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') self.assertEqual(obs.upstream_process, SamplePlatingProcess(10)) 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, 3081) self.assertEqual(obs.study, Study(1)) # Test a control sample obs = SampleComposition(85) self.assertEqual(obs.sample_composition_type, 'blank') self.assertIsNone(obs.sample_id) self.assertEqual(obs.content, 'blank.21.H1') self.assertEqual(obs.upstream_process, SamplePlatingProcess(10)) self.assertEqual(obs.container, Well(4333)) self.assertEqual(obs.total_volume, 10) self.assertIsNone(obs.notes) self.assertEqual(obs.composition_id, 4341) self.assertIsNone(obs.study)
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 plate_map_handler_get_request(process_id): plate_id = None if process_id is not None: try: process = SamplePlatingProcess(process_id) except LabmanUnknownIdError: 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 'template' not in pc.description] return {'plate_confs': plate_confs, 'plate_id': plate_id, 'process_id': process_id}
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: labman.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 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) != 3: raise HTTPError(400, 'Incorrect path parameter') attribute = req_path[0] if attribute == 'well': row = req_path[1] col = req_path[2] if req_value is None or not req_value.strip(): raise HTTPError(400, 'A new value for the well should be provided') SamplePlatingProcess(process_id).update_well(row, col, req_value) 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_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) 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), Well(3253), Well(3433), Well(3613), Well(3793), Well(3973) ], '1.SKB2.640194': [ Well(3088), Well(3268), Well(3448), Well(3628), Well(3808), Well(3988) ], '1.SKB3.640195': [ Well(3103), Well(3283), Well(3463), Well(3643), Well(3823), Well(4003) ], '1.SKB4.640189': [ Well(3118), Well(3298), Well(3478), Well(3658), Well(3838), Well(4018) ], '1.SKB5.640181': [ Well(3133), Well(3313), Well(3493), Well(3673), Well(3853), Well(4033) ], '1.SKB6.640176': [ Well(3148), Well(3328), Well(3508), Well(3688), Well(3868), Well(4048) ], '1.SKB7.640196': [ Well(3163), Well(3343), Well(3523), Well(3703), Well(3883), Well(4063) ], '1.SKB8.640193': [ Well(3178), Well(3358), Well(3538), Well(3718), Well(3898), Well(4078) ], '1.SKB9.640200': [ Well(3193), Well(3373), Well(3553), Well(3733), Well(3913), Well(4093) ], '1.SKD1.640179': [ Well(3208), Well(3388), Well(3568), Well(3748), Well(3928), Well(4108) ], '1.SKD2.640178': [ Well(3223), Well(3403), Well(3583), Well(3763), Well(3943), Well(4123) ], '1.SKD3.640198': [ Well(3238), Well(3418), Well(3598), Well(3778), Well(3958), Well(4138) ] } self.assertEqual(tester.duplicates, exp)
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: labman.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) != 4: raise HTTPError(400, 'Incorrect path parameter') attribute = req_path[0] if attribute == 'well': row = req_path[1] col = req_path[2] well_attribute = req_path[3] 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=[req_value]) 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, req_value) return {'sample_id': content, '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()
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: labman.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_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'))