def get(self, study_id):
try:
study = Study(int(study_id))
term = self.get_argument('term', None)
res = list(study.samples(term, limit=20))
self.write(json_encode(res))
except LabControlUnknownIdError:
self.set_status(404)
self.finish()
def get(self, study_id):
try:
study = Study(int(study_id))
term = self.get_argument('term', None)
limit = self.get_argument('limit', None)
# If the specified limit is somehow invalid, study.samples() will
# raise a ValueError. In this case, we'll set a 400 ("Bad Request")
# status code.
res = list(study.samples(term, limit))
self.write(json_encode(res))
except LabControlUnknownIdError:
self.set_status(404)
except ValueError:
# These will be raised if the limit passed is invalid
self.set_status(400)
self.finish()
def test_samples_with_specimen_id(self):
s = Study(1)
# HACK: the Study object in labcontrol can't modify specimen_id_column
# hence we do this directly in SQL, if a test fails the transaction
# will rollback, otherwise we reset the column to NULL.
sql = """UPDATE qiita.study
SET specimen_id_column = %s
WHERE study_id = 1"""
with sql_connection.TRN as TRN:
TRN.add(sql, ['anonymized_name'])
exp_samples = [
'SKB1', 'SKB2', 'SKB3', 'SKB4', 'SKB5', 'SKB6', 'SKB7', 'SKB8',
'SKB9', 'SKD1', 'SKD2', 'SKD3', 'SKD4', 'SKD5', 'SKD6', 'SKD7',
'SKD8', 'SKD9', 'SKM1', 'SKM2', 'SKM3', 'SKM4', 'SKM5', 'SKM6',
'SKM7', 'SKM8', 'SKM9'
]
self.assertEqual(s.samples(), exp_samples)
exp_samples = [
'SKB1', 'SKB2', 'SKB3', 'SKB4', 'SKB5', 'SKB6', 'SKB7', 'SKB8',
'SKB9'
]
self.assertEqual(s.samples(limit=9), exp_samples)
exp_samples = [
'SKB1', 'SKB2', 'SKB3', 'SKB4', 'SKB5', 'SKB6', 'SKB7', 'SKB8',
'SKB9'
]
self.assertEqual(s.samples('SKB'), exp_samples)
exp_samples = ['SKB1', 'SKB2', 'SKB3']
self.assertEqual(s.samples('SKB', limit=3), exp_samples)
exp_samples = [
'SKM1', 'SKM2', 'SKM3', 'SKM4', 'SKM5', 'SKM6', 'SKM7', 'SKM8',
'SKM9'
]
self.assertEqual(s.samples('SKM'), exp_samples)
exp_samples = [
'SKM1', 'SKM2', 'SKM3', 'SKM4', 'SKM5', 'SKM6', 'SKM7', 'SKM8',
'SKM9'
]
# case insensitive
self.assertEqual(s.samples('Skm'), exp_samples)
self.assertEqual(s.samples('64'), [])
TRN.add(sql, [None])
def test_samples_with_sample_id(self):
s = Study(1)
exp_samples = [
'1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195', '1.SKB4.640189',
'1.SKB5.640181', '1.SKB6.640176', '1.SKB7.640196', '1.SKB8.640193',
'1.SKB9.640200', '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190', '1.SKD7.640191',
'1.SKD8.640184', '1.SKD9.640182', '1.SKM1.640183', '1.SKM2.640199',
'1.SKM3.640197', '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'
]
self.assertEqual(s.samples(), exp_samples)
exp_samples = [
'1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195', '1.SKB4.640189',
'1.SKB5.640181', '1.SKB6.640176', '1.SKB7.640196', '1.SKB8.640193',
'1.SKB9.640200'
]
self.assertEqual(s.samples(limit='9'), exp_samples)
exp_samples = [
'1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195', '1.SKB4.640189',
'1.SKB5.640181', '1.SKB6.640176', '1.SKB7.640196', '1.SKB8.640193',
'1.SKB9.640200'
]
self.assertEqual(s.samples('SKB'), exp_samples)
exp_samples = ['1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195']
self.assertEqual(s.samples('SKB', limit='3'), exp_samples)
exp_samples = [
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197', '1.SKM4.640180',
'1.SKM5.640177', '1.SKM6.640187', '1.SKM7.640188', '1.SKM8.640201',
'1.SKM9.640192'
]
self.assertEqual(s.samples('1.SKM'), exp_samples)
exp_samples = [
'1.SKM1.640183', '1.SKM2.640199', '1.SKM3.640197', '1.SKM4.640180',
'1.SKM5.640177', '1.SKM6.640187', '1.SKM7.640188', '1.SKM8.640201',
'1.SKM9.640192'
]
self.assertEqual(s.samples('1.Skm'), exp_samples) # case insensitive
exp_samples = ['1.SKB1.640202', '1.SKD1.640179', '1.SKM1.640183']
self.assertEqual(s.samples('1.64'), exp_samples)
def test_samples_with_limit(self):
"""Unit-tests the `limit` argument of Study.samples() in particular.
It's worth noting that the `limit` value that StudySamplesHandler.get()
uses when calling Study.samples() is actually a string -- this is due
to our use of tornado.web.RequestHandler.get_argument().
Study.samples() only cares that `int(limit)` succeeds, and is otherwise
agnostic to the actual input type of `limit`.
(For the sake of caution, we test a couple of types besides purely
`str` values within this function.)
"""
s = Study(1)
all_samples = [
'1.SKB1.640202', '1.SKB2.640194', '1.SKB3.640195', '1.SKB4.640189',
'1.SKB5.640181', '1.SKB6.640176', '1.SKB7.640196', '1.SKB8.640193',
'1.SKB9.640200', '1.SKD1.640179', '1.SKD2.640178', '1.SKD3.640198',
'1.SKD4.640185', '1.SKD5.640186', '1.SKD6.640190', '1.SKD7.640191',
'1.SKD8.640184', '1.SKD9.640182', '1.SKM1.640183', '1.SKM2.640199',
'1.SKM3.640197', '1.SKM4.640180', '1.SKM5.640177', '1.SKM6.640187',
'1.SKM7.640188', '1.SKM8.640201', '1.SKM9.640192'
]
# Check cases where the limit is valid but doesn't actually result in
# any filtering being done.
self.assertEqual(s.samples(), all_samples)
for i in [27, 28, 50, 100, 10000]:
self.assertEqual(s.samples(limit=i), all_samples)
self.assertEqual(s.samples(limit=str(i)), all_samples)
# limit=None is the default, but we check it here explicitly anyway.
self.assertEqual(s.samples(limit=None), all_samples)
# Check *all* limit values in the inclusive range [1, 27] -- these
# should, well, limit the output list of samples accordingly
for i in range(1, len(all_samples)):
self.assertEqual(s.samples(limit=i), all_samples[:i])
self.assertEqual(s.samples(limit=str(i)), all_samples[:i])
float_limits_to_test = [1.0, 1.2, 3.0, 27.0, 29.1, 1000.0]
str_of_float_limits_to_test = [str(f) for f in float_limits_to_test]
# Test that various not-castable-to-a-base-10-int inputs don't work
# (This includes string representations of floats, e.g. "1.0", since
# such a string is not a valid "integer literal" -- see
# https://docs.python.org/3/library/functions.html#int.
uncastable_limits_to_test = [[1, 2, 3], "abc", "gibberish", "ten",
(1, ), "0xBEEF", "0b10101", "0o123",
float("inf"),
float("-inf"),
float("nan"), "None", "inf"]
for i in uncastable_limits_to_test + str_of_float_limits_to_test:
with self.assertRaisesRegex(ValueError,
"limit must be castable to an int"):
s.samples(limit=i)
# Calling int(x) where x is a float just truncates x "towards zero"
# according to https://docs.python.org/3/library/functions.html#int.
#
# This behavior is tested, but it should never happen (one, because
# as of writing Study.samples() is only called with a string limit
# value, and two because I can't imagine why someone would pass a float
# in for the "limit" argument).
for i in float_limits_to_test:
self.assertEqual(s.samples(limit=i), all_samples[:floor(i)])
# Check that limits <= 0 cause an error
nonpositive_limits = [0, -1, -2, -27, -53, -100]
for i in nonpositive_limits:
with self.assertRaisesRegex(ValueError,
"limit must be greater than zero"):
s.samples(limit=i)
with self.assertRaisesRegex(ValueError,
"limit must be greater than zero"):
s.samples(limit=str(i))
# Check evil corner case where the limit is nonpositive and not
# castable to an int (this should fail first on the castable check)
with self.assertRaisesRegex(ValueError,
"limit must be castable to an int"):
s.samples(limit="-1.0")