# -*- coding: utf-8 -*- """Tests for utilities for BEL resources.""" import time import unittest from bel_resources import EmptyResourceError, get_bel_resource, split_file_to_annotations_and_definitions from bel_resources.read_document import sanitize_file_lines from bel_resources.utils import get_iso_8601_date from tests.constants import TEST_ANNOTATION_PATH, TEST_NAMESPACE_EMPTY_PATH from tests.examples import simple from tests.mocks import mock_bel_resources class TestUtils(unittest.TestCase): """Test utilities.""" def test_get_date(self): """Test getting the date.""" d = get_iso_8601_date() self.assertIsInstance(d, str) self.assertEqual(d[:4], time.strftime('%Y')) self.assertEqual(d[4:6], time.strftime('%m')) self.assertEqual(d[6:8], time.strftime('%d')) class TestBELResources(unittest.TestCase): """Test utilities for BEL resources.""" def test_raises_on_empty(self): """Test that an error is thrown if an empty resource is downloaded.""" with self.assertRaises(EmptyResourceError): get_bel_resource(TEST_NAMESPACE_EMPTY_PATH) def test_raises_on_missing(self): """Test that an error is thrown if a non-existent resource is specified.""" # TODO def test_raises_on_invalid(self): """Test that an error is thrown if the resource is malformed.""" # TODO def _help_test_annotation(self, res): expected_values = { 'TestAnnot1': 'O', 'TestAnnot2': 'O', 'TestAnnot3': 'O', 'TestAnnot4': 'O', 'TestAnnot5': 'O', } self.assertEqual(expected_values, res['Values']) def test_get_from_path(self): """Test downloading a resource from a file path.""" res = get_bel_resource(TEST_ANNOTATION_PATH) self._help_test_annotation(res) def test_get_from_url(self): """Test downloading a resource by URL.""" with mock_bel_resources: res = get_bel_resource('https://example.com/test_an_1.belanno') self._help_test_annotation(res) class TestSplitLines(unittest.TestCase): """Test splitting file into annotations and definitions.""" def test_parts(self): """Test splitting file into annotations and definitions.""" lines = simple.splitlines() docs, definitions, statements = split_file_to_annotations_and_definitions(lines) self.assertEqual(8, len(list(docs))) self.assertEqual(4, len(list(definitions))) self.assertEqual(14, len(list(statements))) class TestSanitizeLines(unittest.TestCase): """Tests for :py:func:`sanitize_file_lines`.""" def test_count(self): """Test that the right number of lines are retrieved.""" lines = simple.splitlines() lines = list(sanitize_file_lines(lines)) self.assertEqual(26, len(lines)) def _help_test_line(self, statement: str, expect: str) -> None: lines = list(sanitize_file_lines(statement.split('\n'))) self.assertEqual(1, len(lines)) line = lines[0][1] self.assertEqual(expect, line) def test_already_correct(self): """Test when the line is already correct.""" expect = statement = '''SET Evidence = "1.1.1 Easy case"''' self._help_test_line(statement, expect) def test_line_break_operator_no_whitespace(self): """Test when a backward slash break is use without whitespace.""" statement = '''SET Evidence = "3.1 Backward slash break test \\ second line"''' expect = '''SET Evidence = "3.1 Backward slash break test second line"''' self._help_test_line(statement, expect) def test_line_break_operator_with_whitespace(self): """Test when a backward slash break is use with whitespace.""" statement = '''SET Evidence = "3.2 Backward slash break test with whitespace \\ second line"''' expect = '''SET Evidence = "3.2 Backward slash break test with whitespace second line"''' self._help_test_line(statement, expect) def test_line_break_operator_multiple(self): """Test when multiple backward slash break are used.""" statement = '''SET Evidence = "3.3 Backward slash break test \\ second line \\ third line"''' expect = '''SET Evidence = "3.3 Backward slash break test second line third line"''' self._help_test_line(statement, expect) def test_missing_line_break(self): """Test when a backward slash break is omitted in a new line.""" statement = '''SET Evidence = "4.1 Malformed line breakcase second line"''' expect = '''SET Evidence = "4.1 Malformed line breakcase second line"''' self._help_test_line(statement, expect) def test_missing_line_break_2(self): """Test a real example.""" statement = '''SET Evidence = "The phosphorylation of S6K at Thr389, which is the TORC1-mediated site, was not inhibited in the SIN1-/- cells (Figure 5A)."''' expect = ( 'SET Evidence = "The phosphorylation of S6K at Thr389, which is the TORC1-mediated site, was not ' 'inhibited in the SIN1-/- cells (Figure 5A)."' ) self._help_test_line(statement, expect) def test_multiple_missing_line_breaks(self): """Test when a backward slash break is omitted in multiple new lines.""" statement = '''SET Evidence = "4.2 Malformed line breakcase second line third line"''' expect = '''SET Evidence = "4.2 Malformed line breakcase second line third line"''' self._help_test_line(statement, expect) def test_multiple_missing_line_breaks_2(self): """Test forgotten delimiters.""" s = [ 'SET Evidence = "Something', 'or other', 'or other"' ] result = list(sanitize_file_lines(s)) expect = [(1, 'SET Evidence = "Something or other or other"')] self.assertEqual(expect, result) def test_line_numbers(self): """Test the line number follow-through.""" statements = [ '# Set document-defined annotation values\n', 'SET Species = 9606', 'SET Tissue = "t-cells"', '# Create an Evidence Line for a block of BEL Statements', 'SET Evidence = "Here we show that interfereon-alpha (IFNalpha) is a potent producer \\', 'of SOCS expression in human T cells, as high expression of CIS, SOCS-1, SOCS-2, \\', 'and SOCS-3 was detectable after IFNalpha stimulation. After 4 h of stimulation \\', 'CIS, SOCS-1, and SOCS-3 had ret' ] result = list(sanitize_file_lines(statements)) expect = [ (2, 'SET Species = 9606'), (3, 'SET Tissue = "t-cells"'), (5, 'SET Evidence = "Here we show that interfereon-alpha (IFNalpha) is a potent producer of SOCS expression ' 'in human T cells, as high expression of CIS, SOCS-1, SOCS-2, and SOCS-3 was detectable after IFNalpha ' 'stimulation. After 4 h of stimulation CIS, SOCS-1, and SOCS-3 had ret') ] self.assertEqual(expect, result) def test_sanitize_comment(self): """Test that comments are sanitized.""" s = [ 'SET Evidence = "yada yada yada" //this is a comment' ] result = list(sanitize_file_lines(s)) expect = [(1, 'SET Evidence = "yada yada yada"')] self.assertEqual(expect, result)