def setUp(self):
self.dbconfig = 'data/dbconfig.json'
self.platform_json = 'data/platform_db_data.json'
self.seqrun_json = 'data/seqrun_db_data.json'
self.pipeline_json = 'data/pipeline_data.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()
base.start_session()
# load platform data
pl = PlatformAdaptor(**{'session': base.session})
pl.store_platform_data(data=read_json_data(self.platform_json))
# load seqrun data
sra = SeqrunAdaptor(**{'session': base.session})
sra.store_seqrun_and_attribute_data(
data=read_json_data(self.seqrun_json))
# load platform data
pla = PipelineAdaptor(**{'session': base.session})
pla.store_pipeline_data(data=read_json_data(self.pipeline_json))
pipeline_seed_data = [
{
'pipeline_name': 'demultiplexing_fastq',
'seed_id': '1',
'seed_table': 'seqrun'
},
]
pla.create_pipeline_seed(data=pipeline_seed_data)
base.close_session()
def setUp(self):
self.dbconfig='data/dbconfig.json'
self.platform_json='data/platform_db_data.json'
self.seqrun_json='data/seqrun_db_data.json'
self.pipeline_json='data/pipeline_data.json'
self.flowcell_rules_json='data/flowcell_rules.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()
base.start_session()
# load platform data
pl=PlatformAdaptor(**{'session':base.session})
pl.store_platform_data(data=read_json_data(self.platform_json))
pl.store_flowcell_barcode_rule(data=read_json_data(self.flowcell_rules_json))
# load seqrun data
sra=SeqrunAdaptor(**{'session':base.session})
sra.store_seqrun_and_attribute_data(data=read_json_data(self.seqrun_json))
base.close_session()
def load_new_platform_data(data_file, dbconfig):
'''
A method for loading new data for platform table
'''
try:
formatted_data = read_json_data(data_file)
dbparam = read_dbconf_json(dbconfig)
pl = PlatformAdaptor(**dbparam)
pl.start_session()
pl.store_platform_data(data=formatted_data)
pl.close_session()
except:
raise
def load_new_flowcell_data(data_file, dbconfig):
'''
A method for loading new data to flowcell table
'''
try:
flowcell_rule_data = read_json_data(data_file)
dbparam = read_dbconf_json(dbconfig)
pl = PlatformAdaptor(**dbparam)
pl.start_session()
pl.store_flowcell_barcode_rule(data=flowcell_rule_data)
pl.close_session()
except:
raise
def load_new_seqrun_data(data_file, dbconfig):
'''
A method for loading new data for seqrun table
'''
try:
formatted_data=read_json_data(data_file)
dbparam=read_dbconf_json(dbconfig)
sr=SeqrunAdaptor(**dbparam)
sr.start_session()
sr.store_seqrun_and_attribute_data(data=formatted_data)
sr.close_session()
except:
raise
def load_new_pipeline_data(data_file, dbconfig):
'''
A method for loading new data for pipeline table
'''
try:
formatted_data = read_json_data(data_file)
dbparam = read_dbconf_json(dbconfig)
pp = PipelineAdaptor(**dbparam)
pp.start_session()
pp.store_pipeline_data(data=formatted_data)
pp.close_session()
except:
raise
def test_read_json_data(self):
data = read_json_data(data_file=self.data_file)
self.assertIsInstance(data, list)
dbconfig_path = args.dbconfig_path
collection_file_data = args.collection_file_data
calculate_checksum = args.calculate_checksum
if __name__ == '__main__':
try:
dbconnected = False
if not os.path.exists(dbconfig_path):
raise IOError('Dbconfig file {0} not found'.format(dbconfig_path))
if not os.path.exists(collection_file_data):
raise IOError('Collection data json file {0} not found'.format(
collection_file_data))
dbparam = read_dbconf_json(dbconfig_path) # read db config
collection_data = read_json_data(
collection_file_data) # read collection data json
ca = CollectionAdaptor(**dbparam)
ca.start_session() # connect to database
dbconnected = True
ca.load_file_and_create_collection(
data=collection_data,
calculate_file_size_and_md5=calculate_checksum,
autosave=True) # load data and commit changes
ca.close_session()
dbconnected = False
except Exception as e:
if dbconnected:
ca.rollback_session()
ca.close_session()
raise ValueError('Error: {0}'.format(e))