hey there-
The general strategy, if you want to write business logic that checks things,
takes other actions, etc. when changes occur in the session, is to use the
before_flush event handler:
https://docs.sqlalchemy.org/en/14/orm/events.html?highlight=before_flush#sqlalchemy.orm.SessionEvents.before_flush
in this event, you can review the linkages on the objects in question and emit
additional statements if desired. Note this is because you said you didn't
want to use CASCADE rules on your foreign keys; that would allow your script to
pass without change.
The general form of using before_flush(), where I've paraphrased a few of your
business rules below in the form of pseduocode, looks like:
from sqlalchemy import event
@event.listens_for(SomeSessionOrFactory, 'before_flush')
def receive_before_flush(session, flush_context, instances):
for obj in session.deleted:
if isinstance(obj, TestMolecule):
check_obj_not_linked_to_other_test_molecules(obj)
elif isinstance(obj, TestChain):
if should_delete_related_test_mol_sequence(obj):
session.delete(obj.related_test_mol_sequence)
# ... etc
Obviously you'd need to work out the specifics of your model here, but within
before_flush() you can respond to all objects that have pending changes and/or
deletions, and add additional custom rules and actions where you are free to
further modify the state of the Session, which will take effect within this
same flush operation.
On Tue, Apr 13, 2021, at 5:29 PM, Mark Aquino wrote:
> Hi Mike,
>
> Sorry about the indentations.
>
> I'm not sure I understand the changes you made to the script after delete as
> it removes all test_chains, test_var_regions, and test_const regions that are
> still referenced by the other test_molecules. The only way I've been able
> to get the delete to work properly is to manually delete test_var_regions and
> test_const_regions first and then delete the test_molecules, but the ideal
> outcome I'm trying to achieve is that when a test_molecule is deleted:
> 1. that the system checks if the chains connected to it are removed if they
> are not linked to other test_molecules.
> 2. if a test_chain is going to be deleted then
> 1. the test_mol_sequence associated with it is deleted if it is no longer
> associated with any other test_chains
> 2. any test_var_regions and test_const_regions are deleted if they are not
> associated with any other test_chains
> 3. and finally if a test_mol_sequence is deleted that any
> test_mol_sequence_features are deleted if they are not associated with any
> other test_mol_sequences.
>
> To make things a little easier to explain, if we just are dealing with
> molecule1 and molecule4 there are only 3 unique test_chains: heavy_chain_1,
> light_chain_1, and heavy_chain_2
> if I deleted molecule1, I would want to retain heavy_chain_2 and
> light_chain_1 and delete heavy_chain_1 as it was no longer associated with
> any test_molecule. Ideally, then I would remove any test_const_regions and
> test_var_regions that are no longer associated with any test_chains.
> Because heavy_chain_1 shares the same test_var_region as heavy_chain_2, that
> test_var_region would remain in the system but the test_const_region unique
> to heavy_chain_1 would be deleted along with the test_mol_sequence and
> test_mol_sequence_features associated with it.
>
> molecule1.chains.add(heavy_chain_1)
> molecule1.chains.add(light_chain_1)
> #molecule2.chains.add(heavy_chain_2)
> #molecule2.chains.add(light_chain_2)
> #molecule3.chains.add(heavy_chain_1)
> #molecule3.chains.add(light_chain_2)
> molecule4.chains.add(heavy_chain_2)
> molecule4.chains.add(light_chain_1)
>
> light_chain_1_sequence = TestMolSequence(content="taglconst1VAR1")
> heavy_chain_1_sequence = TestMolSequence(content="tagheavyconstant1VAR2")
> heavy_chain_2_sequence = TestMolSequence(content="tagheavyconstant2VAR2")
> light_chain_2_sequence = TestMolSequence(content="taglconst1VAR3")
>
> Does that make sense?
>
>
>
> On Tue, Apr 13, 2021 at 4:50 PM Mike Bayer <mike...@zzzcomputing.com> wrote:
>> __
>> Hi there -
>>
>> I would ask that you try to make sure your formatting is maintained when
>> posting examples especially such long ones as I had to re-indent it in order
>> to run this.
>>
>> The delete at the end is failing because of incomplete cascade rules. The
>> DELETE against "test_mol_sequence" seeks to CASCADE as configured to the
>> other three tables,, which then fail because there are non-cascading FKs in
>> the association tables. We can see this via the message:
>>
>> update or delete on table "test_var_region" violates foreign key constraint
>> "test_chain_var_region_var_region_id_fkey" on table "test_chain_var_region"
>> DETAIL: Key (id)=(1) is still referenced from table "test_chain_var_region".
>>
>> [SQL: DELETE FROM test_mol_sequence WHERE test_mol_sequence.id = %(id)s]
>>
>>
>> it's DELETEing from test_mol_sequence but the error is against a totally
>> different table. That's postgresql's cascade.
>>
>> if you want these CASCADEs to remain in place then you'd need to ensure that
>> those linked rows can be deleted without any rows being present in the
>> association tables.
>>
>> I can modify your test at the end to fully DELETE these rows without
>> qualifying for those that have empty collections only and the script then
>> passes, because now it's deleting those rows that would otherwise be
>> dependent on by "test_var_region" and therefore "test_mol_sequence", so
>> there's nothing unexpected going on. Easiest solution here would be to
>> add CASCADE rules to the association tables also. If you want that to be
>> prevented as you mention, and instead expect the script to explicitly delete
>> those depending rows, then your script is already achieving that. the
>> "business logic" so to speak in this case would be as below:
>>
>> orphan_chains = (
>> session.query(TestChain).
>> # filter(~TestChain.molecules.any()).
>> all()
>> )
>> for chain in orphan_chains:
>> session.delete(chain)
>>
>> orphan_vrs = (
>> session.query(TestVarRegion)
>> # .filter(~TestVarRegion.chains.any())
>> .all()
>> )
>> for orphan_vr in orphan_vrs:
>> session.delete(orphan_vr)
>> orphan_crs = (
>> session.query(TestConstRegion)
>> # .filter(~TestConstRegion.chains.any())
>> .all()
>> )
>> for orphan_cr in orphan_crs:
>> session.delete(orphan_cr)
>> orphan_sequences = (
>> session.query(TestMolSequence)
>> # .filter(~TestMolSequence.chains.any())
>> .all()
>> )
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Tue, Apr 13, 2021, at 10:03 AM, maqui...@gmail.com
>> <mailto:maqui...%40gmail.com> wrote:
>>> I need to delete the association table rows for many to many relationships
>>> when I delete one, but the default behavior (to remove those rows) does not
>>> seem to work in my case.
>>>
>>> I have multiple levels of many to many relationships, as you can see in the
>>> example I'll provide below and when I delete a "parent" afterwards I try to
>>> clean up any children left behind that have no other parents. However,
>>> these children are in many to many relationships with other children and
>>> that's when the ORM fails to attempt to remove those children from their
>>> related association tables (at least, in a way that I expect).
>>>
>>> The issue is error is:
>>> def do_executemany(self, cursor, statement, parameters, context=None):
>>> if self.executemany_mode is EXECUTEMANY_DEFAULT:
>>> > cursor.executemany(statement, parameters)
>>> E sqlalchemy.exc.IntegrityError:
>>> (psycopg2.errors.ForeignKeyViolation) update or delete on table
>>> "test_var_region" violates foreign key constraint
>>> "test_chain_var_region_var_region_id_fkey" on table "test_chain_var_region"
>>> E DETAIL: Key (id)=(1) is still referenced from table
>>> "test_chain_var_region".
>>> E
>>> E [SQL: DELETE FROM test_mol_sequence WHERE test_mol_sequence.id
>>> = %(id)s]
>>> E [parameters: ({'id': 5}, {'id': 6}, {'id': 7}, {'id': 8},
>>> {'id': 9}, {'id': 10})]
>>> E (Background on this error at: http://sqlalche.me/e/gkpj)
>>>
>>> The desired effect, of course, is that the rows in test_chain_var_region
>>> that reference the deleted chains removed. I've tried several strategies
>>> to do this but with no change in this behavior.
>>>
>>> Cascades could be an issue, and I would rather handle removal of any
>>> "orphan" rows in the model tables via business logic than have the database
>>> cascade deletes and potentially remove rows that are associated with other
>>> objects.
>>>
>>> import pytest
>>> from sqlalchemy import (
>>> Table,
>>> Column,
>>> Integer,
>>> String,
>>> ForeignKey,
>>> create_engine,
>>> )
>>> from sqlalchemy.ext.declarative import declarative_base, DeclarativeMeta
>>> from sqlalchemy.orm import relationship, Session
>>> from sqlalchemy.util import OrderedSet
>>>
>>>
>>> Base: DeclarativeMeta = declarative_base()
>>> engine = create_engine(
>>> "postgresql://postgres:postgres@localhost:5432/espresso", echo=True
>>> )
>>> test_chain_const_region = Table(
>>> "test_chain_const_region",
>>> Base.metadata,
>>> Column("chain_id", Integer, ForeignKey("test_chain.id")),
>>> Column("const_region_id", Integer, ForeignKey("test_const_region.id")),
>>> )
>>> test_chain_var_region = Table(
>>> "test_chain_var_region",
>>> Base.metadata,
>>> Column("chain_id", Integer, ForeignKey("test_chain.id")),
>>> Column("var_region_id", Integer, ForeignKey("test_var_region.id")),
>>> )
>>> test_molecule_chain = Table(
>>> "test_molecule_chain",
>>> Base.metadata,
>>> Column("molecule_id", Integer, ForeignKey("test_molecule.id")),
>>> Column("chain_id", Integer, ForeignKey("test_chain.id")),
>>> )
>>>
>>> test_mol_sequence_feat_mol_sequence = Table(
>>> "test_mol_sequence_feat_mol_sequence",
>>> Base.metadata,
>>> Column("mol_sequence_feat_id", Integer,
>>> ForeignKey("test_mol_sequence_feat.id")),
>>> Column("mol_sequence_id", Integer, ForeignKey("test_mol_sequence.id")),
>>> )
>>>
>>>
>>> class TestMolecule(Base):
>>> __tablename__ = "test_molecule"
>>> id = Column(Integer, primary_key=True)
>>> label = Column(String)
>>> chains = relationship(
>>> "TestChain",
>>> secondary=test_molecule_chain,
>>> collection_class=OrderedSet,
>>> back_populates="molecules",
>>> )
>>>
>>>
>>> class TestMolSequence(Base):
>>> __tablename__ = "test_mol_sequence"
>>>
>>> id = Column(Integer, primary_key=True)
>>> content = Column(String, nullable=False, unique=True)
>>> parent_features = relationship(
>>> "TestMolSequenceFeat",
>>> secondary=test_mol_sequence_feat_mol_sequence,
>>> collection_class=OrderedSet,
>>> back_populates="feature_sequences",
>>> single_parent=True,
>>> )
>>> chains = relationship(
>>> "TestChain", back_populates="mol_sequence", collection_class=OrderedSet
>>> )
>>>
>>>
>>> class TestMolSequenceFeat(Base):
>>> __tablename__ = "test_mol_sequence_feat"
>>>
>>> id = Column(Integer, primary_key=True)
>>> molecule_sequence_id = Column(
>>> Integer, ForeignKey("test_mol_sequence.id", ondelete="CASCADE"),
>>> )
>>> molecule_sequence = relationship("TestMolSequence",)
>>> start = Column(Integer)
>>> stop = Column(Integer)
>>> feature_sequences = relationship(
>>> "TestMolSequence",
>>> secondary=test_mol_sequence_feat_mol_sequence,
>>> collection_class=OrderedSet,
>>> back_populates="parent_features",
>>> # single_parent=True,
>>> )
>>>
>>>
>>> class TestChain(Base):
>>> __tablename__ = "test_chain"
>>>
>>> id = Column(Integer, primary_key=True)
>>> label = Column(String)
>>> chain_type = Column(String)
>>> mol_sequence_id = Column(Integer, ForeignKey("test_mol_sequence.id"))
>>> mol_sequence = relationship("TestMolSequence", back_populates="chains")
>>> molecules = relationship(
>>> "TestMolecule",
>>> secondary=test_molecule_chain,
>>> collection_class=OrderedSet,
>>> back_populates="chains",
>>> )
>>> var_regions = relationship(
>>> "TestVarRegion",
>>> secondary=test_chain_var_region,
>>> collection_class=OrderedSet,
>>> back_populates="chains",
>>> )
>>> const_regions = relationship(
>>> "TestConstRegion",
>>> secondary=test_chain_const_region,
>>> collection_class=OrderedSet,
>>> back_populates="chains",
>>> )
>>>
>>>
>>> class TestVarRegion(Base):
>>> __tablename__ = "test_var_region"
>>>
>>> id = Column(Integer, primary_key=True)
>>> molecule_sequence_id = Column(
>>> Integer, ForeignKey("test_mol_sequence.id", ondelete="CASCADE"),
>>> )
>>> description = Column(String)
>>> additional_information = Column(String)
>>> label = Column("label", String, nullable=True, unique=False)
>>> molecule_sequence = relationship("TestMolSequence")
>>> chains = relationship(
>>> "TestChain",
>>> secondary=test_chain_var_region,
>>> collection_class=OrderedSet,
>>> back_populates="var_regions",
>>> passive_deletes=True,
>>> )
>>>
>>>
>>> class TestConstRegion(Base):
>>> __tablename__ = "test_const_region"
>>>
>>> id = Column(Integer, primary_key=True)
>>> molecule_sequence_id = Column(
>>> Integer, ForeignKey("test_mol_sequence.id", ondelete="CASCADE"),
>>> )
>>> description = Column(String)
>>> additional_information = Column(String)
>>> label = Column("label", String, nullable=True, unique=False)
>>> molecule_sequence = relationship("TestMolSequence")
>>> chains = relationship(
>>> "TestChain",
>>> secondary=test_chain_const_region,
>>> collection_class=OrderedSet,
>>> back_populates="const_regions",
>>> passive_deletes=True,
>>> )
>>>
>>>
>>> class TestManyToMany:
>>> @pytest.fixture
>>> def engine(self):
>>> return create_engine(
>>> "postgresql://postgres:postgres@localhost:5432/espresso", echo=True
>>> )
>>>
>>> @pytest.fixture
>>> def session(self):
>>> *"""Returns an sqlalchemy session, and after the test tears down everything
>>> properly."""
** *connection = engine.connect()
>>> # begin the nested transaction
>>> transaction = connection.begin()
>>> # use the connection with the already started transaction
>>> session = Session(bind=connection)
>>>
>>> yield session
>>>
>>> session.close()
>>> # roll back the broader transaction
>>> transaction.commit()
>>> # put back the connection to the connection pool
>>> connection.close()
>>>
>>> @pytest.mark.create_m2m_models
>>> def test_create_m2m_models(self, engine):
>>>
>>> Base.metadata.drop_all(bind=engine)
>>> Base.metadata.create_all(bind=engine)
>>>
>>> @pytest.mark.seed_m2m_data
>>> def test_m2m_seeding_data(self, engine, session):
>>>
>>> molecule1 = TestMolecule(label="molecule1")
>>> molecule2 = TestMolecule(label="molecule2")
>>> molecule3 = TestMolecule(label="molecule3")
>>> molecule4 = TestMolecule(label="molecule4")
>>> light_chain_1_sequence = TestMolSequence(content="taglconst1VAR1")
>>> heavy_chain_1_sequence = TestMolSequence(content="tagheavyconstant1VAR2")
>>> heavy_chain_2_sequence = TestMolSequence(content="tagheavyconstant2VAR2")
>>> light_chain_2_sequence = TestMolSequence(content="taglconst1VAR3")
>>> heavy_chain_1 = TestChain(
>>> chain_type="heavy", mol_sequence=light_chain_1_sequence
>>> )
>>> light_chain_1 = TestChain(
>>> chain_type="light", mol_sequence=heavy_chain_1_sequence
>>> )
>>> light_chain_2 = TestChain(
>>> chain_type="light", mol_sequence=light_chain_2_sequence
>>> )
>>> heavy_chain_2 = TestChain(
>>> chain_type="heavy", mol_sequence=heavy_chain_2_sequence
>>> )
>>>
>>> molecule1.chains.add(heavy_chain_1)
>>> molecule1.chains.add(light_chain_1)
>>> molecule2.chains.add(heavy_chain_2)
>>> molecule2.chains.add(light_chain_2)
>>> molecule3.chains.add(heavy_chain_1)
>>> molecule3.chains.add(light_chain_2)
>>> molecule4.chains.add(heavy_chain_2)
>>> molecule4.chains.add(light_chain_1)
>>>
>>> tag_sequence = TestMolSequence(content="tag")
>>> light_constant_region_seq = TestMolSequence(content="lconst1")
>>> heavy_constant_region_1_seq = TestMolSequence(content="heavyconstant1")
>>> heavy_constant_region_2_seq = TestMolSequence(content="heavyconstant2")
>>> vr1_seq = TestMolSequence(content="VAR1")
>>> vr2_seq = TestMolSequence(content="VAR2")
>>> vr3_seq = TestMolSequence(content="VAR3")
>>> # lc2_const_region_seq = TestMolSequence(content="lconst")
>>> lc1_tag_feature = TestMolSequenceFeat(
>>> start=0, stop=3, molecule_sequence=light_chain_1_sequence
>>> )
>>> lc1_const_region_feature = TestMolSequenceFeat(
>>> start=3, stop=10, molecule_sequence=light_chain_1_sequence
>>> )
>>> lc1_var_region_feature = TestMolSequenceFeat(
>>> start=10, stop=14, molecule_sequence=light_chain_1_sequence
>>> )
>>> hc1_tag_feature = TestMolSequenceFeat(
>>> start=0, stop=3, molecule_sequence=heavy_chain_1_sequence
>>> )
>>> hc1_const_region_feature = TestMolSequenceFeat(
>>> start=3, stop=17, molecule_sequence=heavy_chain_1_sequence
>>> )
>>> hc1_var_region_feature = TestMolSequenceFeat(
>>> start=17, stop=21, molecule_sequence=heavy_chain_1_sequence
>>> )
>>>
>>> hc2_tag_feature = TestMolSequenceFeat(
>>> start=0, stop=3, molecule_sequence=heavy_chain_2_sequence
>>> )
>>> hc2_const_region_feature = TestMolSequenceFeat(
>>> start=3, stop=17, molecule_sequence=heavy_chain_2_sequence
>>> )
>>> hc2_var_region_feature = TestMolSequenceFeat(
>>> start=17, stop=21, molecule_sequence=heavy_chain_2_sequence
>>> )
>>>
>>> lc2_tag_feature = TestMolSequenceFeat(
>>> start=0, stop=3, molecule_sequence=light_chain_2_sequence
>>> )
>>> lc2_const_region_feature = TestMolSequenceFeat(
>>> start=3, stop=10, molecule_sequence=light_chain_2_sequence
>>> )
>>> lc2_var_region_feature = TestMolSequenceFeat(
>>> start=10, stop=14, molecule_sequence=light_chain_2_sequence
>>> )
>>> var_region1 = TestVarRegion(molecule_sequence=vr1_seq)
>>> var_region2 = TestVarRegion(molecule_sequence=vr2_seq)
>>> var_region3 = TestVarRegion(molecule_sequence=vr3_seq)
>>> const_region1 = TestConstRegion(molecule_sequence=light_constant_region_seq)
>>> const_region2 =
>>> TestConstRegion(molecule_sequence=heavy_constant_region_1_seq)
>>> const_region3 =
>>> TestConstRegion(molecule_sequence=heavy_constant_region_2_seq)
>>>
>>> light_chain_1.var_regions.add(var_region1)
>>> heavy_chain_1.var_regions.add(var_region2)
>>> heavy_chain_2.var_regions.add(var_region2)
>>> light_chain_2.var_regions.add(var_region3)
>>>
>>> light_chain_1.const_regions.add(const_region1)
>>> light_chain_2.const_regions.add(const_region1)
>>> heavy_chain_1.const_regions.add(const_region2)
>>> heavy_chain_2.const_regions.add(const_region3)
>>>
>>> lc1_tag_feature.feature_sequences.add(tag_sequence)
>>> lc1_var_region_feature.feature_sequences.add(vr1_seq)
>>> lc1_const_region_feature.feature_sequences.add(light_constant_region_seq)
>>>
>>> hc1_tag_feature.feature_sequences.add(tag_sequence)
>>> hc1_var_region_feature.feature_sequences.add(vr2_seq)
>>> hc1_const_region_feature.feature_sequences.add(heavy_constant_region_1_seq)
>>>
>>> lc2_tag_feature.feature_sequences.add(tag_sequence)
>>> lc2_var_region_feature.feature_sequences.add(vr3_seq)
>>> lc2_const_region_feature.feature_sequences.add(light_constant_region_seq)
>>>
>>> hc2_tag_feature.feature_sequences.add(tag_sequence)
>>> hc2_var_region_feature.feature_sequences.add(vr2_seq)
>>> hc2_const_region_feature.feature_sequences.add(heavy_constant_region_2_seq)
>>>
>>> session.add_all(
>>> [
>>> heavy_chain_1,
>>> light_chain_1,
>>> light_chain_2,
>>> heavy_chain_2,
>>> molecule1,
>>> molecule2,
>>> molecule3,
>>> molecule4,
>>> # tag_sequence,
>>> # lc1_tag_feature,
>>> # lc1_const_region_feature,
>>> # hc1_tag_feature,
>>> # hc1_var_region_feature,
>>> # lc1_tag_feature,
>>> # lc2_const_region_feature,
>>> ]
>>> )
>>> session.commit()
>>>
>>> @pytest.mark.delete_test_m2m_models
>>> def test_create_m2m(self, session):
>>> molecule = session.query(TestMolecule).filter_by(label="molecule1").one()
>>> session.delete(molecule)
>>> session.query(TestChain).filter(~TestChain.molecules.any()).delete(
>>> synchronize_session="fetch"
>>> )
>>> session.expire_all()
>>> orphan_chains = (
>>> session.query(TestChain).filter(~TestChain.molecules.any()).all()
>>> )
>>> for chain in orphan_chains:
>>> session.delete(chain)
>>> orphan_vrs = (
>>> session.query(TestVarRegion).filter(~TestVarRegion.chains.any()).all()
>>> )
>>> for orphan_vr in orphan_vrs:
>>> session.delete(orphan_vr)
>>> orphan_crs = (
>>> session.query(TestConstRegion)
>>> .filter(~TestConstRegion.chains.any())
>>> .all()
>>> )
>>> for orphan_cr in orphan_crs:
>>> session.delete(orphan_cr)
>>> orphan_sequences = (
>>> session.query(TestMolSequence).filter(~TestMolSequence.chains.any()).all()
>>> )
>>> orphan_sequence: TestMolSequence
>>> for orphan_sequence in orphan_sequences:
>>> session.delete(orphan_sequence)
>>> session.commit()
>>>
>>> --
>>> SQLAlchemy -
>>> The Python SQL Toolkit and Object Relational Mapper
>>>
>>> http://www.sqlalchemy.org/
>>>
>>> To post example code, please provide an MCVE: Minimal, Complete, and
>>> Verifiable Example. See http://stackoverflow.com/help/mcve for a full
>>> description.
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>>>
>>> <https://groups.google.com/d/msgid/sqlalchemy/7963c7d7-9053-436e-ae5b-f92519ddeb0en%40googlegroups.com?utm_medium=email&utm_source=footer>.
>>
>>
>> --
>> SQLAlchemy -
>> The Python SQL Toolkit and Object Relational Mapper
>>
>> http://www.sqlalchemy.org/
>>
>> To post example code, please provide an MCVE: Minimal, Complete, and
>> Verifiable Example. See http://stackoverflow.com/help/mcve for a full
>> description.
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>>
>> <https://groups.google.com/d/msgid/sqlalchemy/56bfe88d-8b81-4541-9192-86d42ebcc27f%40www.fastmail.com?utm_medium=email&utm_source=footer>.
>
> --
> SQLAlchemy -
> The Python SQL Toolkit and Object Relational Mapper
>
> http://www.sqlalchemy.org/
>
> To post example code, please provide an MCVE: Minimal, Complete, and
> Verifiable Example. See http://stackoverflow.com/help/mcve for a full
> description.
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>
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--
SQLAlchemy -
The Python SQL Toolkit and Object Relational Mapper
http://www.sqlalchemy.org/
To post example code, please provide an MCVE: Minimal, Complete, and Verifiable
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