import contextlib import datetime import glob import importlib import os import random import shutil import subprocess import sys import tempfile import traceback import urllib import uuid import numpy as np import pytest from numpy.testing import assert_almost_equal, assert_array_equal, assert_equal from packaging.version import Version import tiledb SUPPORTED_DATETIME64_DTYPES = tuple( np.dtype(f"M8[{res}]") for res in "Y M W D h m s ms us ns".split() ) def has_pandas(): try: import pandas as pd except ImportError: return False if Version(pd.__version__) < Version("1.0") or Version(pd.__version__) >= Version( "3.0.0.dev0" ): return False return True def has_pyarrow(): try: import pyarrow as pa if Version(pa.__version__) < Version("1.0"): return False except ImportError: return False return True def assert_tail_equal(a, *rest, **kwargs): """Assert that all arrays in target equal first array""" for target in rest: assert_array_equal(a, target, **kwargs) def create_vfs_dir(path): """Create a directory at the given scheme-prefixed path, first creating the base bucket if needed.""" split_uri = urllib.parse.urlsplit(path) scheme = split_uri.scheme bucket = split_uri.netloc bucket_uri = scheme + "://" + bucket vfs = tiledb.VFS() if not vfs.is_bucket(bucket_uri): vfs.create_bucket(bucket_uri) vfs.create_dir(path) class DiskTestCase: """Helper class to store paths and associated allocation frames. This is both a cleanup step and a test of resource management. Some platforms will refuse to delete an open file, indicating a potentially leaked resource. """ @classmethod def setup_method(self): # .lower: because bucket name must be all lowercase prefix = "tiledb-" + self.__name__.lower() if hasattr(pytest, "tiledb_vfs") and pytest.tiledb_vfs == "s3": self.path_scheme = pytest.tiledb_vfs + "://" self.rootdir = self.path_scheme + prefix + str(random.randint(0, 10e10)) create_vfs_dir(self.rootdir) else: self.path_scheme = "" self.rootdir = tempfile.mkdtemp(prefix=prefix) self.vfs = tiledb.VFS() self.pathmap = dict() @classmethod def teardown_method(self): # Remove every directory starting with rootdir # This is both a clean-up step and an implicit test # of proper resource deallocation (see notes below) for dirpath in glob.glob(self.rootdir + "*"): try: shutil.rmtree(dirpath) except OSError as exc: print( "test '{}' error deleting '{}'".format( self.__class__.__name__, dirpath ) ) print("registered paths and originating functions:") for path, frame in self.pathmap.items(): print(" '{}' <- '{}'".format(path, frame)) raise exc def path(self, basename=None, shared=False): if self.path_scheme: basename = basename if basename else str(uuid.uuid4()) out = os.path.join(self.rootdir, basename) self.vfs.create_dir(out) else: if basename is not None: # Note: this must be `is not None` because we need to match empty string out = os.path.abspath(os.path.join(self.rootdir, basename)) else: out = tempfile.mkdtemp(dir=self.rootdir) if os.name == "nt" and shared: subprocess.run( f'cmd //c "net share tiledb-shared={out}"', shell=True, check=True ) # We have had issues in both py and libtiledb in the past # where files were not released (eg: destructor not called) # Often this is invisible on POSIX platforms, but will # cause errors on Windows because two processes cannot access # the same file at once. # In order to debug this issue, we save the caller where # this path was allocated so that we can determine what # test created an unreleased file frame = traceback.extract_stack(limit=2)[-2][2] self.pathmap[out] = frame return out def assertRaises(self, *args): return pytest.raises(*args) def assertRaisesRegex(self, e, m): return pytest.raises(e, match=m) @contextlib.contextmanager def assertEqual(self, *args): if not len(args) == 2: raise Exception("Unexpected input len > 2 to assertEquals") assert args[0] == args[1] @contextlib.contextmanager def assertNotEqual(self, *args): if not len(args) == 2: raise Exception("Unexpected input len > 2 to assertEquals") assert args[0] != args[1] @contextlib.contextmanager def assertTrue(self, a, msg=None): if msg: assert a, msg else: assert a @contextlib.contextmanager def assertFalse(self, a): assert a is False @contextlib.contextmanager def assertIsInstance(self, v, t): assert isinstance(v, t) @contextlib.contextmanager def assertSetEqual(self, s1, s2): assert all(isinstance(x, set) for x in (s1, s2)) assert s1 == s2 @contextlib.contextmanager def assertIsNone(self, a1): assert a1 is None @contextlib.contextmanager def assertTupleEqual(self, a1, a2): assert a1 == a2 @contextlib.contextmanager def assertAlmostEqual(self, a1, a2): assert_almost_equal(a1, a2) # exclude whitespace: if we generate unquoted newline then pandas will be confused _ws_set = set("\n\t\r") def gen_chr(max, printable=False): while True: # TODO we exclude 0x0 here because the key API does not embedded NULL s = chr(random.randrange(1, max)) if printable and (not s.isprintable()) or (s in _ws_set): continue if len(s) > 0: break return s def rand_utf8(size=5, printable=False): # This is a hack to ensure that all UTF-8 is parseable. It would be nicer to # exclude invalid surrogate pairs, but this will do. while True: try: v = "".join([gen_chr(0xD007F, printable=printable) for _ in range(0, size)]) return v.encode("UTF-8").decode() except UnicodeError: continue def rand_ascii(size=5, printable=False): return "".join([gen_chr(127, printable) for _ in range(0, size)]) def rand_ascii_bytes(size=5, printable=False): return b"".join([gen_chr(127, printable).encode("utf-8") for _ in range(0, size)]) def dtype_max(dtype): if not np.issubdtype(dtype, np.generic): raise TypeError("expected numpy dtype!") if np.issubdtype(dtype, np.floating): finfo = np.finfo(dtype) return finfo.max elif np.issubdtype(dtype, np.integer): iinfo = np.iinfo(dtype) return int(iinfo.max) elif np.issubdtype(dtype, np.datetime64): return np.datetime64(datetime.datetime.max) raise f"Unknown dtype for dtype_max '{dtype}'" def dtype_min(dtype): if not np.issubdtype(dtype, np.generic): raise TypeError("expected numpy dtype!") if np.issubdtype(dtype, np.floating): finfo = np.finfo(dtype) return finfo.min elif np.issubdtype(dtype, np.integer): iinfo = np.iinfo(dtype) return int(iinfo.min) elif np.issubdtype(dtype, np.datetime64): return np.datetime64(datetime.datetime.min) raise f"Unknown dtype for dtype_min '{dtype}'" def rand_datetime64_array( size, start=None, stop=None, include_extremes=True, dtype=None ): if not dtype: dtype = np.dtype("M8[ns]") # generate randint inbounds on the range of the dtype units = np.datetime_data(dtype)[0] intmin, intmax = np.iinfo(np.int64).min, np.iinfo(np.int64).max if start is None: start = np.datetime64(intmin + 1, units) else: start = np.datetime64(start) if stop is None: stop = np.datetime64(intmax, units) else: stop = np.datetime64(stop) arr = np.random.randint( start.astype(dtype).astype(np.int64), stop.astype(dtype).astype(np.int64), size=size, dtype=np.int64, ) arr.sort() arr = arr.astype(dtype) # enable after fix for core issue: ch 7192 if include_extremes: arr[0] = start arr[-1] = stop return arr def intspace(start, stop, num=50, dtype=np.int64): """ Return evenly spaced values over range ensuring that stop is always the maximum (will not overflow with int dtype as linspace) :param start: :param stop: :param num: :param dtype: :return: """ rval = np.zeros(num, dtype=dtype) step = (stop - start) // num nextval = start if np.issubdtype(dtype, np.integer) and step < 1: raise ValueError( "Cannot use non-integral step value '{}' for integer dtype!".format(step) ) for i in range(num): rval[i] = nextval nextval += step rval[-1] = stop return rval def assert_unordered_equal(a1, a2, unordered=True): """Assert that arrays are equal after sorting if `unordered==True`""" if unordered: a1 = np.sort(a1) a2 = np.sort(a2) assert_array_equal(a1, a2) def assert_subarrays_equal(a, b, ordered=True): assert_equal(a.shape, b.shape) if not ordered: a = np.sort(a) b = np.sort(b) for a_el, b_el in zip(a.flat, b.flat): assert_array_equal(a_el, b_el) def assert_dict_arrays_equal(d1, d2, ordered=True): assert d1.keys() == d2.keys(), "Keys not equal" if ordered: for k in d1.keys(): assert_array_equal(d1[k], d2[k]) else: d1_dtypes = [tuple((name, value.dtype)) for name, value in d1.items()] d1_records = [tuple(values) for values in zip(*d1.values())] array1 = np.array(d1_records, dtype=d1_dtypes) d2_dtypes = [tuple((name, value.dtype)) for name, value in d2.items()] d2_records = [tuple(values) for values in zip(*d2.values())] array2 = np.array(d2_records, dtype=d2_dtypes) assert_unordered_equal(array1, array2, True) def assert_captured(cap, expected): if sys.platform != "win32": import ctypes libc = ctypes.CDLL(None) libc.fflush(None) out, err = cap.readouterr() assert not err assert expected in out @pytest.fixture(scope="module", params=["hilbert", "row-major"]) def fx_sparse_cell_order(request): yield request.param