import shutil import tempfile import warnings from pathlib import Path import numpy as np import tables as tb from tables.tests import common # Check read Tables from pytables version 0.8 class BackCompatTablesTestCase(common.PyTablesTestCase): def test01_readTable(self): """Checking backward compatibility of old formats of tables.""" if common.verbose: print("\n", "-=" * 30) print("Running %s.test01_readTable..." % self.__class__.__name__) # Create an instance of an HDF5 Table with warnings.catch_warnings(): warnings.filterwarnings("ignore", category=UserWarning) h5file = tb.open_file(common.test_filename(self.h5fname), "r") try: table = h5file.get_node("/tuple0") # Read the 100 records result = [rec["var2"] for rec in table] if common.verbose: print("Nrows in", table._v_pathname, ":", table.nrows) print("Last record in table ==>", table[-1]) print("Total selected records in table ==> ", len(result)) self.assertEqual(len(result), 100) finally: h5file.close() @common.unittest.skipIf(not common.lzo_avail, "lzo not available") class Table2_1LZO(BackCompatTablesTestCase): # pytables 0.8.x versions and after h5fname = "Table2_1_lzo_nrv2e_shuffle.h5" @common.unittest.skipIf(not common.lzo_avail, "lzo not available") class Tables_LZO1(BackCompatTablesTestCase): h5fname = "Tables_lzo1.h5" # files compressed with LZO1 @common.unittest.skipIf(not common.lzo_avail, "lzo not available") class Tables_LZO1_shuffle(BackCompatTablesTestCase): # files compressed with LZO1 and shuffle h5fname = "Tables_lzo1_shuffle.h5" @common.unittest.skipIf(not common.lzo_avail, "lzo not available") class Tables_LZO2(BackCompatTablesTestCase): h5fname = "Tables_lzo2.h5" # files compressed with LZO2 @common.unittest.skipIf(not common.lzo_avail, "lzo not available") class Tables_LZO2_shuffle(BackCompatTablesTestCase): # files compressed with LZO2 and shuffle h5fname = "Tables_lzo2_shuffle.h5" # Check read attributes from PyTables >= 1.0 properly class BackCompatAttrsTestCase(common.TestFileMixin, common.PyTablesTestCase): FILENAME = "zerodim-attrs-%s.h5" def setUp(self): self.h5fname = common.test_filename(self.FILENAME % self.format) super().setUp() def test01_readAttr(self): """Checking backward compatibility of old formats for attributes.""" if common.verbose: print("\n", "-=" * 30) print("Running %s.test01_readAttr..." % self.__class__.__name__) # Read old formats a = self.h5file.get_node("/a") scalar = np.array(1, dtype="int32") vector = np.array([1], dtype="int32") if self.format == "1.3": self.assertTrue(common.allequal(a.attrs.arrdim1, vector)) self.assertTrue(common.allequal(a.attrs.arrscalar, scalar)) self.assertEqual(a.attrs.pythonscalar, 1) elif self.format == "1.4": self.assertTrue(common.allequal(a.attrs.arrdim1, vector)) self.assertTrue(common.allequal(a.attrs.arrscalar, scalar)) self.assertTrue(common.allequal(a.attrs.pythonscalar, scalar)) class Attrs_1_3(BackCompatAttrsTestCase): format = "1.3" # pytables 1.0.x versions and earlier class Attrs_1_4(BackCompatAttrsTestCase): format = "1.4" # pytables 1.1.x versions and later class VLArrayTestCase(common.TestFileMixin, common.PyTablesTestCase): h5fname = common.test_filename("flavored_vlarrays-format1.6.h5") def test01_backCompat(self): """Checking backward compatibility with old flavors of VLArray.""" # Check that we can read the contents without problems (nor warnings!) vlarray1 = self.h5file.root.vlarray1 self.assertEqual(vlarray1.flavor, "numeric") vlarray2 = self.h5file.root.vlarray2 self.assertEqual(vlarray2.flavor, "python") self.assertEqual(vlarray2[1], [b"5", b"6", b"77"]) # Make sure that 1.x files with TimeXX types continue to be readable # and that its byteorder is correctly retrieved. class TimeTestCase(common.TestFileMixin, common.PyTablesTestCase): # Open a PYTABLES_FORMAT_VERSION=1.x file h5fname = common.test_filename("time-table-vlarray-1_x.h5") def test00_table(self): """Checking backward compatibility with old TimeXX types (tables).""" # Check that we can read the contents without problems (nor warnings!) table = self.h5file.root.table self.assertEqual(table.byteorder, "little") def test01_vlarray(self): """Checking backward compatibility with old TimeXX types (vlarrays).""" # Check that we can read the contents without problems (nor warnings!) vlarray4 = self.h5file.root.vlarray4 self.assertEqual(vlarray4.byteorder, "little") vlarray8 = self.h5file.root.vlarray4 self.assertEqual(vlarray8.byteorder, "little") class OldFlavorsTestCase01(common.PyTablesTestCase): close = False # numeric def test01_open(self): """Checking opening of (X)Array (old 'numeric' flavor)""" # Open the HDF5 with old numeric flavor h5fname = common.test_filename("oldflavor_numeric.h5") with tb.open_file(h5fname) as h5file: # Assert other properties in array self.assertEqual(h5file.root.array1.flavor, "numeric") self.assertEqual(h5file.root.array2.flavor, "python") self.assertEqual(h5file.root.carray1.flavor, "numeric") self.assertEqual(h5file.root.carray2.flavor, "python") self.assertEqual(h5file.root.vlarray1.flavor, "numeric") self.assertEqual(h5file.root.vlarray2.flavor, "python") def test02_copy(self): """Checking (X)Array.copy() method ('numetic' flavor)""" srcfile = common.test_filename("oldflavor_numeric.h5") tmpfile = tempfile.mktemp(".h5") shutil.copy(srcfile, tmpfile) try: # Open the HDF5 with old numeric flavor with tb.open_file(tmpfile, "r+") as h5file: # Copy to another location self.assertWarns( tb.exceptions.FlavorWarning, h5file.root.array1.copy, "/", "array1copy", ) h5file.root.array2.copy("/", "array2copy") h5file.root.carray1.copy("/", "carray1copy") h5file.root.carray2.copy("/", "carray2copy") h5file.root.vlarray1.copy("/", "vlarray1copy") h5file.root.vlarray2.copy("/", "vlarray2copy") if self.close: h5file.close() h5file = tb.open_file(tmpfile) else: h5file.flush() # Assert other properties in array self.assertEqual(h5file.root.array1copy.flavor, "numeric") self.assertEqual(h5file.root.array2copy.flavor, "python") self.assertEqual(h5file.root.carray1copy.flavor, "numeric") self.assertEqual(h5file.root.carray2copy.flavor, "python") self.assertEqual(h5file.root.vlarray1copy.flavor, "numeric") self.assertEqual(h5file.root.vlarray2copy.flavor, "python") finally: Path(tmpfile).unlink() class OldFlavorsTestCase02(common.PyTablesTestCase): close = True def suite(): theSuite = common.unittest.TestSuite() niter = 1 for n in range(niter): theSuite.addTest(common.make_suite(VLArrayTestCase)) theSuite.addTest(common.make_suite(TimeTestCase)) theSuite.addTest(common.make_suite(OldFlavorsTestCase01)) theSuite.addTest(common.make_suite(OldFlavorsTestCase02)) theSuite.addTest(common.make_suite(Table2_1LZO)) theSuite.addTest(common.make_suite(Tables_LZO1)) theSuite.addTest(common.make_suite(Tables_LZO1_shuffle)) theSuite.addTest(common.make_suite(Tables_LZO2)) theSuite.addTest(common.make_suite(Tables_LZO2_shuffle)) return theSuite if __name__ == "__main__": import sys common.parse_argv(sys.argv) common.print_versions() common.unittest.main(defaultTest="suite")