class SampleTestCase(unittest.TestCase):
def setUp(self):
self.series = Series("GSE123456", "GSE123456_family.soft.subset")
self.sample = Sample("GSM1", self.series)
def test_is_info_complete(self):
self.assertFalse(self.sample.is_info_complete())
self.sample.organism = "Mus musculus"
self.assertFalse(self.sample.is_info_complete())
self.sample.url = "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000000"
self.assertTrue(self.sample.is_info_complete())
@mock.patch("rsempipeline.utils.objs.Sample.is_info_complete")
def test_gen_outdir(self, mock_is_info_complete):
self.sample.organism = "Mus musculus"
self.sample.url = "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000000"
self.assertEqual(self.sample.gen_outdir("some_outdir"), "some_outdir/GSE123456/mus_musculus/GSM1")
self.assertEqual(self.sample.outdir, "some_outdir/GSE123456/mus_musculus/GSM1")
mock_is_info_complete.return_value = False
self.assertRaisesRegexp(ValueError, "not information complete", self.sample.gen_outdir, "some_outdir")
def test___str__(self):
self.sample.organism = "Mus musculus"
self.sample.url = "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000000"
self.sample.gen_outdir("some_outdir")
self.assertEqual(str(self.sample), "<GSM1 (0/0/0) of GSE123456 at some_outdir/GSE123456/mus_musculus/GSM1>")
def test___repr__(self):
self.sample.organism = "Mus musculus"
self.sample.url = "ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX000/SRX000000"
self.sample.gen_outdir("some_outdir")
self.assertEqual(str(self.sample), "<GSM1 (0/0/0) of GSE123456 at some_outdir/GSE123456/mus_musculus/GSM1>")
