def test_dataset_io_sanitizing(self):
ssfn = data.getXml(8)
ofn = tempfile.NamedTemporaryFile(suffix=".xml").name
# some smoke tests:
run_filter_dataset(ssfn, ofn, "", "")
run_filter_dataset(ssfn, ofn, 0, "")
run_filter_dataset(ssfn, ofn, 0, "None")
with self.assertRaises(ValueError):
run_filter_dataset(ssfn, ofn, "None", "None")
run_filter_dataset(ssfn, ofn, None, None)
run_filter_dataset(ssfn, ofn, 0, 0)
run_filter_dataset(ssfn, ofn, False, False)
with self.assertRaises(ValueError):
run_filter_dataset(ssfn, ofn, True, False)
run_filter_dataset(ssfn, ofn, False, True)
with self.assertRaises(ValueError):
run_filter_dataset(ssfn, ofn, True, True)
run_filter_dataset(ssfn, ofn, 1, True)
run_filter_dataset(ssfn, ofn, "0", "None")
run_filter_dataset(ssfn, ofn, " 0 ", "None")
run_filter_dataset(ssfn, ofn, "-1", "none")
run_filter_dataset(ssfn, ofn, " -1 ", "none")
run_filter_dataset(ssfn, ofn, -1, "none")
run_filter_dataset(ssfn, ofn, "-1", "blah")
run_filter_dataset(ssfn, ofn, "-1", "None, None")
run_filter_dataset(ssfn, ofn, "1.0", "None, None")
run_filter_dataset(ssfn, ofn, " 1.0 ", "None, None")
with self.assertRaises(ValueError):
run_filter_dataset(ssfn, ofn, " 1. 0 ", "None, None")
with self.assertRaises(ValueError):
run_filter_dataset(ssfn, ofn, "1. 0", "None, None")
run_filter_dataset(ssfn, ofn, "10.0", "None, None")
run_filter_dataset(ssfn, ofn, "0.01", "None, None")
run_filter_dataset(ssfn, ofn, "100000.01", "None, None")
run_filter_dataset(ssfn, ofn, ".00", "None, None")
run_filter_dataset(ssfn, ofn, 1.0, "None, None")
run_filter_dataset(ssfn, ofn, 10.0, "None, None")
run_filter_dataset(ssfn, ofn, 0.01, "None, None")
run_filter_dataset(ssfn, ofn, 100000.01, "None, None")
run_filter_dataset(ssfn, ofn, 100000, "None, None")
run_filter_dataset(ssfn, ofn, .00, "None, None")
run_filter_dataset(ssfn, ofn, 1., "None, None")
run_filter_dataset(ssfn, ofn, "1.", "None, None")
with self.assertRaises(ValueError):
run_filter_dataset(ssfn, ofn, "None.1", "None, None")
with self.assertRaises(ValueError):
run_filter_dataset(ssfn, ofn, "None1", "None, None")
with self.assertRaises(ValueError):
run_filter_dataset(ssfn, ofn, "1.1None", "None, None")
self.assertEqual(None, sanitize_read_length(""))
self.assertEqual(None, sanitize_read_length(0))
self.assertEqual(None, sanitize_read_length(0))
with self.assertRaises(ValueError):
sanitize_read_length("None")
self.assertEqual(None, sanitize_read_length(None))
self.assertEqual(None, sanitize_read_length(0))
self.assertEqual(None, sanitize_read_length(False))
with self.assertRaises(ValueError):
sanitize_read_length(True)
self.assertEqual(None, sanitize_read_length(False))
with self.assertRaises(ValueError):
sanitize_read_length(True)
self.assertEqual(1, sanitize_read_length(1))
self.assertEqual(0, sanitize_read_length("0"))
self.assertEqual(0, sanitize_read_length(" 0 "))
self.assertEqual(-1, sanitize_read_length("-1"))
self.assertEqual(-1, sanitize_read_length(" -1 "))
self.assertEqual(-1, sanitize_read_length(-1))
self.assertEqual(1, sanitize_read_length("1.0"))
self.assertEqual(1, sanitize_read_length(" 1.0 "))
self.assertEqual(1, sanitize_read_length(1.0))
with self.assertRaises(ValueError):
sanitize_read_length(" 1. 0 ")
with self.assertRaises(ValueError):
sanitize_read_length("1. 0")
self.assertEqual(10, sanitize_read_length("10.0"))
self.assertEqual(10, sanitize_read_length(10.0))
self.assertEqual(0, sanitize_read_length("0.01"))
self.assertEqual(0, sanitize_read_length(0.01))
self.assertEqual(100000, sanitize_read_length("100000.01"))
self.assertEqual(100000, sanitize_read_length(100000.01))
self.assertEqual(100000, sanitize_read_length(100000))
# These two are somewhat annoying:
self.assertEqual(0, sanitize_read_length(".00"))
self.assertEqual(None, sanitize_read_length(.00))
self.assertEqual(1, sanitize_read_length(1.))
self.assertEqual(1, sanitize_read_length("1."))
with self.assertRaises(ValueError):
sanitize_read_length("None.1")
with self.assertRaises(ValueError):
sanitize_read_length("None1")
with self.assertRaises(ValueError):
sanitize_read_length("1.1None")
def test_filter_application(self):
ssfn = data.getXml(8)
ofn = tempfile.NamedTemporaryFile(suffix=".xml").name
# some smoke tests:
run_filter_dataset(ssfn, ofn, "0", "None")
ds = openDataSet(ofn)
self.assertEqual(len(ds), 92)
run_filter_dataset(ssfn, ofn, "10000", "None")
ds = openDataSet(ofn)
self.assertEqual(len(ds), 0)
run_filter_dataset(ssfn, ofn, "100", "rq > .7")
ds = openDataSet(ofn)
self.assertEqual(str(ds.filters),
"( rq > .7 AND length >= 100 )")
run_filter_dataset(ssfn, ofn, "100", "rq > .7, length < 5000")
ds = openDataSet(ofn)
self.assertEqual(
str(ds.filters),
'( length < 5000 AND rq > .7 AND length >= 100 )')
run_filter_dataset(ssfn, ofn, 0,
"rq>=.7, length >= 1000, length <= 5000")
ds = openDataSet(ofn)
self.assertEqual(
str(ds.filters),
'( length >= 1000 AND length <= 5000 AND rq >= .7 )')
run_filter_dataset(ssfn, ofn, 0,
"rq>=.7, length gte 1000, length lte 5000")
ds = openDataSet(ofn)
self.assertEqual(
str(ds.filters),
'( length gte 1000 AND length lte 5000 AND rq >= .7 )')
