def get_driver_line(self):
query = '''
SELECT g.name as driver_line
FROM ophys_experiments oe
JOIN ophys_sessions os ON oe.ophys_session_id = os.id
JOIN specimens sp ON sp.id=os.specimen_id
JOIN donors d ON d.id=sp.donor_id
JOIN donors_genotypes dg ON dg.donor_id=d.id
JOIN genotypes g ON g.id=dg.genotype_id
JOIN genotype_types gt ON gt.id=g.genotype_type_id AND gt.name = 'driver'
WHERE oe.id= {};
'''.format(self.get_ophys_experiment_id())
result = self.fetchall(query)
if result is None or len(result) < 1:
raise OneOrMoreResultExpectedError('Expected one or more, but received: {} from query'.format(result))
return result
def from_lims(cls, behavior_session_id: int,
lims_db: PostgresQueryMixin) -> "DriverLine":
query = f"""
SELECT g.name AS driver_line
FROM behavior_sessions bs
JOIN donors d ON bs.donor_id=d.id
JOIN donors_genotypes dg ON dg.donor_id=d.id
JOIN genotypes g ON g.id=dg.genotype_id
JOIN genotype_types gt
ON gt.id=g.genotype_type_id AND gt.name = 'driver'
WHERE bs.id={behavior_session_id};
"""
result = lims_db.fetchall(query)
if result is None or len(result) < 1:
raise OneOrMoreResultExpectedError(
f"Expected one or more, but received: '{result}' "
f"from query:\n'{query}'")
driver_line = sorted(result)
return cls(driver_line=driver_line)
def get_driver_line(self) -> List[str]:
"""Returns the genotype name(s) of the driver line(s).
:rtype: list
"""
query = f"""
SELECT g.name AS driver_line
FROM behavior_sessions bs
JOIN donors d ON bs.donor_id=d.id
JOIN donors_genotypes dg ON dg.donor_id=d.id
JOIN genotypes g ON g.id=dg.genotype_id
JOIN genotype_types gt
ON gt.id=g.genotype_type_id AND gt.name = 'driver'
WHERE bs.id={self.behavior_session_id};
"""
result = self.lims_db.fetchall(query)
if result is None or len(result) < 1:
raise OneOrMoreResultExpectedError(
f"Expected one or more, but received: '{result}' "
f"from query:\n'{query}'")
return result
def get_driver_line(self) -> str:
"""Get the (gene) driver line for the subject associated with an ophys
experiment"""
query = """
SELECT g.name as driver_line
FROM ophys_experiments oe
JOIN ophys_sessions os ON oe.ophys_session_id = os.id
JOIN specimens sp ON sp.id = os.specimen_id
JOIN donors d ON d.id = sp.donor_id
JOIN donors_genotypes dg ON dg.donor_id = d.id
JOIN genotypes g ON g.id = dg.genotype_id
JOIN genotype_types gt ON gt.id = g.genotype_type_id
WHERE gt.name = 'driver'
AND oe.id = {};
""".format(self.get_ophys_experiment_id())
result = self.lims_db.fetchall(query)
if result is None or len(result) < 1:
raise OneOrMoreResultExpectedError(
f"Expected one or more, but received: '{result}' from query")
return result