remove the "secondary" argument from proteins_seed to PDB, the
"homologues" table has no relevance to that relation().
On Feb 1, 2009, at 1:56 PM, Piotrek Byzia wrote:
>
> 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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