I just wanted to clarify, the desire would be for the "test_var_region" and
"test_const_region" entities that are linked to other entities to remain
untouched and only to have their associations removed from the deleted
items. The output from the ORM indicates that the system is actually
attempting to delete them in some sort of cascade event a.) although that
is unspecified in any cascade option and b.) that is undesired in the first
place.
On Tue, Apr 13, 2021 at 10:04 AM maqui...@gmail.com <maquino1...@gmail.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.
> ---
> You received this message because you are subscribed to the Google Groups
> "sqlalchemy" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to sqlalchemy+unsubscr...@googlegroups.com.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/sqlalchemy/7963c7d7-9053-436e-ae5b-f92519ddeb0en%40googlegroups.com
> <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.
---
You received this message because you are subscribed to the Google Groups
"sqlalchemy" group.
To unsubscribe from this group and stop receiving emails from it, send an email
to sqlalchemy+unsubscr...@googlegroups.com.
To view this discussion on the web visit
https://groups.google.com/d/msgid/sqlalchemy/CAL6EnB44ZiTLgUB%2BAZhwnqCDCKiHwWR5X-5oTGxRut_16GLW9g%40mail.gmail.com.
