diff --git a/docs/api/query.md b/docs/api/query.md new file mode 100644 index 0000000..e85bb48 --- /dev/null +++ b/docs/api/query.md @@ -0,0 +1,29 @@ +# Query Filtering + +`omop_alchemy.cdm.query` provides `ConceptFilter`, a shared, reusable way to +filter CDM `concept`-table queries by domain, vocabulary, concept ID, and +standard/active status, with an optional row-count limit. + +It exists so that packages consuming OMOP Alchemy (e.g. `omop-emb`, `omop-graph`) +don't each need to reimplement the same filtering logic against their own copy +of `Concept`'s column names — since this package owns the `Concept` model +directly, the filter can reference real columns rather than duck-typing against +an opaquely-imported table. + +```python +from sqlalchemy import select +from omop_alchemy.cdm.model.vocabulary import Concept +from omop_alchemy.cdm.query import ConceptFilter + +concept_filter = ConceptFilter( + domains=("Condition", "Drug"), + require_standard=True, +) +query = concept_filter.apply(select(Concept)) +``` + +All fields are optional and combinable. + +::: omop_alchemy.cdm.query.ConceptFilter + options: + heading_level: 3 diff --git a/mkdocs.yml b/mkdocs.yml index 1b71f81..ca89aba 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -81,6 +81,7 @@ nav: - CDM Base: api/base.md - Columns: api/columns.md - Relationships: api/relationships.md + - Query Filtering: api/query.md - Typing: api/typing.md - Object-Relational Mappings: diff --git a/omop_alchemy/cdm/model/vocabulary/__init__.py b/omop_alchemy/cdm/model/vocabulary/__init__.py index 909b945..f3a9227 100644 --- a/omop_alchemy/cdm/model/vocabulary/__init__.py +++ b/omop_alchemy/cdm/model/vocabulary/__init__.py @@ -1,6 +1,13 @@ from .concept_ancestor import Concept_Ancestor from .concept_class import Concept_Class -from .concept import Concept, ConceptContext, ConceptView +from .concept import ( + Concept, + ConceptContext, + ConceptView, + InvalidReasonFlag, + StandardConceptFlag, + normalised_flag_expr, +) from .concept_relationship import Concept_Relationship from .domain import Domain from .relationship import Relationship @@ -15,6 +22,9 @@ "Concept", "ConceptContext", "ConceptView", + "InvalidReasonFlag", + "StandardConceptFlag", + "normalised_flag_expr", "Concept_Relationship", "Domain", "Relationship", diff --git a/omop_alchemy/cdm/model/vocabulary/concept.py b/omop_alchemy/cdm/model/vocabulary/concept.py index 6a306e6..7567950 100644 --- a/omop_alchemy/cdm/model/vocabulary/concept.py +++ b/omop_alchemy/cdm/model/vocabulary/concept.py @@ -1,6 +1,7 @@ import sqlalchemy as sa import sqlalchemy.orm as so from sqlalchemy.ext.declarative import declared_attr +from enum import StrEnum, nonmember from typing import Optional, TYPE_CHECKING, List from datetime import date if TYPE_CHECKING: @@ -22,6 +23,43 @@ omop_table_options, ) + +class StandardConceptFlag(StrEnum): + """Allowed non-null values of ``concept.standard_concept`` (OMOP CDM v5.4).""" + + STANDARD = "S" + CLASSIFICATION = "C" + + # Precomputed membership set for the hot Python-side check (Concept.is_standard) -- + # re-deriving this from the enum on every call is measurably expensive (~10x). + values = nonmember(frozenset({STANDARD, CLASSIFICATION})) + + +class InvalidReasonFlag(StrEnum): + """Allowed non-null values of ``concept.invalid_reason`` (OMOP CDM v5.4).""" + + DELETED = "D" + UPDATED = "U" + + +def normalised_flag_expr( + column: sa.SQLColumnExpression[Optional[str]], +) -> sa.SQLColumnExpression[Optional[str]]: + """Return a canonical OMOP flag expression. + + OMOP CDM v5.4 allows only ``NULL``/``'S'``/``'C'`` for ``standard_concept`` + and ``NULL``/``'D'``/``'U'`` for ``invalid_reason``. Some real-world loads + contain blank or whitespace-only strings instead of ``NULL``; those are + normalised here defensively so callers do not need to reimplement the same + tolerance logic. + + Non-empty non-canonical values are left unchanged so downstream validation + can still detect them as bad data rather than silently treating them as a + valid state. + """ + return sa.func.nullif(sa.func.trim(column), "") + + @cdm_table class Concept( ReferenceTable, @@ -54,6 +92,26 @@ class Concept( valid_end_date: so.Mapped[date] = so.mapped_column(sa.Date(), nullable=False) invalid_reason: so.Mapped[Optional[str]] = so.mapped_column(sa.String(1), nullable=True) + @property + def is_standard(self) -> bool: + value = self.standard_concept.strip() if self.standard_concept is not None else "" + return bool(value) and value in StandardConceptFlag.values + + @classmethod + def is_standard_expr(cls) -> sa.SQLColumnExpression[bool]: + """SQL-side counterpart to :attr:`is_standard`, for use in query filters.""" + return normalised_flag_expr(cls.standard_concept).in_(StandardConceptFlag.values) + + @property + def is_valid(self) -> bool: + value = self.invalid_reason.strip() if self.invalid_reason is not None else "" + return not value + + @classmethod + def is_valid_expr(cls) -> sa.SQLColumnExpression[bool]: + """SQL-side counterpart to :attr:`is_valid`, for use in query filters.""" + return normalised_flag_expr(cls.invalid_reason).is_(None) + class ConceptContext(ReferenceContext): """ Navigational relationships for Concept. @@ -119,12 +177,3 @@ class ConceptView(Concept, ConceptContext): """ __tablename__ = "concept" __mapper_args__ = {"concrete": False} - - - @property - def is_standard(self) -> bool: - return self.standard_concept == "S" - - @property - def is_valid(self) -> bool: - return self.invalid_reason is None diff --git a/omop_alchemy/cdm/query.py b/omop_alchemy/cdm/query.py new file mode 100644 index 0000000..7409306 --- /dev/null +++ b/omop_alchemy/cdm/query.py @@ -0,0 +1,87 @@ +"""Shared CDM concept-table query filtering. + +Consolidates filtering logic previously duplicated across downstream packages +""" + +from __future__ import annotations + +from dataclasses import dataclass +from typing import Optional + +import sqlalchemy as sa + +from omop_alchemy.cdm.model.vocabulary import Concept + + +@dataclass(frozen=True) +class ConceptFilter: + """Search constraints for plain CDM ``concept``-table queries. + + All fields are optional. Unset fields impose no constraint. + + Attributes + ---------- + concept_ids : tuple[int, ...], optional + Restrict results to this set of concept IDs. + domains : tuple[str, ...], optional + Restrict results to concepts in these OMOP domains. + vocabularies : tuple[str, ...], optional + Restrict results to concepts from these vocabularies. + require_standard : bool + When ``True``, only concepts where ``Concept.is_standard`` is + ``True`` are returned (``standard_concept`` in ``('S', 'C')``, + tolerating blank/whitespace-only values as unset). Default ``False``. + require_active : bool + When ``True``, only concepts where ``Concept.is_valid`` is ``True`` + are returned (``invalid_reason`` is ``NULL``/blank/whitespace, i.e. + not ``'D'`` or ``'U'``). Default ``False``. + limit : int, optional + Maximum number of rows to return. If not set, all matching rows are + returned. + """ + + concept_ids: Optional[tuple[int, ...]] = None + domains: Optional[tuple[str, ...]] = None + vocabularies: Optional[tuple[str, ...]] = None + require_standard: bool = False + require_active: bool = False + limit: Optional[int] = None + + def __post_init__(self) -> None: + if self.limit is not None and self.limit <= 0: + raise ValueError( + f"ConceptFilter.limit must be a positive integer, got {self.limit}." + ) + + def apply(self, query: sa.Select) -> sa.Select: + """Apply filter constraints to a Select already targeting Concept.""" + if self.concept_ids is not None: + query = query.where(Concept.concept_id.in_(self.concept_ids)) + + if self.domains is not None: + query = query.where(Concept.domain_id.in_(self.domains)) + + if self.vocabularies is not None: + query = query.where(Concept.vocabulary_id.in_(self.vocabularies)) + + if self.require_standard: + query = query.where(Concept.is_standard_expr()) + + if self.require_active: + query = query.where(Concept.is_valid_expr()) + + if self.limit is not None: + query = query.limit(self.limit) + + return query + + def is_empty(self) -> bool: + """Return ``True`` if no constraints are set.""" + return ( + self.concept_ids is None + and self.domains is None + and self.vocabularies is None + and not self.require_standard + and not self.require_active + and self.limit is None + ) diff --git a/pyproject.toml b/pyproject.toml index 25f2ed3..d0a9734 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -50,7 +50,7 @@ dev = [ "requests>=2.33.0", "pytest>=9.0.3", "pytest-cov>=4.0", - "ty>=0.0.59", + "ty==0.0.61", "ruff>=0.4", "mkdocs-material>=9.7.1", "mkdocstrings-python>=2.0.1", diff --git a/tests/test_concept_filter.py b/tests/test_concept_filter.py new file mode 100644 index 0000000..d62f07d --- /dev/null +++ b/tests/test_concept_filter.py @@ -0,0 +1,198 @@ +"""Tests for ConceptFilter.apply(), the shared CDM concept-table WHERE/LIMIT builder.""" + +import pytest +import sqlalchemy as sa + +from omop_alchemy.cdm.model.vocabulary import ( + Concept, + ConceptView, + InvalidReasonFlag, + StandardConceptFlag, + normalised_flag_expr, +) +from omop_alchemy.cdm.query import ConceptFilter + + +class TestConceptFilterApply: + def test_empty_filter_adds_no_clauses(self): + query = sa.select(Concept.concept_id) + result = ConceptFilter().apply(query) + + assert str(result) == str(query) + + def test_concept_ids_adds_in_clause(self): + query = sa.select(Concept.concept_id) + result = ConceptFilter(concept_ids=(1, 2, 3)).apply(query) + + compiled = str(result) + assert "WHERE" in compiled + assert "concept_id IN" in compiled + + def test_domains_adds_in_clause(self): + query = sa.select(Concept.concept_id) + result = ConceptFilter(domains=("Condition", "Drug")).apply(query) + + assert "domain_id IN" in str(result) + + def test_vocabularies_adds_in_clause(self): + query = sa.select(Concept.concept_id) + result = ConceptFilter(vocabularies=("SNOMED",)).apply(query) + + assert "vocabulary_id IN" in str(result) + + def test_require_standard_adds_clause(self): + query = sa.select(Concept.concept_id) + result = ConceptFilter(require_standard=True).apply(query) + + compiled = str(result).lower() + assert "nullif" in compiled + assert "trim" in compiled + assert " in " in compiled + + def test_require_active_adds_clause(self): + query = sa.select(Concept.concept_id) + result = ConceptFilter(require_active=True).apply(query) + + compiled = str(result).lower() + assert "nullif" in compiled + assert "trim" in compiled + assert "is null" in compiled + + def test_require_active_does_not_exclude_null_invalid_reason(self, session): + """Regression test: NULL invalid_reason (the normal, active case) must + not be dropped by a SQL NOT IN three-valued-logic bug.""" + query = sa.select(Concept.concept_id) + result = ConceptFilter(require_active=True).apply(query) + + returned_ids = set(session.scalars(result).all()) + all_ids = set(session.scalars(sa.select(Concept.concept_id)).all()) + assert returned_ids == all_ids + assert returned_ids # sanity: fixtures aren't empty + + def test_require_standard_executes_and_matches_fixtures(self, session): + """Regression test: prove require_standard actually executes and + matches real 'S' rows, not just that the compiled clause looks right.""" + query = sa.select(Concept.concept_id) + result = ConceptFilter(require_standard=True).apply(query) + + returned_ids = set(session.scalars(result).all()) + all_ids = set(session.scalars(sa.select(Concept.concept_id)).all()) + assert returned_ids == all_ids + assert returned_ids # sanity: fixtures aren't empty + + def test_require_standard_compiles_with_literal_binds(self): + """Regression test: StrEnum members passed to .in_() must render as + plain string literals, not enum reprs, so query.compile(literal_binds= + True) (used for debug logging) doesn't raise a CompileError.""" + query = sa.select(Concept.concept_id) + result = ConceptFilter(require_standard=True).apply(query) + + compiled = str(result.compile(compile_kwargs={"literal_binds": True})) + assert "'S'" in compiled + assert "'C'" in compiled + + def test_limit_is_applied(self): + query = sa.select(Concept.concept_id) + result = ConceptFilter(limit=5).apply(query) + + assert "LIMIT" in str(result) + + def test_negative_limit_raises(self): + with pytest.raises(ValueError, match="positive integer"): + ConceptFilter(limit=0) + + def test_is_empty(self): + assert ConceptFilter().is_empty() + assert not ConceptFilter(limit=5).is_empty() + assert not ConceptFilter(domains=("Drug",)).is_empty() + assert not ConceptFilter(require_standard=True).is_empty() + assert not ConceptFilter(require_active=True).is_empty() + + +class TestNormalisedFlagExpr: + """normalised_flag_expr must trim whitespace and turn blank strings into + NULL, while leaving NULL and non-blank values (canonical or not) alone.""" + + @pytest.mark.parametrize( + "raw, expected", + [ + (None, None), + ("", None), + (" ", None), + ("S", "S"), + (" S ", "S"), + ("X", "X"), # non-canonical, non-blank values pass through unchanged + ], + ) + def test_normalises_value(self, session, raw, expected): + result = session.scalar( + sa.select(normalised_flag_expr(sa.literal(raw, type_=sa.String))) + ) + assert result == expected + + +class TestConceptViewFlags: + """ConceptView.is_standard/is_valid must agree with StandardConceptFlag / + the OMOP definition of "standard" (S or C), not just a single literal.""" + + @pytest.mark.parametrize( + "standard_concept, expected", + [ + (StandardConceptFlag.STANDARD, True), + (StandardConceptFlag.CLASSIFICATION, True), + (f" {StandardConceptFlag.STANDARD} ", True), + (None, False), + ("", False), + (" ", False), + ], + ) + def test_is_standard(self, standard_concept, expected): + cv = ConceptView(standard_concept=standard_concept) + assert cv.is_standard is expected + + @pytest.mark.parametrize( + "invalid_reason, expected", + [ + (None, True), + ("", True), + (" ", True), + (InvalidReasonFlag.DELETED, False), + (InvalidReasonFlag.UPDATED, False), + ], + ) + def test_is_valid(self, invalid_reason, expected): + cv = ConceptView(invalid_reason=invalid_reason) + assert cv.is_valid is expected + + @pytest.mark.parametrize( + "invalid_reason", [None, "", " ", "D", "U", "X", " X "] + ) + def test_is_valid_agrees_with_require_active_filter(self, session, invalid_reason): + """PR feedback regression test: a 'dirty' row must not be judged + active by ConceptFilter(require_active=True) but invalid by + ConceptView.is_valid, or vice versa.""" + included_by_filter = session.scalar( + sa.select(normalised_flag_expr(sa.literal(invalid_reason, type_=sa.String)).is_(None)) + ) + cv = ConceptView(invalid_reason=invalid_reason) + assert cv.is_valid == included_by_filter + + @pytest.mark.parametrize( + "standard_concept", [None, "", " ", "S", " S ", "C", " C ", "X", " X "] + ) + def test_is_standard_agrees_with_require_standard_filter(self, session, standard_concept): + """Same consistency check as above, for is_standard/require_standard.""" + # bool(...): a bare SELECT surfaces SQL's three-valued IN() as NULL + # rather than False, but a WHERE clause treats NULL the same as + # False (row excluded) - so this coercion mirrors WHERE semantics. + included_by_filter = bool( + session.scalar( + sa.select( + normalised_flag_expr(sa.literal(standard_concept, type_=sa.String)).in_( + [flag.value for flag in StandardConceptFlag] + ) + ) + ) + ) + cv = ConceptView(standard_concept=standard_concept) + assert cv.is_standard == included_by_filter diff --git a/uv.lock b/uv.lock index 49ef5a0..69eb986 100644 --- a/uv.lock +++ b/uv.lock @@ -13,15 +13,6 @@ resolution-markers = [ "python_full_version < '3.14' and sys_platform != 'emscripten' and sys_platform != 'win32'", ] -[[package]] -name = "alabaster" -version = "1.0.0" -source = { registry = "https://pypi.org/simple" } -sdist 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