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# -*- 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)
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