def setUp(self):
searcher = MagicMock()
cache = MagicMock()
searcher.folders = ['species_taxid',
'taxid',
'organism_name',
'genus',
'species',
'accession']
self.fuse = GenbankFuse(searcher, cache)
class TestParsePath(unittest.TestCase):
def setUp(self):
searcher = MagicMock()
cache = MagicMock()
searcher.folders = ['species_taxid',
'taxid',
'organism_name',
'genus',
'species',
'accession']
self.fuse = GenbankFuse(searcher, cache)
@patch('genbankfs.genbank_fuse.os.path.join')
def test_match_accession_happy(self, join_mock):
join_mock.side_effect = fake_path_join
path_list = '/accession/foo/README.txt'.split('/')
result = self.fuse._match_accession(path_list, {})
self.assertEqual(result.file_path, 'foo/README.txt')
self.assertEqual(result.dir_name, None)
self.assertEqual(result.path_list, [])
self.assertEqual(result.query, {'accession': 'foo'})
@patch('genbankfs.genbank_fuse.os.path.join')
def test_match_accession_unhappy(self, join_mock):
join_mock.side_effect = fake_path_join
path_list = '/foo/bar/README.txt'.split('/')
result = self.fuse._match_accession(path_list, {})
self.assertEqual(result.file_path, None)
self.assertEqual(result.dir_name, 'default')
self.assertEqual(result.path_list, [])
self.assertEqual(result.query, {})
path_list = '/README.txt'.split('/')
result = self.fuse._match_accession(path_list, {})
self.assertEqual(result.file_path, None)
self.assertEqual(result.dir_name, 'default')
self.assertEqual(result.path_list, [])
self.assertEqual(result.query, {})
def test_parser_builder(self):
parser = self.fuse._parser_builder('foo')
self.assertRaises(AssertionError, parser, ['bar'], {})
expected = PathParseResult(None, 'foo', [], {})
self.assertEqual(parser(['foo'], {}), expected)
expected = PathParseResult(None, 'default', [], {'foo': 'bar'})
self.assertEqual(parser(['foo', 'bar'], {}), expected)
expected = PathParseResult(None, 'default', [], {'foo': 'bar', 'baz': 1})
self.assertEqual(parser(['foo', 'bar'], {'foo': 'quux', 'baz': 1}), expected)
expected = PathParseResult(None, 'default', ['baz'], {'foo': 'bar'})
self.assertEqual(parser(['foo', 'bar', 'baz'], {}), expected)
def test_parse_path_single(self):
path = '/accession'
result = self.fuse.parse_path(path, {})
expected = PathParseResult(None, 'accession', [], {})
self.assertEqual(result, expected)
path = '/taxid'
result = self.fuse.parse_path(path, {})
expected = PathParseResult(None, 'taxid', [], {})
self.assertEqual(result, expected)
path = '/species'
result = self.fuse.parse_path(path, {})
expected = PathParseResult(None, 'species', [], {})
self.assertEqual(result, expected)
path = '/genus'
result = self.fuse.parse_path(path, {})
expected = PathParseResult(None, 'genus', [], {})
self.assertEqual(result, expected)
path = '/foo'
result = self.fuse.parse_path(path, {})
expected = PathParseResult(None, 'default', [], {})
self.assertEqual(result, expected)
def test_parse_multi(self):
path = '/genus/foo'
result = self.fuse.parse_path(path, {})
expected = PathParseResult(None, 'default', [], {"genus": "foo"})
self.assertEqual(result, expected)
path = '/genus/foo/taxid'
result = self.fuse.parse_path(path, {})
expected = PathParseResult(None, 'taxid', [], {"genus": "foo"})
self.assertEqual(result, expected)
path = '/genus/foo/taxid/1000'
result = self.fuse.parse_path(path, {})
expected = PathParseResult(None, 'default', [], {"genus": "foo", "taxid": "1000"})
self.assertEqual(result, expected)
path = '/genus/foo/taxid/1000/accession/ABC'
result = self.fuse.parse_path(path, {})
expected_query = {
"genus": "foo",
"taxid": "1000",
'accession': 'ABC'
}
expected = PathParseResult(None, 'default', [], expected_query)
self.assertEqual(result, expected)
path = '/genus/foo/taxid/1000/accession/ABC/README.txt'
result = self.fuse.parse_path(path, {})
expected_query = {
'accession': 'ABC'
}
expected = PathParseResult('ABC/README.txt', None, [], expected_query)
self.assertEqual(result, expected)
def test_parse_nonsense(self):
path = '/genus/foo/taxid/NONSENSE/1000/accession/ABC'
result = self.fuse.parse_path(path, {})
expected_query = {
"genus": "foo",
"taxid": "NONSENSE",
}
expected = PathParseResult(None, 'default', [], expected_query)
self.assertEqual(result, expected)
path = '/genus/foo/taxid/1000/NONSENSE/accession/ABC'
result = self.fuse.parse_path(path, {})
expected_query = {
"genus": "foo",
"taxid": "1000",
}
expected = PathParseResult(None, 'default', [], expected_query)
self.assertEqual(result, expected)
path = '/genus/foo/taxid/1000/NONSENSE/accession/ABC/README.txt'
result = self.fuse.parse_path(path, {})
expected_query = {
'accession': 'ABC'
}
expected = PathParseResult('ABC/README.txt', None, [], expected_query)
self.assertEqual(result, expected)
