new schema mpi fuctions

.env

@@ -1 +1,2 @@
-DB_URI="postgresql+psycopg2://postgres:pw@localhost:5432/postgres"
+DB_URI="postgresql+psycopg2://postgres:pw@localhost:5432/postgres"
+TEST_DB_URI="sqlite:///:memory:"

.github/pull_request_template.md

@@ -7,6 +7,8 @@
 ## Additional Notes
 [Add any additional context or notes that reviewers should know about.]
 
+<--------------------- REMOVE THE LINES BELOW BEFORE MERGING --------------------->
+
 ## Checklist
 Please review and complete the following checklist before submitting your pull request:
 

.gitignore

@@ -27,7 +27,8 @@ temp/
 *.tmp
 
 # macOS
-.DS_Store
+# ignore all files ending in .DS_Store
+**/.DS_Store
 
 # Python-Virtual Environments
 .venv

alembic/env.py

@@ -5,8 +5,6 @@
 
 from alembic import context
 
-import dotenv
-ENV = dotenv.dotenv_values()
 
 # this is the Alembic Config object, which provides
 # access to the values within the .ini file in use.
@@ -16,7 +14,8 @@
 # This line sets up loggers basically.
 if config.config_file_name is not None:
     fileConfig(config.config_file_name)
-config.set_main_option("sqlalchemy.url", ENV["DB_URI"])
+from recordlinker.config import settings
+config.set_main_option("sqlalchemy.url", settings.DB_URI)
 
 # add your model's MetaData object here
 # for 'autogenerate' support

alembic/versions/64ed9566f189_external_person_id_should_be_nullable.py

@@ -0,0 +1,42 @@
+"""external person id should be nullable
+
+Revision ID: 64ed9566f189
+Revises: bfbd015ca466
+Create Date: 2024-09-18 20:22:07.510203
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = '64ed9566f189'
+down_revision: Union[str, None] = 'bfbd015ca466'
+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.drop_index('ix_mpi_blocking_value_value', table_name='mpi_blocking_value')
+    op.alter_column('mpi_patient', 'external_person_id',
+               existing_type=sa.VARCHAR(length=255),
+               nullable=True)
+    op.alter_column('mpi_patient', 'external_person_source',
+               existing_type=sa.VARCHAR(length=100),
+               nullable=True)
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.alter_column('mpi_patient', 'external_person_source',
+               existing_type=sa.VARCHAR(length=100),
+               nullable=False)
+    op.alter_column('mpi_patient', 'external_person_id',
+               existing_type=sa.VARCHAR(length=255),
+               nullable=False)
+    op.create_index('ix_mpi_blocking_value_value', 'mpi_blocking_value', ['value'], unique=False)
+    # ### end Alembic commands ###

alembic/versions/ad18f1d41fad_convert_blockingkey_into_enum.py

@@ -0,0 +1,57 @@
+"""convert BlockingKey into enum
+
+Revision ID: ad18f1d41fad
+Revises: 6052c193a26a
+Create Date: 2024-09-17 21:15:37.714595
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = 'ad18f1d41fad'
+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.drop_table('mpi_blocking_key')
+    op.drop_table('mpi_blocking_value')
+
+    op.create_table('mpi_blocking_value',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('patient_id', sa.Integer(), nullable=False),
+    sa.Column('blockingkey', sa.Integer(), nullable=False),
+    sa.Column('value', sa.String(length=50), nullable=False),
+    sa.ForeignKeyConstraint(['patient_id'], ['mpi_patient.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index('idx_blocking_value_patient_key_value', 'mpi_blocking_value', ['patient_id', 'blockingkey', 'value'], unique=False)
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_table('mpi_blocking_value')
+
+    op.create_table('mpi_blocking_key',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('key', sa.String(length=50), nullable=False),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_table('mpi_blocking_value',
+    sa.Column('id', sa.Integer(), nullable=False),
+    sa.Column('patient_id', sa.Integer(), nullable=False),
+    sa.Column('blockingkey_id', sa.Integer(), nullable=False),
+    sa.Column('value', sa.String(length=50), nullable=False),
+    sa.ForeignKeyConstraint(['blockingkey_id'], ['mpi_blocking_key.id'], ),
+    sa.ForeignKeyConstraint(['patient_id'], ['mpi_patient.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    op.create_index(op.f('ix_mpi_blocking_value_value'), 'mpi_blocking_value', ['value'], unique=False)
+    # ### end Alembic commands ###

alembic/versions/bfbd015ca466_moving_externalperson_to_patient_table.py

@@ -0,0 +1,43 @@
+"""moving ExternalPerson to Patient table
+
+Revision ID: bfbd015ca466
+Revises: ad18f1d41fad
+Create Date: 2024-09-18 20:10:30.193941
+
+"""
+from typing import Sequence, Union
+
+from alembic import op
+import sqlalchemy as sa
+
+
+# revision identifiers, used by Alembic.
+revision: str = 'bfbd015ca466'
+down_revision: Union[str, None] = 'ad18f1d41fad'
+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.drop_table('mpi_external_person')
+    op.create_index(op.f('ix_mpi_blocking_value_value'), 'mpi_blocking_value', ['value'], unique=False)
+    op.add_column('mpi_patient', sa.Column('external_person_id', sa.String(length=255), nullable=False))
+    op.add_column('mpi_patient', sa.Column('external_person_source', sa.String(length=100), nullable=False))
+    # ### end Alembic commands ###
+
+
+def downgrade() -> None:
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column('mpi_patient', 'external_person_source')
+    op.drop_column('mpi_patient', 'external_person_id')
+    op.drop_index(op.f('ix_mpi_blocking_value_value'), table_name='mpi_blocking_value')
+    op.create_table('mpi_external_person',
+    sa.Column('id', sa.INTEGER(), nullable=False),
+    sa.Column('person_id', sa.INTEGER(), nullable=False),
+    sa.Column('external_id', sa.VARCHAR(length=255), nullable=False),
+    sa.Column('source', sa.VARCHAR(length=255), nullable=False),
+    sa.ForeignKeyConstraint(['person_id'], ['mpi_person.id'], ),
+    sa.PrimaryKeyConstraint('id')
+    )
+    # ### end Alembic commands ###

pyproject.toml

@@ -21,6 +21,7 @@ dependencies = [
     "fastapi",
     "pydantic",
     "pydantic-settings",
+    "python-dateutil==2.9.0",
     "sqlalchemy",
     "fhirpathpy",
     "rapidfuzz",
@@ -37,7 +38,6 @@ dev = [
     "pyarrow",
     "httpx",
     "alembic",
-    "python-dotenv"
 ]
 prod = [
     # List any additional production-only dependencies here
@@ -65,6 +65,7 @@ select = ["E4", "E7", "E9", "F", "I", "D102", "D103", "D104", "D105", "D106"] #
 
 [tool.ruff.lint.per-file-ignores]
 "**/__init__.py" = ["D"]
+"tests/*.py" = ["D102", "D103"]  # Ignore the public docstring rules in test files
 
 [tool.ruff.lint.isort]
 # The following settings reduce the number of changes from reorder-python-imports

src/recordlinker/config.py

@@ -10,6 +10,9 @@ class Settings(pydantic_settings.BaseSettings):
     )
 
     db_uri: str = pydantic.Field(description="The URI for the MPI database")
+    # FIXME: A separate URI for testing is temporary, this is necessary right now because
+    # the old schema only works with postgresql.  Once the old schema is removed we can consolidate
+    test_db_uri: str = pydantic.Field(description="The URI for the MPI database to run tests against")
     connection_pool_size: typing.Optional[int] = pydantic.Field(
         description="The number of MPI database connections in the connection pool",
         default=5,