import io import os import pathlib import random import sys import numpy as np import pytest import tiledb from .common import DiskTestCase, rand_utf8 class TestVFS(DiskTestCase): def test_supports(self): vfs = tiledb.VFS() self.assertTrue(vfs.supports("file")) self.assertIsInstance(vfs.supports("s3"), bool) self.assertIsInstance(vfs.supports("hdfs"), bool) self.assertIsInstance(vfs.supports("gcs"), bool) self.assertIsInstance(vfs.supports("azure"), bool) with self.assertRaises(ValueError): vfs.supports("invalid") def test_vfs_config(self): opt = {"region": "us-west-x1234"} params = [opt, tiledb.Config(opt)] for param in params: vfs = tiledb.VFS(param) assert vfs.config()["region"] == opt["region"] def test_dir(self): vfs = tiledb.VFS() dir = self.path("foo") self.assertFalse(vfs.is_dir(dir)) # create vfs.create_dir(dir) if pytest.tiledb_vfs != "s3": self.assertTrue(vfs.is_dir(dir)) # remove vfs.remove_dir(dir) self.assertFalse(vfs.is_dir(dir)) # create nested path dir = self.path("foo/bar") if pytest.tiledb_vfs != "s3": # this fails locally because "foo" base path does not exist # this will not fail on s3 because there is no concept of directory with self.assertRaises(tiledb.TileDBError): vfs.create_dir(dir) vfs.create_dir(self.path("foo")) vfs.create_dir(self.path("foo/bar")) if pytest.tiledb_vfs != "s3": self.assertTrue(vfs.is_dir(dir)) def test_file(self): vfs = tiledb.VFS() file = self.path("foo") self.assertFalse(vfs.is_file(file)) # create vfs.touch(file) self.assertTrue(vfs.is_file(file)) # remove vfs.remove_file(file) self.assertFalse(vfs.is_file(file)) # check nested path file = self.path("foo/bar") if pytest.tiledb_vfs != "s3": # this fails locally because "foo" base path does not exist # this will not fail on s3 because there is no concept of directory with self.assertRaises(tiledb.TileDBError): vfs.touch(file) def test_move(self): vfs = tiledb.VFS() vfs.create_dir(self.path("foo")) vfs.create_dir(self.path("bar")) vfs.touch(self.path("bar/baz")) self.assertTrue(vfs.is_file(self.path("bar/baz"))) vfs.move_file(self.path("bar/baz"), self.path("foo/baz")) self.assertFalse(vfs.is_file(self.path("bar/baz"))) self.assertTrue(vfs.is_file(self.path("foo/baz"))) # moving to invalid dir should raise an error if pytest.tiledb_vfs != "s3": # this fails locally because "foo" base path does not exist # this will not fail on s3 because there is no concept of directory with self.assertRaises(tiledb.TileDBError): vfs.move_dir(self.path("foo/baz"), self.path("do_not_exist/baz")) @pytest.mark.skipif( sys.platform == "win32", reason="VFS copy commands from core are not supported on Windows", ) def test_copy(self): vfs = tiledb.VFS() vfs.create_dir(self.path("foo")) vfs.create_dir(self.path("bar")) vfs.touch(self.path("foo/baz")) self.assertTrue(vfs.is_file(self.path("foo/baz"))) vfs.copy_file(self.path("foo/baz"), self.path("bar/baz")) self.assertTrue(vfs.is_file(self.path("foo/baz"))) self.assertTrue(vfs.is_file(self.path("bar/baz"))) vfs.copy_dir(self.path("foo"), self.path("baz")) self.assertTrue(vfs.is_file(self.path("baz/baz"))) # copying to invalid dir should raise an error if pytest.tiledb_vfs != "s3": # this fails locally because "foo" base path does not exist # this will not fail on s3 because there is no concept of directory with self.assertRaises(tiledb.TileDBError): vfs.copy_dir(self.path("foo/baz"), self.path("do_not_exist/baz")) def test_write_read(self): vfs = tiledb.VFS() buffer = b"bar" fio = vfs.open(pathlib.Path(self.path("foo")), "wb") fio.write(buffer) self.assertEqual(vfs.file_size(self.path("foo")), 3) fio = vfs.open(self.path("foo").encode("utf-8"), "rb") self.assertEqual(fio.read(3), buffer) # test read with numpy integers fio.seek(np.int64(0)) self.assertEqual(fio.read(np.int32(3)), buffer) fio.seek(np.int64(0)) self.assertEqual(fio.read(np.uint64(3)), buffer) fio.close() # write / read empty input fio = vfs.open(self.path("baz"), "wb") fio.write(b"") fio.close() self.assertEqual(vfs.file_size(self.path("baz")), 0) fio = vfs.open(self.path("baz"), "rb") self.assertEqual(fio.read(0), b"") fio.close() # read from file that does not exist with self.assertRaises(tiledb.TileDBError): vfs.open(self.path("do_not_exist"), "rb") def test_io(self): vfs = tiledb.VFS() buffer = b"0123456789" with tiledb.FileIO(vfs, self.path("foo"), mode="wb") as fio: fio.write(buffer) fio.flush() self.assertEqual(fio.tell(), len(buffer)) with tiledb.FileIO(vfs, self.path("foo"), mode="rb") as fio: with self.assertRaises(IOError): fio.write(b"foo") self.assertEqual(vfs.file_size(self.path("foo")), len(buffer)) fio = tiledb.FileIO(vfs, self.path("foo"), mode="rb") self.assertEqual(fio.read(3), b"012") self.assertEqual(fio.tell(), 3) self.assertEqual(fio.read(3), b"345") self.assertEqual(fio.tell(), 6) self.assertEqual(fio.read(10), b"6789") self.assertEqual(fio.tell(), 10) # seek from beginning fio.seek(0) self.assertEqual(fio.tell(), 0) self.assertEqual(fio.read(), buffer) # seek must be positive when SEEK_SET with self.assertRaises(ValueError): fio.seek(-1, 0) # seek from current positfion fio.seek(5) self.assertEqual(fio.tell(), 5) fio.seek(3, 1) self.assertEqual(fio.tell(), 8) fio.seek(-3, 1) self.assertEqual(fio.tell(), 5) # seek from end fio.seek(-4, 2) self.assertEqual(fio.tell(), 6) # Test readall fio.seek(0) self.assertEqual(fio.readall(), buffer) self.assertEqual(fio.tell(), 10) fio.seek(5) self.assertEqual(fio.readall(), buffer[5:]) self.assertEqual(fio.readall(), b"") # Test readinto fio.seek(0) test_bytes = bytearray(10) self.assertEqual(fio.readinto(test_bytes), 10) self.assertEqual(test_bytes, buffer) # Reading from the end should return empty fio.seek(0) fio.read() self.assertEqual(fio.read(), b"") # Test writing and reading lines with TextIOWrapper lines = [rand_utf8(random.randint(0, 50)) + "\n" for _ in range(10)] rand_uri = self.path("test_fio.rand") with tiledb.FileIO(vfs, rand_uri, "wb") as f: txtio = io.TextIOWrapper(f, encoding="utf-8") txtio.writelines(lines) txtio.flush() with tiledb.FileIO(vfs, rand_uri, "rb") as f2: txtio = io.TextIOWrapper(f2, encoding="utf-8") self.assertEqual(txtio.readlines(), lines) def test_sc42569_vfs_memoryview(self): # This test is to ensure that giving np.ndarray buffer to readinto works # when trying to write bytes that cannot be converted to float32 or int32 vfs = tiledb.VFS() buffer = b"012\x00\x01" with tiledb.FileIO(vfs, self.path("foo"), mode="wb") as fio: fio.write(buffer) fio.flush() self.assertEqual(fio.tell(), len(buffer)) fio = tiledb.FileIO(vfs, self.path("foo"), mode="rb") # Test readinto with np.float32 fio.seek(0) test_np_array = np.empty(5, dtype=np.float32) n_bytes = fio.readinto(test_np_array) self.assertEqual(n_bytes, 5) self.assertEqual(test_np_array.tobytes()[:n_bytes], buffer) # Test readinto with np.int32 fio.seek(0) test_np_array = np.empty(5, dtype=np.int32) n_bytes = fio.readinto(test_np_array) self.assertEqual(n_bytes, 5) self.assertEqual(test_np_array.tobytes()[:n_bytes], buffer) def test_ls(self): basepath = self.path("test_vfs_ls") self.vfs.create_dir(basepath) for id in (1, 2, 3): dir = os.path.join(basepath, f"dir{id}") self.vfs.create_dir(dir) fname = os.path.join(basepath, "file_" + str(id)) with tiledb.FileIO(self.vfs, fname, "wb") as fio: fio.write(b"") expected = ("file_1", "file_2", "file_3") # empty directories do not "exist" on s3 if pytest.tiledb_vfs != "s3": expected = expected + ("dir1", "dir2", "dir3") self.assertSetEqual( set(expected), set( map( lambda x: os.path.basename(x.split("test_vfs_ls")[1]), self.vfs.ls(basepath), ) ), ) @pytest.mark.skipif( pytest.tiledb_vfs not in ["file", "s3", "azure", "gcs"], reason="Only test on local, S3, Azure, and GCS", ) def test_ls_recursive(self): # Create a nested directory structure to test recursive listing basepath = self.path("test_vfs_ls_recursive") self.vfs.create_dir(basepath) dir = os.path.join(basepath, "dir1") self.vfs.create_dir(dir) fname = os.path.join(dir, "file_1") with tiledb.FileIO(self.vfs, fname, "wb") as fio: fio.write(b"") fname = os.path.join(dir, "file_2") with tiledb.FileIO(self.vfs, fname, "wb") as fio: fio.write(b"") dir = os.path.join(basepath, "dir2") self.vfs.create_dir(dir) dir2 = os.path.join(dir, "dir2_1") self.vfs.create_dir(dir2) fname = os.path.join(dir2, "file_1") with tiledb.FileIO(self.vfs, fname, "wb") as fio: fio.write(b"") fname = os.path.join(dir2, "file_2") with tiledb.FileIO(self.vfs, fname, "wb") as fio: fio.write(b"") dir2 = os.path.join(dir, "dir2_2") self.vfs.create_dir(dir2) fname = os.path.join(dir2, "file_1") with tiledb.FileIO(self.vfs, fname, "wb") as fio: fio.write(b"") expected = [ "dir1", "dir1/file_1", "dir1/file_2", "dir2", "dir2/dir2_1", "dir2/dir2_1/file_1", "dir2/dir2_1/file_2", "dir2/dir2_2", "dir2/dir2_2/file_1", ] self.assertSetEqual( set(expected), set( map( # # Keep only the paths after the basepath and normalize them to work on all platforms lambda x: os.path.normpath( x.split("test_vfs_ls_recursive/")[1] ).replace("\\", "/"), self.vfs.ls_recursive(basepath), ) ), ) # Check with user provided callback callback_results = [] def callback(uri, _): # we don't use the second argument 'is_dir' callback_results.append(uri) return True self.vfs.ls_recursive(basepath, callback) self.assertSetEqual( set(expected), set( map( # Keep only the paths after the basepath and normalize them to work on all platforms lambda x: os.path.normpath( x.split("test_vfs_ls_recursive/")[1] ).replace("\\", "/"), callback_results, ) ), ) # Can also be called by calling ls with recursive=True self.assertSetEqual( set(expected), set( map( # Keep only the paths after the basepath and normalize them to work on all platforms lambda x: os.path.normpath( x.split("test_vfs_ls_recursive/")[1] ).replace("\\", "/"), self.vfs.ls(basepath, recursive=True), ) ), ) def test_dir_size(self): vfs = tiledb.VFS() path = self.path("test_vfs_dir_size") vfs.create_dir(path) rand_sizes = np.random.choice(100, size=4, replace=False) for size in rand_sizes: file_path = os.path.join(path, "f_" + str(size)) with tiledb.FileIO(vfs, file_path, "wb") as f: data = os.urandom(size) f.write(data) self.assertEqual(vfs.dir_size(path), sum(rand_sizes)) def test_open_with(self): uri = self.path("test_open_with") vfs = tiledb.VFS() buffer = b"0123456789" with vfs.open(uri, mode="wb") as fio: fio.write(buffer) fio.flush() self.assertEqual(fio.tell(), len(buffer)) with vfs.open(uri, mode="rb") as fio: with self.assertRaises(IOError): fio.write(b"foo") self.assertEqual(fio.read(len(buffer)), buffer) def test_vfs_isdir(tmp_path): """isdir is an alias for is_dir.""" fs = tiledb.VFS() assert fs.isdir(tmp_path.as_posix()) def test_vfs_isfile(tmp_path): """isfile is an alias for is_file.""" tmp_file = tmp_path.joinpath("foo") tmp_file.touch() fs = tiledb.VFS() assert fs.isfile(tmp_file.as_posix()) def test_vfs_size(tmp_path): """size is an alias for file_size.""" tmp_file = tmp_path.joinpath("foo") buffer = b"0123456789" tmp_file.write_bytes(buffer) fs = tiledb.VFS() assert fs.size(tmp_file.as_posix()) == len(buffer)