Hi,
I'm using sqla with the following schema (see below). I'm creating a cell
object implicitly, using the function make_cell and the association proxy
pattern.
def make_cell(patient_obj, snp_obj, snpval):
patient_obj.snps[snp_obj] = snpval
return patient_obj
My question is, is there some way to get my hands on the Cell object that
was just created? If possible, I'd like make_cell to return the cell
object. My immediate reason is that this would make it easy to save the
object using session.save() (there might be some indirect way to do this,
of course), but it would be nice anyway.
Thanks in advance. Please CC me on any reply.
Regards, Faheem.
******************************************************************
dbschema.py
******************************************************************
from sqlalchemy import *
from sqlalchemy.orm import *
from sqlalchemy.ext.associationproxy import association_proxy
from sqlalchemy.orm.collections import attribute_mapped_collection
from datetime import datetime
metadata = MetaData('sqlite:///btsnp.sqlite')
# *patients*
# patient_id (PK)
# (Can use actual patient id as unique/alternate identifier
# Create index).
# sex -> list of choices allowed
# age -> (0, 140)
# time of death
patient_table = Table(
'patient', metadata,
Column('id', String(20), primary_key=True, index=True),
Column('celfilename', String(30), nullable=False, index=True, unique=True),
Column('sex', String(1)),
)
cell_table = Table(
'cell', metadata,
Column('patient_id', None, ForeignKey('patient.id', onupdate='CASCADE',
ondelete='CASCADE'), index=True, nullable=False, primary_key=True),
Column('snp_id', None, ForeignKey('snp.rsid', onupdate='CASCADE',
ondelete='CASCADE'), index=True, nullable=False, primary_key=True),
Column('snpval_id', None, ForeignKey('snpval.val', onupdate='CASCADE',
ondelete='CASCADE'), index=True, nullable=False)
)
# *snps*
# snp_id (PK)
# name (name of snp)
snp_table = Table(
'snp', metadata,
Column('rsid', String(20), nullable=False, primary_key=True),
Column('chromosome', Integer, nullable=False),
Column('location', Integer, nullable=False),
Column('probe_set_id', String(20), nullable=False, unique=True),
Column('allele', String(3), nullable=False),
)
# *doublets*
# doublet_id (PK)
# seq (two letters AA, AG)
snpval_table = Table(
'snpval', metadata,
Column('val', Integer, primary_key=True),
)
metadata.create_all()
def create_cell(snp, snpval):
return Cell(snp=snp, snpval=snpval)
class Patient(object):
def __init__(self, id, celfilename, sex):
self.id = id
self.celfilename = celfilename
self.sex = sex
def __repr__(self):
return '<Patient %s>'%self.id
snps = association_proxy('by_rsid', 'snpval', creator=create_cell)
class Cell(object):
def __init__(self, patient=None, snp=None, snpval=None):
self.patient = patient
self.snp = snp
self.snpval = snpval
def __repr__(self):
return '<Cell %s>'%self.snpval
class Snp(object):
def __init__(self, rsid, chromosome, location, probe_set_id, allele):
self.rsid = rsid
self.chromosome = chromosome
self.location = location
self.probe_set_id = probe_set_id
self.allele = allele
def __repr__(self):
return '<SNP %s>'%self.rsid
patients = association_proxy('by_patient', 'snpval', creator=create_cell)
class Snpval(object):
def __init__(self, val):
self.val = val
def __repr__(self):
return '<Snpval %s>'%self.val
# mapper(Broker, brokers_table, properties={
# 'by_stock': relation(Holding,
# collection_class=attribute_mapped_collection('stock'))
# })
# 'cells' corresponds to a 1 to many relation.
mapper(Patient, patient_table, properties={'cells':relation(Cell,
backref='patient'),
'by_rsid': relation(Cell,
collection_class=attribute_mapped_collection('snp'))}
)
# 'patient_snpval' corresponds to a many to 1 relation.
# 'patient_snpval' corresponds to a 1 to 1 relation.
mapper(Cell, cell_table, properties={'snp':relation(Snp, backref='cells'),
'snpval':cell_table.c.snpval_id,
'snpval_obj':relation(Snpval,
uselist=False, backref='cell')})
mapper(Snp, snp_table, properties={'by_patient': relation(Cell,
collection_class=attribute_mapped_collection('patient'))})
mapper(Snpval, snpval_table)
#print patient_mapper.identity_key_from_instance()
# 0) Create doublet (2 letters).
# 1) Enter row names (cols) and patient names( snp ids).
# 2) Look at text files and update linker tables.
**************************************************************************
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