, 12))
for ts in range(1, 4):
with tiledb.open(path, mode="w", timestamp=ts) as A:
A[:] = {"a": data, "b": data}
yield path
shutil.rmtree(path)
def create_test_array_sparse_25x12_mult(temp_rootdir):
"""
Create a simple sparse test array.
"""
path = os.path.abspath(os.path.join(temp_rootdir, "sparse_25x12_mult"))
ctx = tiledb.default_ctx()
rows_dim = tiledb.Dim("row", ctx=ctx, domain=(1, 25), dtype=np.int64)
cols_dim = tiledb.Dim("col", ctx=ctx, domain=(1, 12), dtype=np.int64)
dom = tiledb.Domain(rows_dim, cols_dim, ctx=ctx)
att1 = tiledb.Attr(name="a", ctx=ctx, dtype=np.float64)
att2 = tiledb.Attr(name="b", ctx=ctx, dtype=np.float64)
schema = tiledb.ArraySchema(ctx=ctx, sparse=True, domain=dom, attrs=(att1, att2))
tiledb.SparseArray.create(path, schema)
coords = np.array(list(itertools.product(np.arange(1, 26), np.arange(1, 13))))
rows = coords[:, 0]
cols = coords[:, 1]
data = np.arange(300)
with tiledb.SparseArray(path, mode="w", timestamp=1) as A:
A[rows, cols] = {"a": data, "b": data}
with tiledb.SparseArray(path, mode="w", timestamp=2) as A:
A[rows, cols] = {"a": data / 2, "b": data * 2}
def create_test_array_dense_25x12(temp_rootdir):
"""
Create a simple dense test array.
"""
path = os.path.abspath(os.path.join(temp_rootdir, "dense_25x12"))
ctx = tiledb.default_ctx()
rows_dim = tiledb.Dim("row", ctx=ctx, domain=(1, 25), dtype=np.int64)
cols_dim = tiledb.Dim("col", ctx=ctx, domain=(1, 12), dtype=np.int64)
dom = tiledb.Domain(rows_dim, cols_dim, ctx=ctx)
att = tiledb.Attr(ctx=ctx, dtype=np.int64)
schema = tiledb.ArraySchema(ctx=ctx, domain=dom, attrs=(att,))
tiledb.DenseArray.create(path, schema)
with tiledb.DenseArray(path, mode="w") as A:
A[:] = np.reshape(np.arange(300), (25, 12))
def create_test_array_sparse_25x12(temp_rootdir):
"""
Create a simple sparse test array.
"""
path = os.path.abspath(os.path.join(temp_rootdir, "sparse_25x12"))
ctx = tiledb.default_ctx()
rows_dim = tiledb.Dim("row", ctx=ctx, domain=(1, 25), dtype=np.int64)
cols_dim = tiledb.Dim("col", ctx=ctx, domain=(1, 12), dtype=np.int64)
dom = tiledb.Domain(rows_dim, cols_dim, ctx=ctx)
att = tiledb.Attr(ctx=ctx, dtype=np.int64)
schema = tiledb.ArraySchema(ctx=ctx, sparse=True, domain=dom, attrs=(att,))
tiledb.SparseArray.create(path, schema)
with tiledb.SparseArray(path, mode="w") as A:
coords = np.array(list(itertools.product(np.arange(1, 26), np.arange(1, 13))))
rows = coords[:, 0]
cols = coords[:, 1]
A[rows, cols] = np.arange(300)
def create_test_array_dense_25x12_mult(temp_rootdir):
"""
Create a simple dense test array.
"""
path = os.path.abspath(os.path.join(temp_rootdir, "dense_25x12_mult"))
ctx = tiledb.default_ctx()
rows_dim = tiledb.Dim("row", ctx=ctx, domain=(1, 25), dtype=np.int64)
cols_dim = tiledb.Dim("col", ctx=ctx, domain=(1, 12), dtype=np.int64)
dom = tiledb.Domain(rows_dim, cols_dim, ctx=ctx)
att1 = tiledb.Attr(name="a", ctx=ctx, dtype=np.float64)
att2 = tiledb.Attr(name="b", ctx=ctx, dtype=np.float64)
schema = tiledb.ArraySchema(ctx=ctx, domain=dom, attrs=(att1, att2))
tiledb.DenseArray.create(path, schema)
data = np.reshape(np.arange(300), (25, 12))
with tiledb.DenseArray(path, mode="w", timestamp=1) as A:
A[:] = {"a": data, "b": data}
with tiledb.DenseArray(path, mode="w", timestamp=2) as A:
A[:] = {"a": data / 2, "b": data * 2}