def test_search(self):
with self.assertRaises(ValueError):
Plate.search()
with self.assertRaises(ValueError):
Plate.search(samples=['1.SKB1.640202'], query_type='WRONG')
plate21 = Plate(21)
plate22 = Plate(22)
plate23 = Plate(23)
plate27 = Plate(27)
plate30 = Plate(30)
plate33 = Plate(33)
self.assertEqual(
Plate.search(samples=['1.SKB1.640202', '1.SKB2.640194']),
[plate21, plate27, plate30, plate33])
self.assertEqual(Plate.search(samples=['1.SKB1.640202']),
[plate21, plate27, plate30, plate33])
self.assertEqual(Plate.search(plate_notes='interesting'), [])
# Add comments to a plate so we can actually test the
# search functionality
plate22.notes = 'Some interesting notes'
plate23.notes = 'More boring notes'
self.assertEqual(Plate.search(plate_notes='interesting'), [plate22])
self.assertCountEqual(Plate.search(plate_notes='interesting boring'),
[])
self.assertEqual(
Plate.search(samples=['1.SKB1.640202'], plate_notes='interesting'),
[])
# sample '1.SKB1.640202' is on 4 sample plates, plus there is a
# gdna plate with a note containing the word 'interesting'
self.assertCountEqual(
Plate.search(samples=['1.SKB1.640202'],
plate_notes='interesting',
query_type='UNION'),
[plate21, plate22, plate27, plate30, plate33])
# The search engine ignores common english words
self.assertEqual(Plate.search(plate_notes='more'), [])
# Add comments to some wells
plate23.get_well(1, 1).composition.notes = 'What else should I write?'
self.assertEqual(Plate.search(well_notes='write'), [plate23])
self.assertEqual(
Plate.search(plate_notes='interesting', well_notes='write'), [])
self.assertCountEqual(
Plate.search(plate_notes='interesting',
well_notes='write',
query_type='UNION'), [plate22, plate23])
def test_get_well(self):
# Plate 21 - Defined in the test DB
tester = Plate(21)
self.assertEqual(tester.get_well(1, 1), Well(3073))
self.assertEqual(tester.get_well(1, 2), Well(3088))
self.assertEqual(tester.get_well(7, 2), Well(4168))
self.assertEqual(tester.get_well(8, 12), Well(4498))
with self.assertRaises(LabmanError):
tester.get_well(8, 13)
with self.assertRaises(LabmanError):
tester.get_well(9, 12)
def test_post_plate_search_handler(self):
# Note: these tests don't exercise all the cases covered in
# db/tests/test_plate.py test_search; instead, they focus on
# testing at least one search based on each of the input
# fields, to verify that these are being passed through
# correctly to the db's Plate.search method.
# Test search by sample names:
post_data = {
'sample_names': dumps(['1.SKB1.640202', '1.SKB2.640194']),
'plate_comment_keywords': "",
'well_comment_keywords': "",
'operation': "INTERSECT"
}
response = self.post('/plate_search', post_data)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertCountEqual(obs.keys(), ['data'])
obs_data = obs['data']
self.assertEqual(len(obs_data), 1)
self.assertEqual(obs_data[0], [21, 'Test plate 1'])
# Test search by plate comment keywords:
# It looks like none of the plates in the test database have
# any notes, so it is necessary to add some to be able to
# test the keywords search functionality; the below is lifted
# verbatim from db/tests/test_plate.py test_search
plate22 = Plate(22)
plate23 = Plate(23)
# Add comments to a plate so we can actually test the
# search functionality
plate22.notes = 'Some interesting notes'
plate23.notes = 'More boring notes'
# end verbatim lift
post_data = {
'sample_names': dumps([]),
'plate_comment_keywords': 'interesting boring',
'well_comment_keywords': "",
'operation': "INTERSECT"
}
response = self.post('/plate_search', post_data)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertCountEqual(obs.keys(), ['data'])
obs_data = obs['data']
self.assertEqual(len(obs_data), 0)
# Test search by intersecting or unioning multiple search terms:
post_data = {
'sample_names': dumps(['1.SKB1.640202']),
'plate_comment_keywords': 'interesting boring',
'well_comment_keywords': "",
'operation': "INTERSECT"
}
response = self.post('/plate_search', post_data)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertCountEqual(obs.keys(), ['data'])
obs_data = obs['data']
self.assertEqual(len(obs_data), 0)
post_data = {
'sample_names': dumps(['1.SKB1.640202']),
'plate_comment_keywords': 'interesting boring',
'well_comment_keywords': "",
'operation': "UNION"
}
response = self.post('/plate_search', post_data)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertCountEqual(obs.keys(), ['data'])
obs_data = obs['data']
self.assertEqual(len(obs_data), 1)
self.assertEqual(obs_data[0], [21, 'Test plate 1'])
# Test search by well comment keywords:
# Add comments to some wells so can test well comment search
plate23.get_well(1, 1).composition.notes = 'What should I write?'
post_data = {
'sample_names': dumps([]),
'plate_comment_keywords': '',
'well_comment_keywords': "write",
'operation': "INTERSECT"
}
response = self.post('/plate_search', post_data)
self.assertEqual(response.code, 200)
obs = json_decode(response.body)
self.assertCountEqual(obs.keys(), ['data'])
obs_data = obs['data']
self.assertEqual(len(obs_data), 1)
self.assertEqual(obs_data[0], [23, 'Test 16S plate 1'])
def test_properties(self):
# Plate 21 - Defined in the test DB
tester = Plate(21)
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.assertIsNone(tester.quantification_process)
self.assertEqual(tester.process, SamplePlatingProcess(10))
# 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(
Plate(23).quantification_process, QuantificationProcess(1))
self.assertEqual(Plate(22).process, GDNAExtractionProcess(1))
exp = {
'1.SKB1.640202': [[Well(3073), '1.SKB1.640202.21.A1'],
[Well(3253), '1.SKB1.640202.21.B1'],
[Well(3433), '1.SKB1.640202.21.C1'],
[Well(3613), '1.SKB1.640202.21.D1'],
[Well(3793), '1.SKB1.640202.21.E1'],
[Well(3973), '1.SKB1.640202.21.F1']],
'1.SKB2.640194': [[Well(3088), '1.SKB2.640194.21.A2'],
[Well(3268), '1.SKB2.640194.21.B2'],
[Well(3448), '1.SKB2.640194.21.C2'],
[Well(3628), '1.SKB2.640194.21.D2'],
[Well(3808), '1.SKB2.640194.21.E2'],
[Well(3988), '1.SKB2.640194.21.F2']],
'1.SKB3.640195': [[Well(3103), '1.SKB3.640195.21.A3'],
[Well(3283), '1.SKB3.640195.21.B3'],
[Well(3463), '1.SKB3.640195.21.C3'],
[Well(3643), '1.SKB3.640195.21.D3'],
[Well(3823), '1.SKB3.640195.21.E3'],
[Well(4003), '1.SKB3.640195.21.F3']],
'1.SKB4.640189': [[Well(3118), '1.SKB4.640189.21.A4'],
[Well(3298), '1.SKB4.640189.21.B4'],
[Well(3478), '1.SKB4.640189.21.C4'],
[Well(3658), '1.SKB4.640189.21.D4'],
[Well(3838), '1.SKB4.640189.21.E4'],
[Well(4018), '1.SKB4.640189.21.F4']],
'1.SKB5.640181': [[Well(3133), '1.SKB5.640181.21.A5'],
[Well(3313), '1.SKB5.640181.21.B5'],
[Well(3493), '1.SKB5.640181.21.C5'],
[Well(3673), '1.SKB5.640181.21.D5'],
[Well(3853), '1.SKB5.640181.21.E5'],
[Well(4033), '1.SKB5.640181.21.F5']],
'1.SKB6.640176': [[Well(3148), '1.SKB6.640176.21.A6'],
[Well(3328), '1.SKB6.640176.21.B6'],
[Well(3508), '1.SKB6.640176.21.C6'],
[Well(3688), '1.SKB6.640176.21.D6'],
[Well(3868), '1.SKB6.640176.21.E6'],
[Well(4048), '1.SKB6.640176.21.F6']],
'1.SKB7.640196': [[Well(3163), '1.SKB7.640196.21.A7'],
[Well(3343), '1.SKB7.640196.21.B7'],
[Well(3523), '1.SKB7.640196.21.C7'],
[Well(3703), '1.SKB7.640196.21.D7'],
[Well(3883), '1.SKB7.640196.21.E7'],
[Well(4063), '1.SKB7.640196.21.F7']],
'1.SKB8.640193': [[Well(3178), '1.SKB8.640193.21.A8'],
[Well(3358), '1.SKB8.640193.21.B8'],
[Well(3538), '1.SKB8.640193.21.C8'],
[Well(3718), '1.SKB8.640193.21.D8'],
[Well(3898), '1.SKB8.640193.21.E8'],
[Well(4078), '1.SKB8.640193.21.F8']],
'1.SKB9.640200': [[Well(3193), '1.SKB9.640200.21.A9'],
[Well(3373), '1.SKB9.640200.21.B9'],
[Well(3553), '1.SKB9.640200.21.C9'],
[Well(3733), '1.SKB9.640200.21.D9'],
[Well(3913), '1.SKB9.640200.21.E9'],
[Well(4093), '1.SKB9.640200.21.F9']],
'1.SKD1.640179': [[Well(3208), '1.SKD1.640179.21.A10'],
[Well(3388), '1.SKD1.640179.21.B10'],
[Well(3568), '1.SKD1.640179.21.C10'],
[Well(3748), '1.SKD1.640179.21.D10'],
[Well(3928), '1.SKD1.640179.21.E10'],
[Well(4108), '1.SKD1.640179.21.F10']],
'1.SKD2.640178': [[Well(3223), '1.SKD2.640178.21.A11'],
[Well(3403), '1.SKD2.640178.21.B11'],
[Well(3583), '1.SKD2.640178.21.C11'],
[Well(3763), '1.SKD2.640178.21.D11'],
[Well(3943), '1.SKD2.640178.21.E11'],
[Well(4123), '1.SKD2.640178.21.F11']],
'1.SKD3.640198': [[Well(3238), '1.SKD3.640198.21.A12'],
[Well(3418), '1.SKD3.640198.21.B12'],
[Well(3598), '1.SKD3.640198.21.C12'],
[Well(3778), '1.SKD3.640198.21.D12'],
[Well(3958), '1.SKD3.640198.21.E12'],
[Well(4138), '1.SKD3.640198.21.F12']]
}
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')
def test_properties(self):
# Plate 21 - Defined in the test DB
tester = Plate(21)
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(10))
# 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.SKB1.640202.21.A1'],
[Well(3121), '1.SKB1.640202.21.A2'],
[Well(3169), '1.SKB1.640202.21.A3'],
[Well(3217), '1.SKB1.640202.21.A4'],
[Well(3265), '1.SKB1.640202.21.A5'],
[Well(3313), '1.SKB1.640202.21.A6'],
[Well(3361), '1.SKB1.640202.21.A7'],
[Well(3409), '1.SKB1.640202.21.A8'],
[Well(3457), '1.SKB1.640202.21.A9'],
[Well(3505), '1.SKB1.640202.21.A10'],
[Well(3553), '1.SKB1.640202.21.A11'],
[Well(3601), '1.SKB1.640202.21.A12']],
'1.SKB2.640194': [[Well(3079), '1.SKB2.640194.21.B1'],
[Well(3127), '1.SKB2.640194.21.B2'],
[Well(3175), '1.SKB2.640194.21.B3'],
[Well(3223), '1.SKB2.640194.21.B4'],
[Well(3271), '1.SKB2.640194.21.B5'],
[Well(3319), '1.SKB2.640194.21.B6'],
[Well(3367), '1.SKB2.640194.21.B7'],
[Well(3415), '1.SKB2.640194.21.B8'],
[Well(3463), '1.SKB2.640194.21.B9'],
[Well(3511), '1.SKB2.640194.21.B10'],
[Well(3559), '1.SKB2.640194.21.B11'],
[Well(3607), '1.SKB2.640194.21.B12']],
'1.SKB3.640195': [[Well(3085), '1.SKB3.640195.21.C1'],
[Well(3133), '1.SKB3.640195.21.C2'],
[Well(3181), '1.SKB3.640195.21.C3'],
[Well(3229), '1.SKB3.640195.21.C4'],
[Well(3277), '1.SKB3.640195.21.C5'],
[Well(3325), '1.SKB3.640195.21.C6'],
[Well(3373), '1.SKB3.640195.21.C7'],
[Well(3421), '1.SKB3.640195.21.C8'],
[Well(3469), '1.SKB3.640195.21.C9'],
[Well(3517), '1.SKB3.640195.21.C10'],
[Well(3565), '1.SKB3.640195.21.C11'],
[Well(3613), '1.SKB3.640195.21.C12']],
'1.SKB4.640189': [[Well(3091), '1.SKB4.640189.21.D1'],
[Well(3139), '1.SKB4.640189.21.D2'],
[Well(3187), '1.SKB4.640189.21.D3'],
[Well(3235), '1.SKB4.640189.21.D4'],
[Well(3283), '1.SKB4.640189.21.D5'],
[Well(3331), '1.SKB4.640189.21.D6'],
[Well(3379), '1.SKB4.640189.21.D7'],
[Well(3427), '1.SKB4.640189.21.D8'],
[Well(3475), '1.SKB4.640189.21.D9'],
[Well(3523), '1.SKB4.640189.21.D10'],
[Well(3571), '1.SKB4.640189.21.D11'],
[Well(3619), '1.SKB4.640189.21.D12']],
'1.SKB5.640181': [[Well(3097), '1.SKB5.640181.21.E1'],
[Well(3145), '1.SKB5.640181.21.E2'],
[Well(3193), '1.SKB5.640181.21.E3'],
[Well(3241), '1.SKB5.640181.21.E4'],
[Well(3289), '1.SKB5.640181.21.E5'],
[Well(3337), '1.SKB5.640181.21.E6'],
[Well(3385), '1.SKB5.640181.21.E7'],
[Well(3433), '1.SKB5.640181.21.E8'],
[Well(3481), '1.SKB5.640181.21.E9'],
[Well(3529), '1.SKB5.640181.21.E10'],
[Well(3577), '1.SKB5.640181.21.E11'],
[Well(3625), '1.SKB5.640181.21.E12']],
'1.SKB6.640176': [[Well(3103), '1.SKB6.640176.21.F1'],
[Well(3151), '1.SKB6.640176.21.F2'],
[Well(3199), '1.SKB6.640176.21.F3'],
[Well(3247), '1.SKB6.640176.21.F4'],
[Well(3295), '1.SKB6.640176.21.F5'],
[Well(3343), '1.SKB6.640176.21.F6'],
[Well(3391), '1.SKB6.640176.21.F7'],
[Well(3439), '1.SKB6.640176.21.F8'],
[Well(3487), '1.SKB6.640176.21.F9'],
[Well(3535), '1.SKB6.640176.21.F10'],
[Well(3583), '1.SKB6.640176.21.F11'],
[Well(3631), '1.SKB6.640176.21.F12']]
}
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)
self.assertEqual(
tester2.quantification_processes[0].date,
datetime.strptime("2017-10-25 19:10:25-0700",
'%Y-%m-%d %H:%M:%S%z'))
self.assertEqual(
tester2.quantification_processes[1].date,
datetime.strptime("2017-10-26 03:10:25-0700",
'%Y-%m-%d %H:%M:%S%z'))