omop-alchemy 0.5.1__tar.gz

omop_alchemy-0.5.1/LICENSE

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omop_alchemy-0.5.1/PKG-INFO

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+Metadata-Version: 2.4
+Name: omop-alchemy
+Version: 0.5.1
+Summary: SQLAlchemy-based models, validation, and utilities for the OHDSI OMOP Common Data Model
+Author-email: Georgie Kennedy <georgie.kennedy@unsw.edu.au>
+License: Apache-2.0
+Project-URL: Homepage, https://github.com/AustralianCancerDataNetwork/OMOP_Alchemy
+Project-URL: Repository, https://github.com/AustralianCancerDataNetwork/OMOP_Alchemy
+Project-URL: Issues, https://github.com/AustralianCancerDataNetwork/OMOP_Alchemy/issues
+Keywords: OMOP,OHDSI,clinical-data,health-informatics,sqlalchemy,ETL,real-world-evidence
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: sqlalchemy>=2.0.45
+Requires-Dist: pandas>=2.0
+Requires-Dist: pyyaml>=6.0
+Requires-Dist: python-dotenv>=1.0
+Requires-Dist: orm-loader>=0.1.1
+Provides-Extra: dev
+Requires-Dist: ipython>=8.0; extra == "dev"
+Requires-Dist: pytest>=7.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.0; extra == "dev"
+Requires-Dist: mypy>=1.8; extra == "dev"
+Requires-Dist: ruff>=0.4; extra == "dev"
+Requires-Dist: rich>=13.0; extra == "dev"
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: myst-parser; extra == "docs"
+Dynamic: license-file
+
+# OMOP Alchemy
+
+**OMOP Alchemy** provides a canonical, typed, SQLAlchemy-first representation of the
+[OHDSI OMOP Common Data Model (CDM)](https://ohdsi.github.io/CommonDataModel/).
+
+It is designed to support **research-ready analytics, validation, and exploration**
+of OMOP data using modern Python tooling, without imposing ETL conventions or
+execution-time side effects.
+
+---
+
+## Design goals
+
+OMOP Alchemy is intentionally:
+
+- **Declarative**  
+  Defines tables, columns, relationships, and constraints 
+
+- **SQLAlchemy-native**  
+  Built for SQLAlchemy 2.x ORM usage
+
+- **Safe to import anywhere**  
+  No implicit engine creation, no global state, no environment assumptions.
+
+- **Typed and inspectable**  
+  Models are fully typed and introspectable for validation, tooling, and IDE support.
+
+- **Backend-agnostic**  
+  Designed to work across PostgreSQL, SQLite, and other SQLAlchemy-supported databases.
+
+---
+
+## What this package does *not* do
+
+OMOP Alchemy deliberately avoids:
+
+- Enforcing ETL conventions or data pipelines
+- Auto-creating databases or loading vocabularies
+- Imposing analytics frameworks or dashboards
+- Making assumptions about deployment environments
+
+These concerns are intentionally left to downstream tooling.
+
+---
+
+## Core features
+
+- SQLAlchemy ORM models for OMOP CDM tables
+- Explicit foreign key and relationship definitions
+- Read-only *View* classes for safe navigation and analytics
+- Domain validation helpers for OMOP concept integrity
+- CSV loading utilities for controlled ingestion and testing
+- Lightweight schema and model validation against CDM specs
+
+---
+
+## Example (concept navigation)
+
+```python
+from omop_alchemy.model.vocabulary import ConceptView
+
+concept = session.get(ConceptView, 320128)  # Lung cancer
+concept.domain.domain_id        # "Condition"
+concept.vocabulary.vocabulary_id  # "SNOMED"
+concept.is_standard             # True
+```
+
+---
+
+## Status
+
+This project is currently beta.
+
+The API is stabilising, but some modules may change as real-world use cases expand. Feedback and issues are welcome.
+
+### Some additional background
+
+This work builds on earlier research and tooling presented at the 2023 OHDSI APAC Symposium
+> see [background paper](https://github.com/AustralianCancerDataNetwork/OMOP_Alchemy/blob/main/notebooks/ORMforResearchReadyData_APAC2023.pdf).

omop_alchemy-0.5.1/README.md

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+# OMOP Alchemy
+
+**OMOP Alchemy** provides a canonical, typed, SQLAlchemy-first representation of the
+[OHDSI OMOP Common Data Model (CDM)](https://ohdsi.github.io/CommonDataModel/).
+
+It is designed to support **research-ready analytics, validation, and exploration**
+of OMOP data using modern Python tooling, without imposing ETL conventions or
+execution-time side effects.
+
+---
+
+## Design goals
+
+OMOP Alchemy is intentionally:
+
+- **Declarative**  
+  Defines tables, columns, relationships, and constraints 
+
+- **SQLAlchemy-native**  
+  Built for SQLAlchemy 2.x ORM usage
+
+- **Safe to import anywhere**  
+  No implicit engine creation, no global state, no environment assumptions.
+
+- **Typed and inspectable**  
+  Models are fully typed and introspectable for validation, tooling, and IDE support.
+
+- **Backend-agnostic**  
+  Designed to work across PostgreSQL, SQLite, and other SQLAlchemy-supported databases.
+
+---
+
+## What this package does *not* do
+
+OMOP Alchemy deliberately avoids:
+
+- Enforcing ETL conventions or data pipelines
+- Auto-creating databases or loading vocabularies
+- Imposing analytics frameworks or dashboards
+- Making assumptions about deployment environments
+
+These concerns are intentionally left to downstream tooling.
+
+---
+
+## Core features
+
+- SQLAlchemy ORM models for OMOP CDM tables
+- Explicit foreign key and relationship definitions
+- Read-only *View* classes for safe navigation and analytics
+- Domain validation helpers for OMOP concept integrity
+- CSV loading utilities for controlled ingestion and testing
+- Lightweight schema and model validation against CDM specs
+
+---
+
+## Example (concept navigation)
+
+```python
+from omop_alchemy.model.vocabulary import ConceptView
+
+concept = session.get(ConceptView, 320128)  # Lung cancer
+concept.domain.domain_id        # "Condition"
+concept.vocabulary.vocabulary_id  # "SNOMED"
+concept.is_standard             # True
+```
+
+---
+
+## Status
+
+This project is currently beta.
+
+The API is stabilising, but some modules may change as real-world use cases expand. Feedback and issues are welcome.
+
+### Some additional background
+
+This work builds on earlier research and tooling presented at the 2023 OHDSI APAC Symposium
+> see [background paper](https://github.com/AustralianCancerDataNetwork/OMOP_Alchemy/blob/main/notebooks/ORMforResearchReadyData_APAC2023.pdf).

omop_alchemy-0.5.1/omop_alchemy/__init__.py

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+from .config import load_environment, get_engine_name, TEST_PATH, ROOT_PATH
+from .errors import CDMValidationError
+
+# from .cdm.base import Base, create_db
+# from .cdm.utils import get_logger, configure_logging
+# from .cdm.model.vocabulary import Concept
+
+__all__ = [
+ #   "Base",
+ #   "Concept",
+ #   "create_db",
+ #   "get_logger",
+ #   "configure_logging",
+    "load_environment",
+    "get_engine_name",
+    "TEST_PATH",
+    "ROOT_PATH",
+]
+
+#logger = get_logger(__name__)

omop_alchemy-0.5.1/omop_alchemy/cdm/base/__init__.py

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+from .domain_checking import ExpectedDomain
+from .cdm_table_base import CDMTableBase
+from .decorators import cdm_table
+from .column_helpers import required_concept_fk, optional_concept_fk, optional_int, required_int
+from .column_mixins import ValueMixin, ReferenceTable, DatedEvent, PersonScoped, HealthSystemContext, FactTable
+from .domain_checking import DomainValidationMixin
+from .reference_context import ReferenceContext
+from .typing import HasConceptId, HasEpisodeId, HasPersonId, DomainSemanticTable, ClinicalEvent
+from .modifier_interface import ModifierTargetMixin
+from .cdm_constants import ModifierFieldConcepts
+__all__ = [
+    "ExpectedDomain",
+    "CDMTableBase",
+    "cdm_table",
+    "required_concept_fk",
+    "optional_concept_fk",
+    "optional_int",
+    "required_int",
+    "ValueMixin",
+    "ReferenceTable",
+    "ReferenceContext",
+    "HasConceptId",
+    "HasEpisodeId",
+    "HasPersonId",
+    "DomainSemanticTable",
+    "ClinicalEvent",
+    "DatedEvent",
+    "PersonScoped",
+    "HealthSystemContext",
+    "DomainValidationMixin",
+    "FactTable",
+    "ModifierTargetMixin",
+    "ModifierFieldConcepts",
+]

omop_alchemy-0.5.1/omop_alchemy/cdm/base/cdm_constants.py

@@ -0,0 +1,5 @@
+class ModifierFieldConcepts:
+    CONDITION_OCCURRENCE = 1147127
+    PROCEDURE_OCCURRENCE = 1147082
+    DRUG_EXPOSURE = 1147707
+    EPISODE = 756290

omop_alchemy-0.5.1/omop_alchemy/cdm/base/cdm_table_base.py

@@ -0,0 +1,14 @@
+from orm_loader.tables import CSVLoadableTableInterface, SerialisableTableInterface
+
+
+class CDMTableBase(CSVLoadableTableInterface, SerialisableTableInterface):  
+    """
+    Base class for CDM tables that support CSV loading and validation.
+    """
+    __abstract__ = True
+
+    """
+    Adds structural validation of ORM models against
+    the official OMOP CDM CSV specifications.
+    """
+    __cdm_extra_checks__: list[str] = []

omop_alchemy-0.5.1/omop_alchemy/cdm/base/column_helpers.py

@@ -0,0 +1,42 @@
+import sqlalchemy as sa
+import sqlalchemy.orm as so
+from typing import Optional
+
+def required_concept_fk(*, index: bool = True):
+    """
+    OMOP-required concept foreign key.
+
+    Semantics:
+    - Must exist
+    - Unknown allowed (concept_id = 0)
+    - Matches CDM Field-Level spec
+    """
+    return so.mapped_column(
+        sa.ForeignKey("concept.concept_id"),
+        nullable=False,
+        default=0,
+        index=index,
+    )
+
+def optional_concept_fk(*, index: bool = False):
+    """
+    Optional concept foreign key.
+    """
+    return so.mapped_column(
+        sa.ForeignKey("concept.concept_id"),
+        nullable=True,
+        index=index,
+    )
+
+def optional_fk(target: str, *, index: bool = False):
+    return so.mapped_column(
+        sa.ForeignKey(target),
+        nullable=True,
+        index=index,
+    )
+
+def required_int():
+    return so.mapped_column(sa.Integer, nullable=False)
+
+def optional_int():
+    return so.mapped_column(sa.Integer, nullable=True)

omop_alchemy-0.5.1/omop_alchemy/cdm/base/column_mixins.py

@@ -0,0 +1,107 @@
+from __future__ import annotations
+
+from datetime import date, datetime
+from typing import Optional, List, TYPE_CHECKING, Type, Any
+from dataclasses import dataclass
+import sqlalchemy as sa
+import sqlalchemy.orm as so
+from orm_loader.helpers import get_model_by_tablename
+
+
+"""
+OMOP CDM structural mixins.
+
+These mixins encode *structural semantics* of the OMOP Common Data Model
+as defined in the Table-Level and Field-Level CSV specifications.
+
+They intentionally do NOT encode clinical or analytical meaning.
+"""
+
+class PersonScoped:
+    """
+    Mixin for tables scoped to a person.
+    """
+    person_id: so.Mapped[int] = so.mapped_column(sa.ForeignKey("person.person_id"), nullable=False, index=True)
+
+class ConceptTyped:
+    """
+    Mixin for tables whose primary meaning is encoded by a concept_id.
+    Subclasses MUST define <something>_concept_id.
+
+    Not currently used TBC if there is a use-case to retain that supports EAV queries?
+    """
+
+    @so.declared_attr
+    def concept_id(cls: Any) -> so.Mapped[int]:
+        raise NotImplementedError(
+            f"{cls.__name__} must define its own <x>_concept_id column"
+        )
+
+class ValueMixin:
+    value_as_number: so.Mapped[Optional[float]] = so.mapped_column(sa.Float, nullable=True)
+    value_as_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.ForeignKey("concept.concept_id"), nullable=True)
+
+    __table_args__ = (
+        sa.CheckConstraint(
+            "value_as_number IS NOT NULL OR value_as_concept_id IS NOT NULL",
+            name="ck_value_present",
+        ),
+    )
+
+    @so.validates("value_as_number", "value_as_concept_id")
+    def _validate_value(self, key, value):
+        other = (
+            self.value_as_concept_id
+            if key == "value_as_number"
+            else self.value_as_number
+        )
+
+        if value is None and other is None:
+            raise ValueError(
+                "At least one of value_as_number or value_as_concept_id must be set"
+            )
+        return value
+
+class DatedEvent:
+    """
+    Mixin for tables with start/end date and datetime pairs.
+    """
+    start_date: so.Mapped[date] = so.mapped_column(nullable=False)
+    start_datetime: so.Mapped[Optional[datetime]] = so.mapped_column(nullable=True)
+
+    end_date: so.Mapped[Optional[date]] = so.mapped_column(nullable=True)
+    end_datetime: so.Mapped[Optional[datetime]] = so.mapped_column(nullable=True)
+
+
+class HealthSystemContext:
+    """
+    Mixin for tables attributed to a provider.
+    """
+    provider_id: so.Mapped[Optional[int]] = so.mapped_column(sa.ForeignKey("provider.provider_id"),index=True,nullable=True)
+    visit_occurrence_id: so.Mapped[Optional[int]] = so.mapped_column(sa.ForeignKey("visit_occurrence.visit_occurrence_id"),index=True,nullable=True)
+    visit_detail_id: so.Mapped[Optional[int]] = so.mapped_column(sa.ForeignKey("visit_detail.visit_detail_id"),index=True,nullable=True)
+
+class FactTable:
+    """
+    Marker mixin for OMOP fact tables.
+
+    Used for introspection, tooling, and documentation only.
+    """
+    pass
+
+class ReferenceTable:
+    """Marker mixin for OMOP reference tables."""
+    pass
+
+class SourceAttribution:
+    """
+    Mixin for *_source_value and *_source_concept_id patterns.
+    """
+    source_value: so.Mapped[Optional[str]] = so.mapped_column(sa.String, nullable=True)
+    source_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.ForeignKey("concept.concept_id"), nullable=True)     
+
+class UnitConcept:
+    """
+    Mixin for unit_concept_id.
+    """
+    unit_concept_id: so.Mapped[Optional[int]] = so.mapped_column(sa.ForeignKey("concept.concept_id"), index=True, nullable=True)

omop_alchemy-0.5.1/omop_alchemy/cdm/base/decorators.py

@@ -0,0 +1,31 @@
+from typing import Type, TypeVar
+from .cdm_table_base import CDMTableBase
+
+T = TypeVar("T", bound=type)
+
+def cdm_table(cls: T) -> T:
+    """
+    Mark a SQLAlchemy declarative class as a concrete OMOP CDM table.
+
+    - Forces __abstract__ = False
+    - Ensures __tablename__ is defined
+    - Inherits from CDMTableBase
+    - Used to clearly distinguish real CDM tables from mixins
+    """
+
+    # Safety: require an explicit tablename
+    if not hasattr(cls, "__tablename__"):
+        raise TypeError(
+            f"@cdm_table applied to {cls.__name__} "
+            "but __tablename__ is not defined"
+        )
+
+    if not issubclass(cls, CDMTableBase):
+        raise TypeError(
+            f"{cls.__name__} must inherit from CDMTableBase "
+        )
+
+    # Explicitly mark as concrete
+    cls.__abstract__ = False
+
+    return cls