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):
# Get all arguments that DataTables send us
res = {"data": [
[s['study_id'], s['study_title'], s['study_alias'], s['owner'],
s['num_samples']] for s in Study.list_studies()]}
self.write(res)
self.finish()
def test_sample_composition_attributes(self):
# Test a sample
obs = SampleComposition(1)
self.assertEqual(obs.sample_composition_type, 'experimental sample')
self.assertEqual(obs.sample_id, '1.SKB1.640202')
self.assertEqual(obs.content, '1.SKB1.640202.Test.plate.1.A1')
self.assertEqual(obs.upstream_process, SamplePlatingProcess(11))
self.assertEqual(obs.container, Well(3073))
self.assertEqual(obs.total_volume, 10)
self.assertIsNone(obs.notes)
obs.notes = 'New Notes'
self.assertEqual(obs.notes, 'New Notes')
obs.notes = None
self.assertIsNone(obs.notes)
self.assertEqual(obs.composition_id, 3082)
self.assertEqual(obs.study, Study(1))
# Test a control sample
obs = SampleComposition(8)
self.assertEqual(obs.sample_composition_type, 'blank')
self.assertIsNone(obs.sample_id)
self.assertEqual(obs.content, 'blank.Test.plate.1.H1')
self.assertEqual(obs.upstream_process, SamplePlatingProcess(11))
self.assertEqual(obs.container, Well(3115))
self.assertEqual(obs.total_volume, 10)
self.assertIsNone(obs.notes)
self.assertEqual(obs.composition_id, 3124)
self.assertIsNone(obs.study)
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_gDNA_composition_attributes(self):
obs = GDNAComposition(1)
self.assertEqual(obs.sample_composition, SampleComposition(1))
self.assertEqual(obs.upstream_process, GDNAExtractionProcess(1))
self.assertEqual(obs.container, Well(3074))
self.assertEqual(obs.total_volume, 10)
self.assertIsNone(obs.notes)
self.assertEqual(obs.composition_id, 3083)
self.assertEqual(obs.study, Study(1))
def get(self, study_id):
try:
study = Study(int(study_id))
except LabControlUnknownIdError:
raise HTTPError(404, reason="Study %s doesn't exist" % study_id)
study_numbers = study.sample_numbers_summary
self.render('study.html', study_id=study.id,
study_title=study.title, study_numbers=study_numbers)
def test_library_prep_16S_composition_attributes(self):
obs = LibraryPrep16SComposition(1)
self.assertEqual(obs.container, Well(3075))
self.assertEqual(obs.total_volume, 10)
self.assertIsNone(obs.notes)
self.assertEqual(obs.gdna_composition, GDNAComposition(1))
self.assertEqual(obs.primer_composition, PrimerComposition(1))
self.assertEqual(obs.composition_id, 3084)
self.assertEqual(obs.study, Study(1))
def get(self, study_id):
try:
study = Study(int(study_id))
self.write({'study_id': study.id,
'study_title': study.title,
'total_samples': study.num_samples})
except LabControlUnknownIdError:
self.set_status(404)
self.finish()
def test_library_prep_shotgun_composition_attributes(self):
obs = LibraryPrepShotgunComposition(1)
self.assertEqual(obs.container, Well(3078))
self._baseAssertEqual(obs.total_volume, 4000)
self.assertIsNone(obs.notes)
self.assertEqual(obs.normalized_gdna_composition,
NormalizedGDNAComposition(1))
self.assertEqual(obs.i5_composition, PrimerComposition(769))
self.assertEqual(obs.i7_composition, PrimerComposition(770))
self.assertEqual(obs.composition_id, 3087)
self.assertEqual(obs.study, Study(1))
def test_normalized_gDNA_composition_attributes(self):
obs = NormalizedGDNAComposition(1)
self.assertEqual(obs.container, Well(3077))
self.assertEqual(obs.total_volume, 3500)
self.assertIsNone(obs.notes)
self.assertEqual(obs.compressed_gdna_composition,
CompressedGDNAComposition(1))
self.assertEqual(obs.dna_volume, 415)
self.assertEqual(obs.water_volume, 3085)
self.assertEqual(obs.composition_id, 3086)
self.assertEqual(obs.study, Study(1))
def test_list_studies(self):
obs = Study.list_studies()
exp = [{
'study_id': 1,
'study_title': 'Identification of the Microbiomes for '
'Cannabis Soils',
'study_alias': 'Cannabis Soils',
'owner': '*****@*****.**',
'num_samples': 27
}]
self.assertEqual(obs, exp)
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_translate_ids_with_sample_id(self):
# Tests sample_id_to_specimen_id and specimen_id_to_sample_id when
# there is no specimen identifier set for the study
s = Study(1)
obs = s.sample_id_to_specimen_id('1.SKM4.640180')
self.assertEqual(obs, '1.SKM4.640180')
# doesn't even need to be a valid sample id
obs = s.sample_id_to_specimen_id('SKM3')
self.assertEqual(obs, 'SKM3')
with self.assertRaisesRegex(ValueError, 'Could not find "SKM4"'):
s.specimen_id_to_sample_id('SKM4')
with self.assertRaisesRegex(ValueError, 'Could not find "SSSS"'):
s.specimen_id_to_sample_id('SSSS')
def test_translate_ids_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'])
obs = s.sample_id_to_specimen_id('1.SKM4.640180')
self.assertEqual(obs, 'SKM4')
obs = s.specimen_id_to_sample_id('SKM4')
self.assertEqual(obs, '1.SKM4.640180')
# should be an exact match
with self.assertRaisesRegex(ValueError,
'Could not find \"1\.skm4\.640180\"'):
s.sample_id_to_specimen_id('1.skm4.640180')
with self.assertRaisesRegex(ValueError, 'Could not find \"skm4\"'):
s.specimen_id_to_sample_id('skm4')
# raise an error in the rare case that the specimen_id_column was
# set to something that's not unique (this could only accidentally
# happen)
TRN.add(sql, ['taxon_id'])
with self.assertRaisesRegex(
RuntimeError, 'There are several '
'matches found for "1118232"; there is'
' a problem with the specimen id '
'column'):
s.specimen_id_to_sample_id('1118232')
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_attributes(self):
s = Study(1)
self.assertEqual(
s.title, 'Identification of the Microbiomes '
'for Cannabis Soils')
self.assertEqual(s.creator, User('*****@*****.**'))
self.assertEqual(s.num_samples, 27)
exp = {
'num_samples': 27,
'number_samples_plated': 10,
'number_samples_extracted': 10,
'number_samples_amplicon_libraries': 10,
'number_samples_amplicon_pools': 10,
'number_samples_amplicon_sequencing_pools': 10,
'number_samples_amplicon_sequencing_runs': 10,
'number_samples_compressed': 10,
'number_samples_normalized': 10,
'number_samples_shotgun_libraries': 10,
'number_samples_shotgun_pool': 10,
'number_samples_shotgun_sequencing_runs': 10
}
self.assertEqual(s.sample_numbers_summary, exp)
def test_specimen_id_column(self):
s = Study(1)
self.assertIsNone(s.specimen_id_column)
def test_properties(self):
# Plate 21 - Defined in the test DB
tester = Plate(21)
obs = tester.creation_timestamp
obs = str(datetime.datetime(obs.year, obs.month, obs.day))
exp = datetime.datetime.now()
exp = str(datetime.datetime(exp.year, exp.month, exp.day))
self.assertEqual(obs, exp)
self.assertEqual(tester.external_id, 'Test plate 1')
self.assertEqual(tester.plate_configuration, PlateConfiguration(1))
self.assertFalse(tester.discarded)
tester.discarded = True
self.assertTrue(tester.discarded)
self.assertIsNone(tester.notes)
obs_layout = tester.layout
self.assertEqual(len(obs_layout), 8)
for row in obs_layout:
self.assertEqual(len(row), 12)
self.assertEqual(tester.studies, {Study(1)})
self.assertListEqual(tester.quantification_processes, [])
self.assertEqual(tester.process, SamplePlatingProcess(11))
# Test changing the name of the plate
tester.external_id = 'Some new name'
self.assertEqual(tester.external_id, 'Some new name')
tester.external_id = 'Test plate 1'
self.assertEqual(tester.external_id, 'Test plate 1')
self.assertEqual(len(Plate(23).quantification_processes), 1)
self.assertEqual(
Plate(23).quantification_processes[0], QuantificationProcess(1))
self.assertEqual(Plate(22).process, GDNAExtractionProcess(1))
exp = {
'1.SKB1.640202': [[Well(3073), '1.SKB1.640202.Test.plate.1.A1'],
[Well(3121), '1.SKB1.640202.Test.plate.1.A2'],
[Well(3169), '1.SKB1.640202.Test.plate.1.A3'],
[Well(3217), '1.SKB1.640202.Test.plate.1.A4'],
[Well(3265), '1.SKB1.640202.Test.plate.1.A5'],
[Well(3313), '1.SKB1.640202.Test.plate.1.A6'],
[Well(3361), '1.SKB1.640202.Test.plate.1.A7'],
[Well(3409), '1.SKB1.640202.Test.plate.1.A8'],
[Well(3457), '1.SKB1.640202.Test.plate.1.A9'],
[Well(3505), '1.SKB1.640202.Test.plate.1.A10'],
[Well(3553), '1.SKB1.640202.Test.plate.1.A11'],
[Well(3601), '1.SKB1.640202.Test.plate.1.A12']],
'1.SKB2.640194': [[Well(3079), '1.SKB2.640194.Test.plate.1.B1'],
[Well(3127), '1.SKB2.640194.Test.plate.1.B2'],
[Well(3175), '1.SKB2.640194.Test.plate.1.B3'],
[Well(3223), '1.SKB2.640194.Test.plate.1.B4'],
[Well(3271), '1.SKB2.640194.Test.plate.1.B5'],
[Well(3319), '1.SKB2.640194.Test.plate.1.B6'],
[Well(3367), '1.SKB2.640194.Test.plate.1.B7'],
[Well(3415), '1.SKB2.640194.Test.plate.1.B8'],
[Well(3463), '1.SKB2.640194.Test.plate.1.B9'],
[Well(3511), '1.SKB2.640194.Test.plate.1.B10'],
[Well(3559), '1.SKB2.640194.Test.plate.1.B11'],
[Well(3607), '1.SKB2.640194.Test.plate.1.B12']],
'1.SKB3.640195': [[Well(3085), '1.SKB3.640195.Test.plate.1.C1'],
[Well(3133), '1.SKB3.640195.Test.plate.1.C2'],
[Well(3181), '1.SKB3.640195.Test.plate.1.C3'],
[Well(3229), '1.SKB3.640195.Test.plate.1.C4'],
[Well(3277), '1.SKB3.640195.Test.plate.1.C5'],
[Well(3325), '1.SKB3.640195.Test.plate.1.C6'],
[Well(3373), '1.SKB3.640195.Test.plate.1.C7'],
[Well(3421), '1.SKB3.640195.Test.plate.1.C8'],
[Well(3469), '1.SKB3.640195.Test.plate.1.C9'],
[Well(3517), '1.SKB3.640195.Test.plate.1.C10'],
[Well(3565), '1.SKB3.640195.Test.plate.1.C11'],
[Well(3613), '1.SKB3.640195.Test.plate.1.C12']],
'1.SKB4.640189': [[Well(3091), '1.SKB4.640189.Test.plate.1.D1'],
[Well(3139), '1.SKB4.640189.Test.plate.1.D2'],
[Well(3187), '1.SKB4.640189.Test.plate.1.D3'],
[Well(3235), '1.SKB4.640189.Test.plate.1.D4'],
[Well(3283), '1.SKB4.640189.Test.plate.1.D5'],
[Well(3331), '1.SKB4.640189.Test.plate.1.D6'],
[Well(3379), '1.SKB4.640189.Test.plate.1.D7'],
[Well(3427), '1.SKB4.640189.Test.plate.1.D8'],
[Well(3475), '1.SKB4.640189.Test.plate.1.D9'],
[Well(3523), '1.SKB4.640189.Test.plate.1.D10'],
[Well(3571), '1.SKB4.640189.Test.plate.1.D11'],
[Well(3619), '1.SKB4.640189.Test.plate.1.D12']],
'1.SKB5.640181': [[Well(3097), '1.SKB5.640181.Test.plate.1.E1'],
[Well(3145), '1.SKB5.640181.Test.plate.1.E2'],
[Well(3193), '1.SKB5.640181.Test.plate.1.E3'],
[Well(3241), '1.SKB5.640181.Test.plate.1.E4'],
[Well(3289), '1.SKB5.640181.Test.plate.1.E5'],
[Well(3337), '1.SKB5.640181.Test.plate.1.E6'],
[Well(3385), '1.SKB5.640181.Test.plate.1.E7'],
[Well(3433), '1.SKB5.640181.Test.plate.1.E8'],
[Well(3481), '1.SKB5.640181.Test.plate.1.E9'],
[Well(3529), '1.SKB5.640181.Test.plate.1.E10'],
[Well(3577), '1.SKB5.640181.Test.plate.1.E11'],
[Well(3625), '1.SKB5.640181.Test.plate.1.E12']],
'1.SKB6.640176': [[Well(3103), '1.SKB6.640176.Test.plate.1.F1'],
[Well(3151), '1.SKB6.640176.Test.plate.1.F2'],
[Well(3199), '1.SKB6.640176.Test.plate.1.F3'],
[Well(3247), '1.SKB6.640176.Test.plate.1.F4'],
[Well(3295), '1.SKB6.640176.Test.plate.1.F5'],
[Well(3343), '1.SKB6.640176.Test.plate.1.F6'],
[Well(3391), '1.SKB6.640176.Test.plate.1.F7'],
[Well(3439), '1.SKB6.640176.Test.plate.1.F8'],
[Well(3487), '1.SKB6.640176.Test.plate.1.F9'],
[Well(3535), '1.SKB6.640176.Test.plate.1.F10'],
[Well(3583), '1.SKB6.640176.Test.plate.1.F11']]
}
self.assertEqual(tester.duplicates, exp)
self.assertEqual(tester.unknown_samples, [])
exp = tester.get_well(1, 1)
exp.composition.update('Unknown')
self.assertEqual(tester.unknown_samples, [exp])
exp.composition.update('1.SKB1.640202')
# test that the quantification_processes attribute correctly
# orders multiple processes in order from oldest to newest
tester2 = Plate(26)
self.assertEqual(len(tester2.quantification_processes), 2)
# we are going to test the dates as string because in the database we
# have the full date (including seconds)
obs_date = str(tester2.quantification_processes[0].date)
self.assertEqual(obs_date, "2017-10-25 19:10:25")
obs_date = str(tester2.quantification_processes[1].date)
self.assertEqual(obs_date, "2017-10-26 03:10:25")
def sample_plating_process_handler_patch_request(user, process_id, req_op,
req_path, req_value,
req_from):
"""Performs the patch operation on the sample plating process
Parameters
----------
user: labcontrol.db.user.User
User performing the request
process_id: int
The SamplePlatingProcess to apply the patch operation
req_op: string
JSON PATCH op parameter
req_path: string
JSON PATCH path parameter
req_value: string
JSON PATCH value parameter
req_from: string
JSON PATCH from parameter
Returns
-------
dict
The results of the patch operation
Raises
------
HTTPError
400: If req_op is not a supported operation
400: If req_path is incorrect
"""
if req_op == 'replace':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 5:
raise HTTPError(400, 'Incorrect path parameter')
attribute = req_path[0]
if attribute == 'well':
row = req_path[1]
col = req_path[2]
study_id = int(req_path[3])
well_attribute = req_path[4]
# The default values of the variables sample_id and
# blank_or_unknown are set before the try, and these are the values
# that are used if either (a) study_id is not 0 OR (b) the try
# fails with a ValueError (see comment in try below). If the try
# fails with anything other than a ValueError then the entire
# function bails, so it doesn't matter what these variables are set
# to. If and only if the try succeeds are these variables set to
# the values within the try.
sample_id = req_value
blank_or_unknown = True
# It actually IS possible to plate a plate without specifying
# separate study id(s); can plate just all blanks, or can provide
# the fully qualified sample id(s)--i.e., <studyid>.<sampleid>.
if study_id != 0:
try:
# Note that the try fails iff the
# Study(study_id).specimen_id_to_sample_id() call fails,
# as the blank_or_unknown = False can't really fail ...
# this assures that we can't realistically end up in an
# inconsistent situation where sample_id has been set
# during the try but blank_or_unknown has not.
#
# Thus, the ordering of these two statements within the try
# is really important: do not change it unless you
# understand all of the above!
the_study = Study(study_id)
sample_id = the_study.specimen_id_to_sample_id(req_value)
blank_or_unknown = False
except ValueError:
pass
# end try/except
# end if
if well_attribute == 'sample':
if req_value is None or not req_value.strip():
raise HTTPError(
400, 'A new value for the well should be provided')
plates = Plate.search(samples=[sample_id])
process = SamplePlatingProcess(process_id)
plates = set(plates) - {process.plate}
prev_plates = [{
'plate_id': p.id,
'plate_name': p.external_id
} for p in plates]
content, sample_ok = process.update_well(row, col, sample_id)
if blank_or_unknown:
req_value = content
return {
'sample_id': req_value,
'previous_plates': prev_plates,
'sample_ok': sample_ok
}
elif well_attribute == 'notes':
if req_value is not None:
# If the user provides an empty string, just store None
# in the database
req_value = (req_value.strip()
if req_value.strip() else None)
SamplePlatingProcess(process_id).comment_well(
row, col, req_value)
return {'comment': req_value}
else:
raise HTTPError(404,
'Well attribute %s not found' % well_attribute)
else:
raise HTTPError(404, 'Attribute %s not found' % attribute)
else:
raise HTTPError(
400, 'Operation %s not supported. Current supported '
'operations: replace' % req_op)
def test_init(self):
with self.assertRaises(LabControlUnknownIdError):
Study(1000000)
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")