add setting.db_table_prefix variable (#100)

## Description
Adding `setting.db_table_prefix` so customers can optionally change all
the table names with a prefix.

## Additional Notes
Allowing customers to use an existing database for storing the MPI
tables comes at a risk of not knowing what existing tables, the customer
might have in their database. To guarantee that the customer doesn't
have any naming conflicts with the tables created by Record Linker, we
can allow for an optional prefix ENV variable, given them the opportunity
to override the table names.

src/recordlinker/config.py

@@ -22,6 +22,10 @@ class Settings(pydantic_settings.BaseSettings):
     )
 
     db_uri: str = pydantic.Field(description="The URI for the MPI database")
+    db_table_prefix: str = pydantic.Field(
+        description="The prefix for all database tables",
+        default="",
+    )
     test_db_uri: str = pydantic.Field(
         description="The URI for the MPI database to run tests against",
         default="sqlite:///testdb.sqlite3",

src/recordlinker/models/algorithm.py

@@ -75,7 +75,7 @@ class AlgorithmPass(Base):
 
     id: orm.Mapped[int] = orm.mapped_column(primary_key=True)
     algorithm_id: orm.Mapped[int] = orm.mapped_column(
-        schema.ForeignKey("algorithm.id", ondelete="CASCADE")
+        schema.ForeignKey(f"{Algorithm.__tablename__}.id", ondelete="CASCADE")
     )
     algorithm: orm.Mapped["Algorithm"] = orm.relationship(back_populates="passes")
     blocking_keys: orm.Mapped[list[str]] = orm.mapped_column(sqltypes.JSON)

src/recordlinker/models/base.py

@@ -1,9 +1,19 @@
 from sqlalchemy import orm
 from sqlalchemy import types as sqltypes
 
+from recordlinker.config import settings
 
-class Base(orm.DeclarativeBase):
-    pass
+
+class PrefixerMeta(orm.DeclarativeMeta):
+
+    def __init__(cls, name, bases, dict_):
+        name = dict_.get("__tablename__")
+        if name:
+            cls.__tablename__ = f"{settings.db_table_prefix}{name}"
+            dict_["__tablename__"] = f"{settings.db_table_prefix}{name}"
+        return super().__init__(name, bases, dict_)
+
+Base = orm.declarative_base(metaclass=PrefixerMeta)
 
 
 def get_bigint_pk():

src/recordlinker/models/mpi.py

@@ -39,7 +39,7 @@ class Patient(Base):
     __tablename__ = "mpi_patient"
 
     id: orm.Mapped[int] = orm.mapped_column(get_bigint_pk(), autoincrement=True, primary_key=True)
-    person_id: orm.Mapped[int] = orm.mapped_column(schema.ForeignKey("mpi_person.id"))
+    person_id: orm.Mapped[int] = orm.mapped_column(schema.ForeignKey(f"{Person.__tablename__}.id"))
     person: orm.Mapped["Person"] = orm.relationship(back_populates="patients")
     # NOTE: We're using a protected attribute here to store the data string, as we
     # want getter/setter access to the data dictionary to trigger updating the
@@ -157,7 +157,7 @@ class BlockingValue(Base):
     )
 
     id: orm.Mapped[int] = orm.mapped_column(get_bigint_pk(), autoincrement=True, primary_key=True)
-    patient_id: orm.Mapped[int] = orm.mapped_column(schema.ForeignKey("mpi_patient.id"))
+    patient_id: orm.Mapped[int] = orm.mapped_column(schema.ForeignKey(f"{Patient.__tablename__}.id"))
     patient: orm.Mapped["Patient"] = orm.relationship(back_populates="blocking_values")
     blockingkey: orm.Mapped[int] = orm.mapped_column(sqltypes.SmallInteger)
     value: orm.Mapped[str] = orm.mapped_column(sqltypes.String(BLOCKING_VALUE_MAX_LENGTH))