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 downstream packages do not 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 whose FROM clause includes Concept.

is_empty ¶

is_empty() -> bool

Return True if no constraints are set.