def setUp(self):
self.case = ContigUploader()
self.mock_contigswrapper = mock.MagicMock(spec=ContigsWrapper)
class ContigUploaderTestCase(unittest.TestCase):
def setUp(self):
self.case = ContigUploader()
self.mock_contigswrapper = mock.MagicMock(spec=ContigsWrapper)
def tearDown(self):
del self.case
@mock.patch('superphy.upload.contig_upload.ContigUploader.error_logging')
@mock.patch('superphy.upload.contig_upload.SequenceValidator')
@mock.patch('superphy.upload.contig_upload.ContigUploader.upload')
@mock.patch('superphy.upload.contig_upload.ContigUploader.get_seqdata')
@mock.patch('superphy.upload.contig_upload.ContigsWrapper')
@mock.patch('superphy.upload.contig_upload.find_missing_sequences')
def test_upload_missing_contigs(self, mock_find, mock_wrapper, mock_data, mock_upload, mock_valid, mock_error):
self.mock_contigswrapper.dict = {}
# Test: No genomes with missing contig data
mock_find.return_value = []
self.case.upload_missing_contigs()
self.assertEqual(len(mock_find.mock_calls), 1)
mock_wrapper.assert_not_called()
mock_data.assert_not_called()
mock_upload.assert_not_called()
mock_valid.assert_not_called()
mock_error.assert_not_called()
# Test: One genome returned from find_missing_contig (from Plasmid)
mock_find.return_value = [("AAAA", "AAAA")]
self.mock_contigswrapper.dict["is_from"] = "PLASMID"
mock_wrapper.return_value = self.mock_contigswrapper
self.case.upload_missing_contigs()
self.assertEqual(len(mock_find.mock_calls), 2)
self.assertEqual(len(mock_wrapper.mock_calls), 1)
self.assertEqual(len(mock_data.mock_calls), 1)
self.assertEqual(len(mock_upload.mock_calls), 1)
mock_valid.assert_not_called()
mock_error.assert_not_called()
# Test: One genome returned from find_missing_contig (not from Plasmid)
mock_find.return_value = [("AAAA", "AAAA")]
self.mock_contigswrapper.dict["is_from"] = "CORE"
mock_wrapper.return_value = self.mock_contigswrapper
self.case.upload_missing_contigs()
self.assertEqual(len(mock_find.mock_calls), 3)
self.assertEqual(len(mock_wrapper.mock_calls), 2)
self.assertEqual(len(mock_data.mock_calls), 2)
self.assertEqual(len(mock_upload.mock_calls), 2)
self.assertEqual(len(mock_valid.mock_calls), 2)
mock_error.assert_not_called()
# Test: One genome returned from find_missing_contig (not from Plasmid), raise type_error in try/except [ERROR]
mock_find.return_value = [("AAAA", "AAAA")]
self.mock_contigswrapper.dict["is_from"] = "WGS"
mock_wrapper.return_value = self.mock_contigswrapper
mock_data.side_effect = TypeError
self.case.upload_missing_contigs()
self.assertEqual(len(mock_find.mock_calls), 4)
self.assertEqual(len(mock_data.mock_calls), 3)
self.assertEqual(len(mock_wrapper.mock_calls), 3)
self.assertEqual(len(mock_upload.mock_calls), 2)
self.assertEqual(len(mock_valid.mock_calls), 2)
self.assertEqual(len(mock_error.mock_calls), 1)
@mock.patch('superphy.upload.contig_upload.BlazegraphUploader', autospec=True)
@mock.patch('superphy.upload.contig_upload.Contig')
def test_upload(self, mock_rdf, mock_bg):
contig_ref = mock.MagicMock(spec=Contig, create=True)
mock_rdf.return_value = contig_ref
sample_func = mock.Mock()
self.mock_contigswrapper.contigs = [("ANVW01000001", "ACGTTGCA")]
self.case.upload(self.mock_contigswrapper, sample_func)
self.assertEqual(self.mock_contigswrapper.generate_kwargs.call_count, 1)
sample_func.assert_called_once_with(mock.ANY, mock.ANY)
mock_rdf.assert_called_once_with(mock.ANY)
mock_bg.assert_called_once_with()
def test_plasmid_rdf(self):
contig_ref = mock.MagicMock(spec=Contig, create=True)
self.mock_contigswrapper.accession = "AAAA"
self.mock_contigswrapper.genome = "AAAA"
self.case.plasmid_rdf(self.mock_contigswrapper, contig_ref)
self.assertEqual(len(contig_ref.mock_calls), 2)
contig_ref.reset_mock()
self.mock_contigswrapper.accession = "AAAA"
self.mock_contigswrapper.genome = "BBBB"
self.case.plasmid_rdf(self.mock_contigswrapper, contig_ref)
self.assertEqual(len(contig_ref.mock_calls), 1)
def test_nonplasmid_rdf(self):
"""
Mainly tests the if case in the nonplasmid_rdf method
"""
contig_ref = mock.MagicMock(spec=Contig, create=True)
self.mock_contigswrapper.valid = True
self.mock_contigswrapper.hits = []
self.case.nonplasmid_rdf(self.mock_contigswrapper, contig_ref)
self.assertEqual(len(contig_ref.mock_calls), 2)
contig_ref.reset_mock()
self.mock_contigswrapper.valid = False
self.mock_contigswrapper.hits = []
self.case.nonplasmid_rdf(self.mock_contigswrapper, contig_ref)
self.assertEqual(len(contig_ref.mock_calls), 1)
def test_error_logging(self):
pass
@mock.patch('superphy.upload.contig_upload.ContigUploader.download_file')
@mock.patch('superphy.upload.contig_upload.open')
@mock.patch('superphy.upload.contig_upload.ContigUploader.load_contigs')
@mock.patch('superphy.upload.contig_upload.SeqIO.parse')
@mock.patch('superphy.upload.contig_upload.Entrez', autospec=True)
def test_get_seqdata(self, mock_entrez, mock_SeqIO, mock_load, mock_open, mock_download):
mock_entrez.efetch.return_value = mock.MagicMock(spec=file)
mock_handle = mock.MagicMock(spec=file)
self.mock_contigswrapper.accession = None
self.mock_contigswrapper.dict = {}
self.mock_contigswrapper.genome = "BA000007"
#complete genome
record1 = SeqRecord(seq="abcd", description="complete genome")
mock_SeqIO.return_value = [record1]
self.case.get_seqdata(self.mock_contigswrapper)
self.assertEqual(len(mock_load.mock_calls), 1)
self.assertEqual(self.mock_contigswrapper.dict["is_from"], "CORE")
#non-complete genome
self.mock_contigswrapper.reset_mock()
mock_SeqIO.reset_mock()
record2 = SeqRecord(seq="actg", description="some genome")
mock_SeqIO.return_value = [record2]
self.case.get_seqdata(self.mock_contigswrapper)
mock_open.return_value = mock.MagicMock(spec=file)
mock_download.assert_called_once_with(mock.ANY, mock.ANY)
mock_open.assert_called_once_with(mock.ANY, mock.ANY)
self.assertEqual(self.mock_contigswrapper.dict["is_from"], "WGS")
@mock.patch('superphy.upload.contig_upload.open')
@mock.patch('superphy.upload.contig_upload.FTP', autospec=True)
def test_download_file(self, mock_FTP, mock_open):
mock_FTP().nlst.return_value = ["wgs.JHNI.1.fsa_nt.gz", "wgs.ABCD.1.fsa_nt.gz", "wgs.IDLE.1.fsa_nt.gz"]
mock_open.return_value = mock.MagicMock(spec=file)
self.case.download_file("JHNI", "fsa_nt.gz")
self.assertEqual(mock_open.call_count, 2)
mock_open.reset_mock()
with self.assertRaises(TypeError):
self.case.download_file("NYAN", "fsa_nt.gz")
mock_open.assert_not_called()
