def test_fetch_project_and_sample_for_experiment(self):
ea = ExperimentAdaptor(**{'session_class':self.session_class})
ea.start_session()
project_id,sample_id=ea.fetch_project_and_sample_for_experiment(experiment_igf_id='ExperimentA')
self.assertEqual(project_id,'ProjectA')
self.assertEqual(sample_id,'SampleA')
ea.close_session()
def test_update_metadta_from_sample_attribute1(self):
ea = ExperimentAdaptor(**{'session_class': self.session_class})
ea.start_session()
exp1 = ea.fetch_experiment_records_id(
experiment_igf_id='IGF00001_HISEQ4000')
self.assertEqual(exp1.library_strategy, 'UNKNOWN')
exp2 = ea.fetch_experiment_records_id(
experiment_igf_id='IGF00002_HISEQ4000')
self.assertEqual(exp2.library_strategy, 'UNKNOWN')
exp3 = ea.fetch_experiment_records_id(
experiment_igf_id='IGF00003_HISEQ4000')
self.assertEqual(exp3.library_source, 'UNKNOWN')
ea.close_session()
emu = Experiment_metadata_updator(dbconfig_file=self.dbconfig,
log_slack=False)
emu.update_metadta_from_sample_attribute()
ea = ExperimentAdaptor(**{'session_class': self.session_class})
ea.start_session()
exp1 = ea.fetch_experiment_records_id(
experiment_igf_id='IGF00001_HISEQ4000')
self.assertEqual(exp1.library_strategy, 'RNA-SEQ')
exp2 = ea.fetch_experiment_records_id(
experiment_igf_id='IGF00002_HISEQ4000')
self.assertEqual(exp2.library_strategy, 'UNKNOWN')
exp3 = ea.fetch_experiment_records_id(
experiment_igf_id='IGF00003_HISEQ4000')
self.assertEqual(exp3.library_source, 'TRANSCRIPTOMIC_SINGLE_CELL')
ea.close_session()
def run(self):
try:
project_igf_id = self.param_required('project_igf_id')
experiment_igf_id = self.param_required('experiment_igf_id')
sample_igf_id = self.param_required('sample_igf_id')
igf_session_class = self.param_required('igf_session_class')
ea = ExperimentAdaptor(**{'session_class': igf_session_class})
ea.start_session()
runs = ea.fetch_runs_for_igf_id(
experiment_igf_id=experiment_igf_id,
include_active_runs=True,
output_mode='dataframe') # fetch active runs for an experiment
ea.close_session()
runs = runs.to_dict(orient='records') # convert run ids to a list
self.param('sub_tasks', runs) # pass on run factory output list
except Exception as e:
message='project: {2}, sample:{3}, Error in {0}: {1}'.format(self.__class__.__name__, \
e, \
project_igf_id,
sample_igf_id)
self.warning(message)
self.post_message_to_slack(
message, reaction='fail') # post msg to slack for failed jobs
raise
def test_check_experiment_records_id(self):
ea = ExperimentAdaptor(**{'session_class':self.session_class})
ea.start_session()
self.assertTrue(ea.check_experiment_records_id(experiment_igf_id='ExperimentA'))
self.assertFalse(ea.check_experiment_records_id(experiment_igf_id='ExperimentB'))
ea.close_session()
def setUp(self):
self.dbconfig = 'data/dbconfig.json'
dbparam = read_dbconf_json(self.dbconfig)
base = BaseAdaptor(**dbparam)
self.engine = base.engine
self.dbname = dbparam['dbname']
Base.metadata.create_all(self.engine)
self.session_class = base.get_session_class()
# load platform data
platform_data=\
[{"platform_igf_id" : "M03291" ,
"model_name" : "MISEQ" ,
"vendor_name" : "ILLUMINA" ,
"software_name" : "RTA" ,
"software_version" : "RTA1.18.54"
},
{"platform_igf_id" : "NB501820",
"model_name" : "NEXTSEQ",
"vendor_name" : "ILLUMINA",
"software_name" : "RTA",
"software_version" : "RTA2"
},
{"platform_igf_id" : "K00345",
"model_name" : "HISEQ4000",
"vendor_name" : "ILLUMINA",
"software_name" : "RTA",
"software_version" : "RTA2"
}]
flowcell_rule_data=\
[{"platform_igf_id":"K00345",
"flowcell_type":"HiSeq 3000/4000 SR",
"index_1":"NO_CHANGE",
"index_2":"NO_CHANGE"},
{"platform_igf_id":"K00345",
"flowcell_type":"HiSeq 3000/4000 PE",
"index_1":"NO_CHANGE",
"index_2":"REVCOMP"},
{"platform_igf_id":"NB501820",
"flowcell_type":"NEXTSEQ",
"index_1":"NO_CHANGE",
"index_2":"REVCOMP"},
{"platform_igf_id":"M03291",
"flowcell_type":"MISEQ",
"index_1":"NO_CHANGE",
"index_2":"NO_CHANGE"}]
pl = PlatformAdaptor(**{'session_class': base.session_class})
pl.start_session()
pl.store_platform_data(data=platform_data)
pl.store_flowcell_barcode_rule(data=flowcell_rule_data)
pl.close_session()
# load project data
project_data = [{'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA'}]
pa = ProjectAdaptor(**{'session_class': base.session_class})
pa.start_session()
pa.store_project_and_attribute_data(data=project_data)
pa.close_session()
# load samples
sample_data = [
{
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109792',
'expected_read': 40000000
},
{
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109793',
'expected_read': 40000000
},
{
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109794',
'expected_read': 40000000
},
{
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109795',
'expected_read': 40000000
},
{
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109796',
'expected_read': 40000000
},
{
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109797',
'expected_read': 40000000
},
{
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109797_1',
'expected_read': 40000000
},
]
sa = SampleAdaptor(**{'session_class': base.session_class})
sa.start_session()
sa.store_sample_and_attribute_data(data=sample_data)
sa.close_session()
# load seqrun data
seqrun_data = [{
'flowcell_id': 'HV2GJBBXX',
'platform_igf_id': 'K00345',
'seqrun_igf_id': '180518_K00345_0047_BHV2GJBBXX'
}]
sra = SeqrunAdaptor(**{'session_class': base.session_class})
sra.start_session()
sra.store_seqrun_and_attribute_data(data=seqrun_data)
sra.close_session()
# load experiment data
experiment_data=\
[{'experiment_igf_id': 'IGF109792_HISEQ4000',
'library_name': 'IGF109792',
'platform_name': 'HISEQ4000',
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109792',
},
{'experiment_igf_id': 'IGF109793_HISEQ4000',
'library_name': 'IGF109793',
'platform_name': 'HISEQ4000',
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109793',
},
{'experiment_igf_id': 'IGF109794_HISEQ4000',
'library_name': 'IGF109794',
'platform_name': 'HISEQ4000',
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109794',
},
{'experiment_igf_id': 'IGF109795_HISEQ4000',
'library_name': 'IGF109795',
'platform_name': 'HISEQ4000',
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109795',
},
{'experiment_igf_id': 'IGF109796_HISEQ4000',
'library_name': 'IGF109796',
'platform_name': 'HISEQ4000',
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109796',
},
{'experiment_igf_id': 'IGF109797_HISEQ4000',
'library_name': 'IGF109797',
'platform_name': 'HISEQ4000',
'project_igf_id': 'IGFQ000472_avik_28-3-2018_RNA',
'sample_igf_id': 'IGF109797',
},
]
ea = ExperimentAdaptor(**{'session_class': base.session_class})
ea.start_session()
ea.store_project_and_attribute_data(data=experiment_data)
ea.close_session()
# load run data
run_data=\
[{'experiment_igf_id': 'IGF109792_HISEQ4000',
'lane_number': '7',
'run_igf_id': 'IGF109792_HISEQ4000_H2N3MBBXY_7',
'seqrun_igf_id': '180518_K00345_0047_BHV2GJBBXX',
'R1_READ_COUNT':288046541
},
{'experiment_igf_id': 'IGF109793_HISEQ4000',
'lane_number': '7',
'run_igf_id': 'IGF109793_HISEQ4000_H2N3MBBXY_7',
'seqrun_igf_id': '180518_K00345_0047_BHV2GJBBXX',
'R1_READ_COUNT':14666330
},
{'experiment_igf_id': 'IGF109794_HISEQ4000',
'lane_number': '7',
'run_igf_id': 'IGF109794_HISEQ4000_H2N3MBBXY_7',
'seqrun_igf_id': '180518_K00345_0047_BHV2GJBBXX',
'R1_READ_COUNT':5009143
},
{'experiment_igf_id': 'IGF109795_HISEQ4000',
'lane_number': '7',
'run_igf_id': 'IGF109795_HISEQ4000_H2N3MBBXY_7',
'seqrun_igf_id': '180518_K00345_0047_BHV2GJBBXX',
'R1_READ_COUNT':1391747
},
{'experiment_igf_id': 'IGF109796_HISEQ4000',
'lane_number': '7',
'run_igf_id': ' IGF109796_HISEQ4000_H2N3MBBXY_7',
'seqrun_igf_id': '180518_K00345_0047_BHV2GJBBXX',
'R1_READ_COUNT':1318008
},
{'experiment_igf_id': 'IGF109797_HISEQ4000',
'lane_number': '7',
'run_igf_id': 'IGF109797_HISEQ4000_H2N3MBBXY_7',
'seqrun_igf_id': '180518_K00345_0047_BHV2GJBBXX',
'R1_READ_COUNT':1216324
},
]
ra = RunAdaptor(**{'session_class': base.session_class})
ra.start_session()
ra.store_run_and_attribute_data(data=run_data)
ra.close_session()