On Dec 5, 2008, at 3:01 PM, Faheem Mitha wrote:
>
>
> 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.
there's no need to session.save() any objects created within
associationproxy - when the parent object is saved, or if the parent
is already saved, any attachments are also saved using the on-by-
default "save-update" cascade.
>
>
> 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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