First version

.github/workflows/lint.yml

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+name: Ruff
+on: [push, pull_request]
+jobs:
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

.github/workflows/python-package.yml

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+# This workflow will install Python dependencies, run tests with a range of Python versions
+
+name: tests
+
+on: [push, pull_request]
+
+jobs:
+  tests:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: [
+          '3.8',
+          '3.9',
+          '3.10',
+          '3.11',
+          '3.12',
+        ]
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
+    - name: Install package and dependencies
+      run: poetry install
+    - name: Test with pytest
+      run: poetry run pytest -vs

.pre-commit-config.yaml

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+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.3.2
+    hooks:
+      # Run the linter.
+      - id: ruff
+        args: [ --fix ]
+      # Run the formatter.
+      - id: ruff-format

README.md

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+# OMOP-CDM
+
+Python SQLAlchemy table definitions of the [OHDSI OMOP CDM](https://ohdsi.github.io/CommonDataModel/).
+
+## Installation
+
+Install from PyPI:
+```shell
+pip install omop-cdm
+```
+
+## Usage
+TODO:
+See [User documentation](docs/index.md)
+
+## Development
+
+### Setup steps
+
+Make sure the following tooling is installed:
+- [Poetry](https://python-poetry.org/docs/#installation)
+- [pre-commit](https://pre-commit.com/#install)
+
+Install the project and dependencies via `poetry install`.
+
+Then set up the git hook scripts via `pre-commit install`.

noxfile.py

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+import nox  # type: ignore
+
+nox.options.sessions = [
+    "tests",
+    "lint",
+]
+
+python = [
+    "3.8",
+    "3.9",
+    "3.10",
+    "3.11",
+    "3.12",
+]
+
+
+@nox.session(python=python)
+def tests(session):
+    session.run("poetry", "install", external=True)
+    session.run("pytest")
+
+
+@nox.session(python="3.12")
+def lint(session):
+    session.run("poetry", "install", external=True)
+    session.run("ruff", "check")

pyproject.toml

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+[tool.poetry]
+name = "omop-cdm"
+version = "0.1.0"
+description = "SQLAlchemy ORM of the OHDSI OMOP CDM"
+authors = [
+    "Spayralbe <[email protected]>",
+]
+readme = "README.md"
+
+[tool.poetry.dependencies]
+python = "^3.8"
+sqlalchemy = "^2.0.0"
+
+
+[tool.poetry.group.test.dependencies]
+testcontainers-postgres = "^0.0.1rc1"
+pytest = "^8.1.1"
+nox = "^2024.3.2"
+ruff = "^0.3.2"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"
+
+
+[tool.pytest.ini_options]
+addopts = "--import-mode=importlib"
+pythonpath = [
+    ".",
+]
+
+# Ignore import violations in all `__init__.py` files
+[tool.ruff.lint.per-file-ignores]
+"__init__.py" = ["E402", "F401"]

src/omop_cdm/__init__.py

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+from omop_cdm.constants import NAMING_CONVENTION

src/omop_cdm/constants.py

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+"""Module containing the placeholder schema names as used in the ORM."""
+
+# These are the placeholder schema names as used in the ORM table
+# definitions and as keys in the schema_translate_map.
+# Actual schema names will be different at runtime, as determined by the
+# provided parameters in the config.yml file.
+VOCAB_SCHEMA = "vocabulary_schema"
+CDM_SCHEMA = "cdm_schema"
+
+# Some often used foreign keys are added as variables for convenience.
+FK_CONCEPT_ID = f"{VOCAB_SCHEMA}.concept.concept_id"
+FK_VOCABULARY_ID = f"{VOCAB_SCHEMA}.vocabulary.vocabulary_id"
+FK_DOMAIN_ID = f"{VOCAB_SCHEMA}.domain.domain_id"
+FK_CONCEPT_CLASS_ID = f"{VOCAB_SCHEMA}.concept_class.concept_class_id"
+FK_PERSON_ID = f"{CDM_SCHEMA}.person.person_id"
+FK_VISIT_OCCURRENCE_ID = f"{CDM_SCHEMA}.visit_occurrence.visit_occurrence_id"
+FK_VISIT_DETAIL_ID = f"{CDM_SCHEMA}.visit_detail.visit_detail_id"
+FK_PROVIDER_ID = f"{CDM_SCHEMA}.provider.provider_id"
+FK_CARE_SITE_ID = f"{CDM_SCHEMA}.care_site.care_site_id"
+FK_LOCATION_ID = f"{CDM_SCHEMA}.location.location_id"
+
+# This object should be used to set the naming_convention parameter of
+# the SQLAlchemy MetaData object. Using it makes sure that the naming of
+# constraints and indexes is deterministic and not left up to the DBMS.
+# It's also needed when dropping these, as SQLAlchemy requires that
+# they have a name for them to be dropped. See:
+# https://docs.sqlalchemy.org/en/20/core/constraints.html#configuring-constraint-naming-conventions
+NAMING_CONVENTION = {
+    "ix": "ix_%(table_name)s_%(column_0_N_name)s",
+    "uq": "uq_%(table_name)s_%(column_0_name)s",
+    "ck": "ck_%(table_name)s_%(constraint_name)s",
+    "fk": "fk_%(table_name)s_%(column_0_name)s_%(referred_table_name)s",
+    "pk": "pk_%(table_name)s",
+}

src/omop_cdm/dynamic/cdm531/__init__.py

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+"""
+OMOP CDM Version 5.3.1.
+
+Generated from OMOP CDM release 5.3.1 using sqlacodegen 3.0.0rc5.
+DDL from https://github.com/OHDSI/CommonDataModel/tree/v5.3.1.
+
+
+
+Deviations from standard model
+
+Removed
+
+attribute_definition
+cohort_attribute
+
+
+Added
+
+stem_table
+source_to_concept_map_version
+
+
+Updated
+
+source_to_concept_map
+    source_code from VARCHAR(50) --> VARCHAR(1000)
+    If using a separate vocab schema, STCM is created in the CDM schema
+
+"""