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.

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.

Search constraints for plain CDM concept-table queries.

All fields are optional. Unset fields impose no constraint.

Attributes:

Name	Type	Description
`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 == 'S'`, tolerating surrounding whitespace). Classification concepts (`'C'`) are excluded because they are not valid mapping targets. Default `False`.
`include_classification`	`bool`	Only meaningful with `require_standard`. When `True`, classification concepts (`'C'`) are admitted alongside standard ones. 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.

apply ¶

apply(query: Select) -> sa.Select

Apply filter constraints to a Select already targeting Concept.

is_empty ¶

is_empty() -> bool

Return True if no constraints are set.