# Test methods with long descriptive names can omit docstrings # pylint: disable=missing-docstring import io import os from os import path, remove import unittest import shutil import time from collections import OrderedDict from tempfile import NamedTemporaryFile, mkdtemp import numpy as np from Orange.data import Table, DiscreteVariable from Orange.data.io import TabReader def read_tab_file(filename): return TabReader(filename).read() class TestTabReader(unittest.TestCase): def setUp(self): self.data = Table.from_numpy(None, [[1, 2, 3]]) def test_read_easy(self): simplefile = """\ Feature 1\tFeature 2\tClass 1\tClass 42 d \tM F \td \td \t \tclass \tclass 1.0 \tM \t5 \trich \tF \t7 \tpoor 2.0 \tM \t4 \t """ with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(simplefile) table = read_tab_file(tmp.name) os.unlink(tmp.name) f1, f2, c1, c2 = table.domain.variables self.assertIsInstance(f1, DiscreteVariable) self.assertEqual(f1.name, "Feature 1") self.assertIsInstance(f2, DiscreteVariable) self.assertEqual(f2.name, "Feature 2") self.assertIsInstance(c1, DiscreteVariable) self.assertEqual(c1.name, "Class 1") self.assertIsInstance(c2, DiscreteVariable) self.assertEqual(c2.name, "Class 42") np.testing.assert_almost_equal(table.X, np.array([[0, 0], [np.nan, 1], [1, 0]])) np.testing.assert_almost_equal(table.Y, np.array([[1, 1], [2, 0], [0, np.nan]])) def test_read_save_quoted(self): quoted = '''\ S\tA s\td m\t """a"""\ti """b"""\tj """c\td"""\tk ''' expected = ['"a"', '"b"', '"c\td"'] with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(quoted) table = read_tab_file(tmp.name) os.unlink(tmp.name) self.assertSequenceEqual(table.metas[:, 0].tolist(), expected) with NamedTemporaryFile(mode="w", delete=False) as tmp: pass TabReader.write_file(tmp.name, table) with open(tmp.name, encoding="utf-8") as f: saved = f.read() os.unlink(tmp.name) with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(saved) table1 = read_tab_file(tmp.name) os.unlink(tmp.name) self.assertSequenceEqual(table1.metas[:, 0].tolist(), expected) def test_read_and_save_attributes(self): samplefile = """\ Feature 1\tFeature 2\tClass 1\tClass 42 d \tM F \td \td \ta=1 b=2 \tclass x=a\\ longer\\ string \tclass 1.0 \tM \t5 \trich """ with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(samplefile) table = read_tab_file(tmp.name) os.unlink(tmp.name) _, f2, c1, _ = table.domain.variables self.assertIsInstance(f2, DiscreteVariable) self.assertEqual(f2.name, "Feature 2") self.assertEqual(f2.attributes, {'a': 1, 'b': 2}) self.assertIn(c1, table.domain.class_vars) self.assertIsInstance(c1, DiscreteVariable) self.assertEqual(c1.name, "Class 1") self.assertEqual(c1.attributes, {'x': 'a longer string'}) with NamedTemporaryFile(mode="w", delete=False) as tmp: pass TabReader.write_file(tmp.name, table) with open(tmp.name, encoding="utf-8") as f: saved = f.read() os.unlink(tmp.name) with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(saved) table = read_tab_file(tmp.name) os.unlink(tmp.name) _, f2, c1, _ = table.domain.variables self.assertIsInstance(f2, DiscreteVariable) self.assertEqual(f2.name, "Feature 2") self.assertEqual(f2.attributes, {'a': 1, 'b': 2}) self.assertIn(c1, table.domain.class_vars) self.assertIsInstance(c1, DiscreteVariable) self.assertEqual(c1.name, "Class 1") self.assertEqual(c1.attributes, {'x': 'a longer string'}) spath = "/path/to/somewhere" c1.attributes["path"] = spath with NamedTemporaryFile(mode="w", delete=False) as tmp: pass TabReader.write_file(tmp.name, table) table = read_tab_file(tmp.name) os.unlink(tmp.name) _, _, c1, _ = table.domain.variables self.assertEqual(c1.attributes["path"], spath) def test_read_data_oneline_header(self): samplefile = """\ data1\tdata2\tdata3 0.1\t0.2\t0.3 1.1\t1.2\t1.5 """ with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(samplefile) table = read_tab_file(tmp.name) os.unlink(tmp.name) self.assertEqual(len(table), 2) self.assertEqual(len(table.domain.variables), 3) self.assertEqual(table.domain[0].name, 'data1') def test_read_data_no_header(self): samplefile = """\ 0.1\t0.2\t0.3 1.1\t1.2\t1.5 """ with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(samplefile) table = read_tab_file(tmp.name) os.unlink(tmp.name) self.assertEqual(len(table), 2) self.assertEqual(len(table.domain.variables), 3) self.assertTrue(table.domain[0].is_continuous) self.assertEqual(table.domain[0].name, 'Feature 1') def test_read_data_no_header_feature_reuse(self): samplefile = """\ 0.1\t0.2\t0.3 1.1\t1.2\t1.5 """ with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(samplefile) t1 = read_tab_file(tmp.name) os.unlink(tmp.name) with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write(samplefile) t2 = read_tab_file(tmp.name) os.unlink(tmp.name) self.assertEqual(t1.domain[0], t2.domain[0]) def test_renaming(self): simplefile = """\ a\t b\t a\t a\t b\t a\t c\t a\t b c\t c\t c\t c\t c\t c\t c\t c\t c \t \t \t \t class\t class\t \t \t meta 0\t 0\t 0\t 0\t 0\t 0\t 0\t 0 """ file = NamedTemporaryFile("wt", delete=False, suffix=".tab") filename = file.name try: file.write(simplefile) file.close() table = read_tab_file(filename) domain = table.domain self.assertEqual([x.name for x in domain.attributes], ["a (1)", "b (1)", "a (2)", "a (3)", "c", "a (5)"]) self.assertEqual([x.name for x in domain.class_vars], ["b (2)", "a (4)"]) self.assertEqual([x.name for x in domain.metas], ["b (3)"]) finally: remove(filename) def test_dataset_with_weird_names_and_column_attributes(self): data = Table(path.join(path.dirname(__file__), 'datasets/weird.tab')) self.assertEqual(len(data), 6) self.assertEqual(len(data.domain.variables), 1) self.assertEqual(len(data.domain.metas), 1) NAME = ['5534fab7fad58d5df50061f1', '5534fab8fad58d5de20061f8'] self.assertEqual(data.domain[0].name, str(NAME)) ATTRIBUTES = dict( Timepoint=20, id=NAME, Name=['Gene expressions (dd_AX4_on_Ka_20Hr_bio1_mapped.bam)', 'Gene expressions (dd_AX4_on_Ka_20Hr_bio2_mapped.bam)'], Replicate=['1', '2'], ) self.assertEqual(data.domain[0].attributes, ATTRIBUTES) def test_sheets(self): file1 = io.StringIO("\n".join("xd dbac")) reader = TabReader(file1) self.assertEqual(reader.sheets, []) def test_attributes_saving(self): tempdir = mkdtemp() try: self.assertEqual(self.data.attributes, {}) self.data.attributes[1] = "test" self.data.save(path.join(tempdir, "out.tab")) table = Table(path.join(tempdir, "out.tab")) self.assertEqual(table.attributes[1], "test") finally: shutil.rmtree(tempdir) def test_attributes_saving_as_txt(self): tempdir = mkdtemp() try: self.data.attributes = OrderedDict() self.data.attributes["a"] = "aa" self.data.attributes["b"] = "bb" self.data.save(path.join(tempdir, "out.tab")) table = Table(path.join(tempdir, "out.tab")) self.assertIsInstance(table.attributes, OrderedDict) self.assertEqual(table.attributes["a"], "aa") self.assertEqual(table.attributes["b"], "bb") finally: shutil.rmtree(tempdir) def test_data_name(self): table1 = Table('iris') table2 = TabReader(table1.__file__).read() self.assertEqual(table1.name, 'iris') self.assertEqual(table2.name, 'iris') def test_metadata(self): tempdir = mkdtemp() try: self.data.attributes = OrderedDict() self.data.attributes["a"] = "aa" self.data.attributes["b"] = "bb" fname = path.join(tempdir, "out.tab") TabReader.write_table_metadata(fname, self.data) self.assertTrue(path.isfile(fname + ".metadata")) finally: shutil.rmtree(tempdir) def test_no_metadata(self): tempdir = mkdtemp() try: self.data.attributes = OrderedDict() fname = path.join(tempdir, "out.tab") TabReader.write_table_metadata(fname, self.data) self.assertFalse(path.isfile(fname + ".metadata")) finally: shutil.rmtree(tempdir) def test_had_metadata_now_there_is_none(self): tempdir = mkdtemp() try: self.data.attributes["a"] = "aa" fname = path.join(tempdir, "out.tab") TabReader.write_table_metadata(fname, self.data) self.assertTrue(path.isfile(fname + ".metadata")) del self.data.attributes["a"] TabReader.write_table_metadata(fname, self.data) self.assertFalse(path.isfile(fname + ".metadata")) finally: shutil.rmtree(tempdir) def test_number_of_decimals(self): data = Table("heart_disease") self.assertEqual(data.domain["age"].number_of_decimals, 0) self.assertEqual(data.domain["ST by exercise"].number_of_decimals, 1) data = Table("housing") self.assertEqual(data.domain["CRIM"].number_of_decimals, 5) self.assertEqual(data.domain["INDUS"].number_of_decimals, 2) self.assertEqual(data.domain["AGE"].number_of_decimals, 1) @staticmethod def test_many_discrete(): with NamedTemporaryFile(mode="w", delete=False) as tmp: tmp.write("Poser\nd\n\n") tmp.writelines("K" + str(i) + "\n" for i in range(30000)) start = time.time() _ = TabReader(tmp.name).read() elapsed = time.time() - start os.unlink(tmp.name) if elapsed > 2: raise AssertionError() if __name__ == "__main__": unittest.main()