Michael, Thanks for that hint! However, I still don't know how should I include association table 'homologues' relation :-(
I sketched a schema of my DB: http://flickr.com/photos/piotrbyzia/3244490067/ and relevant code is under: http://pastie.org/376811 The similar problem is with Interactions table - how should I define many-to-many relation there? SQLA seems pretty mature, but to be honest, I struggle to find one complete example to use as a boiler plate... Best, Piotrek Byzia On Feb 1, 7:02 pm, Michael Bayer <mike...@zzzcomputing.com> wrote: > 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) --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "sqlalchemy" group. To post to this group, send email to sqlalchemy@googlegroups.com To unsubscribe from this group, send email to sqlalchemy+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/sqlalchemy?hl=en -~----------~----~----~----~------~----~------~--~---
