Features/ibis custom eras

circe/__init__.py

@@ -19,7 +19,7 @@
 License: Apache License 2.0
 """
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"
 __author__ = "CIRCE Python Implementation Team"
 __email__ = "circe-python@ohdsi.org"
 __license__ = "Apache License 2.0"

circe/execution/engine/custom_era.py

@@ -0,0 +1,171 @@
+from __future__ import annotations
+
+import ibis
+
+from ..plan.schema import PERSON_ID, START_DATE
+from .end_strategy import _replace_end_date, attach_observation_bounds
+
+
+def _compute_exposure_end_date(table, *, days_supply_override: int | None):
+    start = table["drug_exposure_start_date"].cast("date")
+
+    if days_supply_override is not None:
+        return start + ibis.interval(days=days_supply_override)
+
+    raw_end = (
+        table["drug_exposure_end_date"].cast("date")
+        if "drug_exposure_end_date" in table.columns
+        else ibis.null().cast("date")
+    )
+    days_supply = (
+        table["days_supply"].cast("int64") if "days_supply" in table.columns else ibis.null().cast("int64")
+    )
+    supply_end = start + days_supply.as_interval("D")
+
+    return ibis.coalesce(raw_end, supply_end, start + ibis.interval(days=1))
+
+
+def _compute_eras(exposures, *, gap_days: int, offset: int):
+    padded = exposures.mutate(
+        _padded_end=(exposures._exposure_end + ibis.interval(days=int(gap_days + offset)))
+    )
+
+    ordering = [
+        padded.start_date,
+        padded._padded_end.desc(),
+        padded._exposure_end.desc(),
+    ]
+
+    cumulative_window = ibis.cumulative_window(group_by=padded.person_id, order_by=ordering)
+    ordered_window = ibis.window(group_by=padded.person_id, order_by=ordering)
+
+    with_cummax = padded.mutate(_cummax_padded_end=padded._padded_end.max().over(cumulative_window))
+
+    with_prev = with_cummax.mutate(_prev_max=with_cummax._cummax_padded_end.lag().over(ordered_window))
+
+    marked = with_prev.mutate(
+        _is_new=ibis.ifelse(
+            with_prev._prev_max.isnull() | (with_prev._prev_max < with_prev.start_date),
+            ibis.literal(1, type="int64"),
+            ibis.literal(0, type="int64"),
+        )
+    )
+
+    group_window = ibis.cumulative_window(
+        group_by=marked.person_id,
+        order_by=[
+            marked.start_date,
+            marked._padded_end.desc(),
+            marked._exposure_end.desc(),
+            marked._is_new.desc(),
+        ],
+    )
+    era_indexed = marked.mutate(_era_id=marked._is_new.sum().over(group_window))
+
+    collapsed = era_indexed.group_by(era_indexed.person_id, era_indexed._era_id).aggregate(
+        era_start_date=era_indexed.start_date.min(),
+        _max_exposure_end=era_indexed._exposure_end.max(),
+    )
+
+    return collapsed.select(
+        collapsed.person_id.cast("int64").name(PERSON_ID),
+        collapsed.era_start_date.cast("date").name("era_start_date"),
+        (collapsed._max_exposure_end + ibis.interval(days=int(offset))).cast("date").name("era_end_date"),
+    )
+
+
+def compute_drug_eras(
+    ctx,
+    *,
+    drug_codeset_id: int,
+    gap_days: int,
+    offset: int,
+    days_supply_override: int | None,
+    cohort_person_ids=None,
+):
+    concept_ids = ctx.concept_ids_for_codeset(drug_codeset_id)
+
+    if not concept_ids:
+        de = ctx.table("drug_exposure")
+        return de.filter(ibis.literal(False)).select(
+            de.person_id.cast("int64").name(PERSON_ID),
+            ibis.null().cast("date").name("era_start_date"),
+            ibis.null().cast("date").name("era_end_date"),
+        )
+
+    de = ctx.table("drug_exposure")
+    if cohort_person_ids is not None:
+        de = de.semi_join(
+            cohort_person_ids,
+            predicates=[de.person_id == cohort_person_ids.person_id],
+        )
+
+    if "drug_source_concept_id" in de.columns:
+        filtered = de.filter(
+            de.drug_concept_id.isin(concept_ids) | de.drug_source_concept_id.isin(concept_ids)
+        )
+    else:
+        filtered = de.filter(de.drug_concept_id.isin(concept_ids))
+
+    prepared = filtered.select(
+        filtered.person_id.cast("int64").name("person_id"),
+        filtered.drug_exposure_start_date.cast("date").name("start_date"),
+        _compute_exposure_end_date(filtered, days_supply_override=days_supply_override).name("_exposure_end"),
+    )
+
+    return _compute_eras(prepared, gap_days=gap_days, offset=offset)
+
+
+def apply_custom_era_strategy(events, strategy, ctx):
+    payload = strategy.payload
+    drug_codeset_id = payload["drug_codeset_id"]
+    gap_days = payload["gap_days"]
+    offset = payload["offset"]
+    days_supply_override = payload.get("days_supply_override")
+
+    if drug_codeset_id is None:
+        with_bounds = attach_observation_bounds(events, ctx)
+        return _replace_end_date(events, with_bounds, with_bounds.op_end_date)
+
+    cohort_person_ids = events.select(events.person_id).distinct()
+
+    eras = compute_drug_eras(
+        ctx,
+        drug_codeset_id=drug_codeset_id,
+        gap_days=gap_days,
+        offset=offset,
+        days_supply_override=days_supply_override,
+        cohort_person_ids=cohort_person_ids,
+    )
+
+    eras_for_join = eras.select(
+        eras.person_id.name("_era_person_id"),
+        eras.era_start_date,
+        eras.era_end_date,
+    )
+
+    with_bounds = attach_observation_bounds(events, ctx)
+
+    joined = with_bounds.left_join(
+        eras_for_join,
+        predicates=[
+            with_bounds.person_id == eras_for_join._era_person_id,
+            with_bounds[START_DATE] >= eras_for_join.era_start_date,
+            with_bounds[START_DATE] <= eras_for_join.era_end_date,
+        ],
+    )
+
+    event_window = ibis.window(
+        group_by=[joined.person_id, joined.event_id],
+        order_by=[joined.era_end_date.asc()],
+    )
+    ranked = joined.mutate(_rn=ibis.row_number().over(event_window))
+    one_per_event = ranked.filter(ranked._rn == 0)
+
+    effective_end = ibis.coalesce(
+        one_per_event.era_end_date,
+        one_per_event.op_end_date,
+    )
+    final_end = ibis.least(effective_end, one_per_event.op_end_date)
+
+    return _replace_end_date(events, one_per_event, final_end)

circe/execution/engine/end_strategy.py

@@ -64,7 +64,9 @@ def apply_end_strategy(events, strategy, ctx):
         return _replace_end_date(events, with_bounds, end_date_expr)
 
     if strategy.kind == "custom_era":
-        raise UnsupportedFeatureError("Ibis executor end-strategy error: custom_era is not supported.")
+        from .custom_era import apply_custom_era_strategy
+
+        return apply_custom_era_strategy(events, strategy, ctx)
 
     # Fallback: preserve default semantics of op_end_date clipping.
     return _replace_end_date(events, with_bounds, with_bounds.op_end_date)

circe/execution/normalize/cohort.py

@@ -3,7 +3,7 @@
 from ...cohortdefinition import CohortExpression
 from ...vocabulary.concept import ConceptSet
 from .._dataclass import frozen_slots_dataclass
-from ..errors import ExecutionNormalizationError, UnsupportedFeatureError
+from ..errors import ExecutionNormalizationError
 from .collapse import NormalizedCollapseSettings, normalize_collapse_settings
 from .criteria import NormalizedCriterion, normalize_criterion
 from .end_strategy import NormalizedEndStrategy, normalize_end_strategy
@@ -149,10 +149,6 @@ def normalize_cohort(
     )
 
     normalized_end_strategy = normalize_end_strategy(expression.end_strategy)
-    if normalized_end_strategy is not None and normalized_end_strategy.kind == "custom_era":
-        raise UnsupportedFeatureError(
-            "Ibis executor normalization error: custom_era end strategy is not supported."
-        )
 
     return NormalizedCohort(
         title=expression.title,

circe/execution/normalize/end_strategy.py

@@ -32,6 +32,7 @@ def normalize_end_strategy(
                 "drug_codeset_id": value.drug_codeset_id,
                 "offset": int(value.offset),
                 "gap_days": int(value.gap_days),
+                "days_supply_override": value.days_supply_override,
             },
         )
     return NormalizedEndStrategy(kind="end_strategy", payload={})

docs/conf.py

@@ -13,8 +13,8 @@
 project = "OHDSI CIRCE Python"
 copyright = "2024, OHDSI Community"
 author = "CIRCE Python Implementation Team"
-release = "0.2.0"
-version = "0.2.0"
+release = "0.3.0"
+version = "0.3.0"
 
 # -- General configuration ---------------------------------------------------
 extensions = [

tests/execution/test_api_ibis.py

@@ -26,8 +26,7 @@
     VisitDetail,
     VisitOccurrence,
 )
-from circe.cohortdefinition.core import CustomEraStrategy, NumericRange
-from circe.execution.errors import UnsupportedFeatureError
+from circe.cohortdefinition.core import NumericRange
 from circe.vocabulary import Concept, ConceptSet, ConceptSetExpression, ConceptSetItem
 
 
@@ -1213,10 +1212,12 @@ def test_build_cohort_location_region_keeps_repeated_location_history_rows():
     assert sorted(result.start_date.astype(str).tolist()) == ["2020-01-01", "2020-02-01"]
 
 
-def test_build_cohort_rejects_unsupported_features():
-    expression = CohortExpression(
-        primary_criteria=PrimaryCriteria(criteria_list=[ConditionOccurrence()]),
-        end_strategy=CustomEraStrategy(drug_codeset_id=1, gap_days=30, offset=0),
-    )
-    with pytest.raises(UnsupportedFeatureError, match="custom_era"):
-        _ = build_cohort(expression, backend=object(), cdm_schema="main")
+def test_build_cohort_rejects_unsupported_criteria():
+    """Unsupported base criteria type is rejected at normalization time."""
+    from circe.cohortdefinition.criteria import Criteria as RawCriteria
+    from circe.execution.errors import UnsupportedCriterionError
+
+    with pytest.raises(UnsupportedCriterionError):
+        from circe.execution.normalize.criteria import normalize_criterion
+
+        normalize_criterion(RawCriteria())