remove old schema and code (#68)

## Description 5000 lines removed 😮 ## Related Issues #63 ## Additional Notes - Making SQLite the default database for testing and local_server, now the old code is removed. HOWEVER, we will continue to use postgres in CI - Removed assets and migrations related to old schema - explicitly added DB adapters (postgres, mysql, microsoft sql server) to pyproject.toml - consolidating testing session fixtures by creating a new contextmanager function, `get_test_session`, in database.py and adding [conftest.py](https://docs.pytest.org/en/7.1.x/reference/fixtures.html#conftest-py-sharing-fixtures-across-multiple-files) to assist with creating reusable testing fixtures - removed all `recordlinker.linkage` code and tests, except for matchers, this was copied to `recordlinker.linking.old_matchers` (we need to port these methods before we can move them) - removed old schema calls from the link-record API endpoint - removed pyway helpers from `recordlinker.utils` - renamed test_record_linkage to test_main (as its really just testing the API endpoints in main.py). Rewrote some of the tests to make use of the new client fixture.
CDCgov · Oct 9, 2024 · 1a2f7ce · 1a2f7ce
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diff --git a/.env b/.env
@@ -1,2 +1 @@
-DB_URI="postgresql+psycopg2://postgres:pw@localhost:5432/postgres"
-TEST_DB_URI="sqlite:///:memory:"
+DB_URI="sqlite:///db.sqlite3"
diff --git a/.github/workflows/check_unit_tests.yml b/.github/workflows/check_unit_tests.yml
@@ -39,7 +39,7 @@ jobs:
 
       - name: Run unit tests
         env:
-          DB_URI: "postgresql+psycopg2://postgres:pw@localhost:5432/postgres"
+          TEST_DB_URI: "postgresql+psycopg2://postgres:pw@localhost:5432/postgres"
         run: |
           pytest --cov=recordlinker --cov-report=xml tests/unit
       - name: Upload test results to Codecov

diff --git a/README.md b/README.md
@@ -44,7 +44,7 @@ To run all the unit tests, use the following command:
 
 To run a single unit test, use the following command:
 ```bash
-./scripts/test_unit.sh tests/unit/test_linkage.py::test_link_record_against_mpi
+./scripts/test_unit.sh tests/unit/test_main.py::test_linkage_success
 ```
 
 ## Standard Notices

diff --git a/assets/linkage/dibbs_basic_algorithm.json b/assets/linkage/dibbs_basic_algorithm.json
diff --git a/assets/linkage/dibbs_enhanced_algorithm.json b/assets/linkage/dibbs_enhanced_algorithm.json
diff --git a/assets/linkage/patient_lol.csv b/assets/linkage/patient_lol.csv
diff --git a/assets/linkage/synthetic_patient_mpi_seed_data.parquet b/assets/linkage/synthetic_patient_mpi_seed_data.parquet
diff --git a/...kage/patient_bundle_to_link_with_mpi.json → ...king/patient_bundle_to_link_with_mpi.json b/...kage/patient_bundle_to_link_with_mpi.json → ...king/patient_bundle_to_link_with_mpi.json
diff --git a/migrations/V01_01__flat_schema.sql b/migrations/V01_01__flat_schema.sql
diff --git a/migrations/V01_02__indexes.sql b/migrations/V01_02__indexes.sql