My fault, I haven't included Proteins_putative, PDB is just another
table..
But anyway, the problem is with definition of many-to-many relaction()
in Protein_seed.
class Protein_putative(Base):
__tablename__ = 'Proteins_putative'
id = Column(Integer, primary_key=True)
name = Column(String, nullable=False, unique=True)
primary_accession_number = Column(String, nullable=False)
description = Column(String)
sequence = Column(String, nullable=False)
length = Column(Integer, nullable=False)
alignment = Column(String, nullable=False)
def __init__(self, name, primary_accession_number, description,
sequence, length, alignment):
self.name = name
self.primary_accession_number = primary_accession_number
self.description = description
self.sequence = sequence
self.length = length
self.alignment = alignment
def __repr__(self):
return "<Protein_putative('%s', '%s')>" % (self.name,
self.primary_accession_number)
On Feb 1, 6:18 pm, Michael Bayer <mike...@zzzcomputing.com> wrote:
> you're using homologues to link Protein_seed to PDB. so the two
> foreign keys should be between the tables named "Proteins_seed" and
> "PDB", not "Proteins_putative", which seems to be otherwise
> unmentioned here.
>
> On Feb 1, 2009, at 11:57 AM, Piotrek Byzia wrote:
>
>
>
> > Hi,
>
> > I'm a fresh user of SQLA, and this is my first attempt to use it.
>
> > Based on the official tutorial example I created a many to many
> > relation between two tables, but I have some issues with getting it
> > working. It returns error "Could not determine join condition between
> > parent/child tables on relation Protein_seed.pdb_entry. Specify a
> > 'primaryjoin' expression. If this is a many-to-many relation,
> > 'secondaryjoin' is needed as well." I don't know how to define
> > secondary key, while my association table "homologues" is not
> > declarative and doesn't have it's own primary key. Can anybody help,
> > please?
>
> > meta = MetaData()
> > Base = declarative_base(metadata=meta)
>
> > homologues = Table('Homologues', meta,
> > Column('protein_seed_id', Integer, ForeignKey
> > ('Proteins_seed.id')),
> > Column('protein_putative_id', Integer, ForeignKey
> > ('Proteins_putative.id'))
> > )
>
> > class PDB(Base):
> > __tablename__ = 'PDB'
>
> > id = Column(Integer, primary_key=True)
> > name = Column(String, nullable=False, unique=True)
> > chain = Column(String, nullable=False)
>
> > def __init__(self, name, chain):
> > self.name = name
> > self.chain = chain
>
> > def __repr__(self):
> > return "<PDB('%s', '%s')>" % (self.name, self.chain)
>
> > class Protein_seed(Base):
> > __tablename__ = 'Proteins_seed'
>
> > id = Column(Integer, primary_key=True)
> > name = Column(String, nullable=False)
> > sequence = Column(String, nullable=False)
> > length = Column(Integer, nullable=False)
> > alignment = Column(String, nullable=False)
> > pdb_id = Column(Integer, ForeignKey('PDB.id'))
>
> > # many-to-one Protein_seed * 1 PDB
> > pdb_entry = relation('PDB', secondary=homologues, backref=backref
> > ('Proteins_seed'),
> > primaryjoin=pdb_id == PDB.id)
>
> > def __init__(self, name, sequence, length, alignment):
> > self.name = name
> > self.sequence = sequence
> > self.length = length
> > self.alignment = alignment
>
> > def __repr__(self):
> > return "<Protein_seed('%s', '%s', '%s', '%s')>" % (self.name,
> > self.sequence, self.length, self.alignment)
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