UniqueConstraint not enforced in CompartmentalizedComponent

[psalvy]

UniqueConstraint not enforced in CompartmentalizedComponent

[steve-federowicz]

Awesome!! Thanks Pierre.

Assigning @jslu9 as this could be critical for BiGG and he has the closest familiarity with that code.

@jslu9 we could probably also use this to develop a test case to make sure we don't get similar issues in other areas of the code.

Thanks Pierre!

[psalvy]

My pleasure ! I'm sorry, I did not know about this get_or_create function, thanks for showing it to me !
I'll keep you updated if I find new stuff.

Pierre

EDIT:
I think I kinow why the unique constraint is not enforced: it is not declared as a table_args, but placed 'naked' in the column declaration. As we are using the declarative mode of SQLAlchemy, the line

    UniqueConstraint('compartment_id', 'component_id')

should be replaced by:

    __table_args__ = (
        UniqueConstraint('compartment_id', 'component_id'),
        {})

EDIT2: This goes also for the classes:

Model
ModelReaction
ReactionMatrix

in models.py that have the same problem

[jslu9]

Ok, I'm looking into it. It's strange that the unique constraint is not
being enforced by sqlalchemy. I'm going to put the unique constraints into
the table args and see if it configures the table correctly that way.

On Mon, Nov 3, 2014 at 11:32 AM, Pierre SALVY [email protected]
wrote:

My pleasure ! I'm sorry, I did not know about this get_or_create function,
thanks for showing it to me !
I'll keep you updated if I find new stuff.

Pierre

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#9 (comment).

[psalvy]

Also, in the declaration of the Model class, as follows:

class Model(Base):
    __tablename__='model'
    id = Column(Integer, Sequence('wids'), primary_key=True)
    bigg_id = Column(String)
    first_created = Column(DateTime)
    genome_id = Column(Integer, ForeignKey('genome.id'))
    genome = relationship('Genome', backref='model')
    UniqueConstraint('name', 'firstcreated')
    notes = Column(String)
    __table_args__ = (UniqueConstraint('bigg_id'),{})
    def __repr__(self):
        return "Model (#%d) %s %s" % (self.id, self.bigg_id, self.first_created)

I noticed a double declaration of the UniqueConstraint, one of which is invalid according to what I posted above, and I also noticed that they do not ask for the same uniqueness.

[zakandrewking]

@jslu9 Is this still happening?