feat: add orm classes

.env

@@ -1 +1,7 @@
-DB_URI="postgresql+psycopg2://postgres:pw@localhost:5432/postgres"
+MPI_DB_TYPE=postgres
+MPI_DBNAME=testdb
+MPI_HOST=localhost
+MPI_PORT=5432
+MPI_USER=postgres
+MPI_PASSWORD=pw
+DB_URI="sqlite:///db.sqlite3"

alembic/versions/0db31a429322_create_algorithm_tables.py

@@ -0,0 +1,51 @@
+"""create algorithm tables
+
+Revision ID: 0db31a429322
+Revises: 6052c193a26a
+Create Date: 2024-09-19 11:45:31.232579
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = '0db31a429322'
+down_revision: Union[str, None] = '6052c193a26a'
+branch_labels: Union[str, Sequence[str], None] = None
+depends_on: Union[str, Sequence[str], None] = None
+
+
+def upgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.create_table('algorithm',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('is_default', sa.Boolean(), nullable=False),
+    sa.Column('label', sa.String(length=255), nullable=False),
+    sa.Column('description', sa.String(), nullable=False),
+    sa.PrimaryKeyConstraint('id'),
+    sa.UniqueConstraint('label')
+    )
+    op.create_table('algorithm_pass',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('algorithm_id', sa.Integer(), nullable=False),
+    sa.Column('blocking_keys', sa.JSON(), nullable=False),
+    sa.Column('evaluators', sa.JSON(), nullable=False),
+    sa.Column('rule', sa.String(length=255), nullable=False),
+    sa.Column('cluster_ratio', sa.Float(), nullable=False),
+    sa.Column('kwargs', sa.JSON(), nullable=False),
+    sa.ForeignKeyConstraint(['algorithm_id'], ['algorithm.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_mpi_blocking_key_key'), 'mpi_blocking_key', ['key'], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_index(op.f('ix_mpi_blocking_key_key'), table_name='mpi_blocking_key')
+    op.drop_table('algorithm_pass')
+    op.drop_table('algorithm')
+    # ### end Alembic commands ###

src/recordlinker/linkage/models.py

@@ -1,5 +1,6 @@
 import uuid
 
+from sqlalchemy import event
 from sqlalchemy import ForeignKey
 from sqlalchemy import JSON
 from sqlalchemy import orm
@@ -9,14 +10,12 @@
 class Base(orm.DeclarativeBase):
     pass
 
-
 class Person(Base):
     __tablename__ = "mpi_person"
 
     id: orm.Mapped[int] = orm.mapped_column(primary_key=True)
     internal_id: orm.Mapped[uuid.UUID] = orm.mapped_column(default=uuid.uuid4)
 
-
 class ExternalPerson(Base):
     __tablename__ = "mpi_external_person"
 
@@ -25,15 +24,13 @@ class ExternalPerson(Base):
     external_id: orm.Mapped[str] = orm.mapped_column(String(255))
     source: orm.Mapped[str] = orm.mapped_column(String(255))
 
-
 class Patient(Base):
     __tablename__ = "mpi_patient"
 
     id: orm.Mapped[int] = orm.mapped_column(primary_key=True)
     person_id: orm.Mapped[int] = orm.mapped_column(ForeignKey("mpi_person.id"))
     data: orm.Mapped[dict] = orm.mapped_column(JSON)
 
-
 class BlockingKey(Base):
     __tablename__ = "mpi_blocking_key"
 
@@ -47,3 +44,48 @@ class BlockingValue(Base):
     patient_id: orm.Mapped[int] = orm.mapped_column(ForeignKey("mpi_patient.id"))
     blockingkey_id: orm.Mapped[int] = orm.mapped_column(ForeignKey("mpi_blocking_key.id"))
     value: orm.Mapped[str] = orm.mapped_column(String(50), index=True)
+
+class Algorithm(Base):
+    __tablename__ = "algorithm"
+
+    id: orm.Mapped[int] = orm.mapped_column(primary_key=True)
+    is_default: orm.Mapped[bool] = orm.mapped_column(default=False)
+    label: orm.Mapped[str] = orm.mapped_column(String(255), unique=True)
+    description: orm.Mapped[str]
+
+def check_only_one_default(connection, target):
+    """
+    Check if there is already a default algorithm before inserting or updating.
+
+    Called before an insert or update operation on the
+    Algorithm table. If the `is_default` attribute of the target object is
+    set to True, it checks the database to ensure that no other algorithm
+    is marked as default. If another default algorithm exists, an exception
+    is raised to prevent the operation.
+
+    Parameters:
+    connection: The database connection being used for the operation.
+    target: The instance of the Algorithm class being inserted or updated.
+    
+    Raises:
+    Exception: If another algorithm is already marked as default.
+    """
+
+    if target.is_default:
+        existing_default = connection.execute("SELECT COUNT(*) FROM algorithm WHERE is_default = TRUE").scalar()
+        if(existing_default > 0):
+            raise ValueError("There can only be one default algorithm.")
+
+event.listen(Algorithm, 'before_insert', check_only_one_default)
+event.listen(Algorithm, 'before_update', check_only_one_default)
+
+class AlgorithmPass(Base):
+    __tablename__ = "algorithm_pass"
+
+    id: orm.Mapped[int] = orm.mapped_column(primary_key=True)
+    algorithm_id: orm.Mapped[int] = orm.mapped_column(ForeignKey("algorithm.id"))
+    blocking_keys: orm.Mapped[list[int]] = orm.mapped_column(JSON)
+    evaluators: orm.Mapped[list[str]] = orm.mapped_column(JSON)     
+    rule: orm.Mapped[str] = orm.mapped_column(String(255))
+    cluster_ratio: orm.Mapped[float]
+    kwargs: orm.Mapped[dict] = orm.mapped_column(JSON)