def test_data_type_tuple(self, collection_mock, data_mock):
collection_mock.configure_mock(data=[1, 2], resolwe=MagicMock())
data_mock.side_effect = [DATA1, DATA2]
BaseCollection.download(collection_mock, data_type=('data:expression:', 'output.exp'))
flist = [u'2/output.exp']
collection_mock.resolwe.download_files.assert_called_once_with(flist, None)
def test_data_type_short(self, collection_mock, data_mock):
collection_mock.configure_mock(data=[1, 2], resolwe=MagicMock())
data_mock.side_effect = [DATA1, DATA2]
BaseCollection.download(collection_mock, data_type='fastq')
flist = [u'1/reads.fq', u'1/arch.gz']
collection_mock.resolwe.download_files.assert_called_once_with(flist, None)
def test_field_name(self, collection_mock):
collection_mock.configure_mock(data=[DATA0, DATA2], resolwe=MagicMock())
BaseCollection.download(collection_mock, field_name='output.exp')
flist = ['2/outfile.exp']
collection_mock.resolwe._download_files.assert_called_once_with(flist, None)
# Check if ok to also provide ``output_field`` that does not start with 'output'
collection_mock.reset_mock()
collection_mock.configure_mock(data=[DATA1, DATA0], resolwe=MagicMock())
BaseCollection.download(collection_mock, field_name='fastq')
flist = ['1/reads.fq', '1/arch.gz']
collection_mock.resolwe._download_files.assert_called_once_with(flist, None)
def test_field_name(self, collection_mock):
collection_mock.configure_mock(data=[DATA0, DATA2],
resolwe=MagicMock())
BaseCollection.download(collection_mock, field_name="output.exp")
flist = ["2/outfile.exp"]
collection_mock.resolwe._download_files.assert_called_once_with(
flist, None)
# Check if ``output_field`` does not start with 'output'
collection_mock.reset_mock()
collection_mock.configure_mock(data=[DATA1, DATA0],
resolwe=MagicMock())
BaseCollection.download(collection_mock, field_name="fastq")
flist = ["1/reads.fq", "1/arch.gz"]
collection_mock.resolwe._download_files.assert_called_once_with(
flist, None)
def test_data_types(self, collection_mock):
get_mock = MagicMock(**{'get.return_value': DATA_SAMPLE[0]})
api_mock = MagicMock(**{'data.return_value': get_mock})
collection_mock.configure_mock(data=[1, 2], resolwe=MagicMock(api=api_mock))
types = BaseCollection.data_types(collection_mock)
self.assertEqual(types, [u'data:reads:fastq:single:'])
def test_data_types(self, collection_mock):
payload = {
'id': 123,
'process_type': 'data:reads:fastq:single:',
# ...
}
get_mock = MagicMock(**{'get.return_value': payload})
api_mock = MagicMock(**{'data.return_value': get_mock})
collection_mock.configure_mock(data=[1, 2], resolwe=MagicMock(api=api_mock))
types = BaseCollection.data_types(collection_mock)
self.assertEqual(types, ['data:reads:fastq:single:'])
def test_bad_field_name(self, collection_mock):
message = "Invalid argument value `field_name`."
with self.assertRaisesRegex(ValueError, message):
BaseCollection.download(collection_mock, field_name=123)
def test_files(self, collection_mock):
collection_mock.configure_mock(data=[DATA1, DATA2], resolwe=" ")
flist = BaseCollection.files(collection_mock)
self.assertEqual(set(flist), set(['arch.gz', 'reads.fq', 'outfile.exp']))
def test_bad_file_type(self, collection_mock):
message = "Invalid argument value `file_type`."
with six.assertRaisesRegex(self, ValueError, message):
BaseCollection.download(collection_mock, file_type=123)
def test_print_annotation(self, collection_mock):
with self.assertRaises(NotImplementedError):
BaseCollection.print_annotation(collection_mock)
def test_bad_data_type(self, collection_mock, data_mock):
message = "Invalid argument value data_type."
with six.assertRaisesRegex(self, ValueError, message):
BaseCollection.download(collection_mock, data_type=123)
def test_print_annotation(self, collection_mock):
with self.assertRaises(NotImplementedError):
BaseCollection.print_annotation(collection_mock)
def test_data_types(self, collection_mock):
api_mock = MagicMock(**{'data.return_value': MagicMock(**{'get.return_value': DATA_SAMPLE[0]})})
collection_mock.configure_mock(data=[1, 2], resolwe=MagicMock(api=api_mock))
types = BaseCollection.data_types(collection_mock)
self.assertEqual(types, [u'data:reads:fastq:single:'])
def test_init(self, collection_mock):
collection_mock.configure_mock(endpoint="fake_endpoint")
BaseCollection.__init__(collection_mock, id=1, resolwe=MagicMock())