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 post(self):
user = self.current_user
plate_config_id = self.get_argument('plate_configuration')
plate_ext_id = self.get_argument('plate_name')
spp = SamplePlatingProcess.create(user,
PlateConfiguration(plate_config_id),
plate_ext_id)
self.write({'plate_id': spp.plate.id, 'process_id': spp.id})
def test_properties(self):
tester = Well(3073)
self.assertEqual(tester.plate, Plate(21))
self.assertEqual(tester.row, 1)
self.assertEqual(tester.column, 1)
self.assertEqual(tester.remaining_volume, 10)
self.assertIsNone(tester.notes)
self.assertEqual(tester.latest_process, SamplePlatingProcess(11))
self.assertEqual(tester.container_id, 3082)
self.assertEqual(tester.composition, SampleComposition(1))
def create_sample_plate_process(user, samples, is_96):
plate_config = get_target_plate_configuration(is_96)
num_rows = plate_config.num_rows
num_cols = plate_config.num_columns
sp_process = SamplePlatingProcess.create(user, plate_config,
'Test plate %s' % datetime.now())
# Plate the samples
for idx, sample in enumerate(samples):
i = int(idx / num_cols) + 1
j = (idx % num_cols) + 1
# Make sure that the user didn't pass more samples than wells
if i > num_rows:
break
sp_process.update_well(i, j, sample)
sample_plate = sp_process.plate
return sp_process, sample_plate
def plate_map_handler_get_request(process_id):
plate_id = None
if process_id is not None:
try:
process = SamplePlatingProcess(process_id)
except LabControlUnknownIdError:
raise HTTPError(404,
reason="Plating process %s doesn't exist" %
process_id)
plate_id = process.plate.id
plate_confs = [[pc.id, pc.description, pc.num_rows, pc.num_columns]
for pc in PlateConfiguration.iter()
if 'plate map' not in pc.description]
cdesc = SampleComposition.get_control_sample_types_description()
return {
'plate_confs': plate_confs,
'plate_id': plate_id,
'process_id': process_id,
'controls_description': cdesc
}
def test_get_previously_plated_wells(self):
tester = Plate(21)
three_plates_list = [Plate(27), Plate(30), Plate(33)]
exp = {
Well(3073): three_plates_list,
Well(3079): three_plates_list,
Well(3085): three_plates_list,
Well(3091): three_plates_list,
Well(3097): three_plates_list,
Well(3103): three_plates_list,
Well(3121): three_plates_list,
Well(3127): three_plates_list,
Well(3133): three_plates_list,
Well(3139): three_plates_list,
Well(3145): three_plates_list,
Well(3151): three_plates_list,
Well(3169): three_plates_list,
Well(3175): three_plates_list,
Well(3181): three_plates_list,
Well(3187): three_plates_list,
Well(3193): three_plates_list,
Well(3199): three_plates_list,
Well(3217): three_plates_list,
Well(3223): three_plates_list,
Well(3229): three_plates_list,
Well(3235): three_plates_list,
Well(3241): three_plates_list,
Well(3247): three_plates_list,
Well(3265): three_plates_list,
Well(3271): three_plates_list,
Well(3277): three_plates_list,
Well(3283): three_plates_list,
Well(3289): three_plates_list,
Well(3295): three_plates_list,
Well(3313): three_plates_list,
Well(3319): three_plates_list,
Well(3325): three_plates_list,
Well(3331): three_plates_list,
Well(3337): three_plates_list,
Well(3343): three_plates_list,
Well(3361): three_plates_list,
Well(3367): three_plates_list,
Well(3373): three_plates_list,
Well(3379): three_plates_list,
Well(3385): three_plates_list,
Well(3391): three_plates_list,
Well(3409): three_plates_list,
Well(3415): three_plates_list,
Well(3421): three_plates_list,
Well(3427): three_plates_list,
Well(3433): three_plates_list,
Well(3439): three_plates_list,
Well(3457): three_plates_list,
Well(3463): three_plates_list,
Well(3469): three_plates_list,
Well(3475): three_plates_list,
Well(3481): three_plates_list,
Well(3487): three_plates_list,
Well(3505): three_plates_list,
Well(3511): three_plates_list,
Well(3517): three_plates_list,
Well(3523): three_plates_list,
Well(3529): three_plates_list,
Well(3535): three_plates_list,
Well(3553): three_plates_list,
Well(3559): three_plates_list,
Well(3565): three_plates_list,
Well(3571): three_plates_list,
Well(3577): three_plates_list,
Well(3583): three_plates_list,
Well(3601): three_plates_list,
Well(3607): three_plates_list,
Well(3613): three_plates_list,
Well(3619): three_plates_list,
Well(3625): three_plates_list
}
obs = tester.get_previously_plated_wells()
self.assertEqual(obs, exp)
# Create another plate and put a sample on it that isn't anywhere else
spp = SamplePlatingProcess.create(User('*****@*****.**'),
PlateConfiguration(1),
'New Plate For Prev')
spp.update_well(1, 1, '1.SKM1.640184')
obs = spp.plate.get_previously_plated_wells()
self.assertEqual(obs, {})
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 post(self):
process = SamplePlatingProcess(self.get_argument('process_id'))
process.notes = self.get_argument('notes')
self.finish()