Merge pull request #245 from CODEX-CELIDA/add-presence-indicator

feat: add AnyTime temporal criterion

execution_engine/omop/criterion/combination/temporal.py

@@ -16,6 +16,7 @@ class TimeIntervalType(StrEnum):
     AFTERNOON_SHIFT = "afternoon_shift"
     NIGHT_SHIFT = "night_shift"
     DAY = "day"
+    ANY_TIME = "any_time"
 
 
 class TemporalIndicatorCombination(CriterionCombination):
@@ -272,3 +273,15 @@ def Day(
         """
 
         return cls.Presence(criterion, category, TimeIntervalType.DAY)
+
+    @classmethod
+    def AnyTime(
+        cls,
+        criterion: Union[Criterion, "CriterionCombination"],
+        category: CohortCategory,
+    ) -> "TemporalIndicatorCombination":
+        """
+        Create a AnyTime combination of criteria.
+        """
+
+        return cls.Presence(criterion, category, TimeIntervalType.ANY_TIME)

execution_engine/task/process/rectangle.py

@@ -639,17 +639,6 @@ def create_time_intervals(
     Raises:
         ValueError: If start_datetime and end_datetime are not in the same timezone.
     """
-
-    # if start_datetime.tzinfo is not None or end_datetime.tzinfo is not None:
-    #     if start_datetime.tzinfo != end_datetime.tzinfo:
-    #         raise ValueError(
-    #             "start_datetime and end_datetime must have the same timezone"
-    #         )
-    #     timezone = start_datetime.tzinfo
-    # else:
-    #     # use local timezone if no timezone is provided
-    #     timezone = datetime.datetime.now().astimezone().tzinfo
-
     if isinstance(timezone, str):
         timezone = cast(pytz.tzinfo.DstTzInfo, pytz.timezone(timezone))
 

execution_engine/task/task.py

@@ -13,7 +13,7 @@
 from execution_engine.omop.db.celida.tables import ResultInterval
 from execution_engine.omop.sqlclient import OMOPSQLClient
 from execution_engine.settings import get_config
-from execution_engine.task.process import get_processing_module
+from execution_engine.task.process import Interval, get_processing_module
 from execution_engine.util.interval import IntervalType
 from execution_engine.util.types import PersonIntervals, TimeRange
 
@@ -467,23 +467,32 @@ def get_start_end_from_interval_type(
 
         assert isinstance(self.expr, logic.TemporalCount), "Invalid expression type"
 
-        if self.expr.interval_type is not None:
-            start_time, end_time = get_start_end_from_interval_type(
-                self.expr.interval_type
-            )
-        elif self.expr.start_time is not None and self.expr.end_time is not None:
-            start_time, end_time = self.expr.start_time, self.expr.end_time
+        if self.expr.interval_type == TimeIntervalType.ANY_TIME:
+            indicator_windows = [
+                Interval(
+                    lower=observation_window.start.timestamp(),
+                    upper=observation_window.end.timestamp(),
+                    type=IntervalType.POSITIVE,
+                )
+            ]
         else:
-            raise ValueError("Invalid time interval settings")
-
-        indicator_windows = process.create_time_intervals(
-            start_datetime=observation_window.start,
-            end_datetime=observation_window.end,
-            start_time=start_time,
-            end_time=end_time,
-            interval_type=IntervalType.POSITIVE,
-            timezone=get_config().timezone,
-        )
+            if self.expr.interval_type is not None:
+                start_time, end_time = get_start_end_from_interval_type(
+                    self.expr.interval_type
+                )
+            elif self.expr.start_time is not None and self.expr.end_time is not None:
+                start_time, end_time = self.expr.start_time, self.expr.end_time
+            else:
+                raise ValueError("Invalid time interval settings")
+
+            indicator_windows = process.create_time_intervals(
+                start_datetime=observation_window.start,
+                end_datetime=observation_window.end,
+                start_time=start_time,
+                end_time=end_time,
+                interval_type=IntervalType.POSITIVE,
+                timezone=get_config().timezone,
+            )
 
         result = process.find_overlapping_windows(indicator_windows, data_p)
 

scripts/execute.py

@@ -37,6 +37,7 @@
 import os
 import re
 import sys
+import time
 
 import pendulum
 from sqlalchemy import text
@@ -106,6 +107,7 @@
 e = ExecutionEngine()
 logging.getLogger().setLevel(logging.DEBUG)
 
+start_time = time.time()
 
 for recommendation_url in urls:
     print(recommendation_url)
@@ -115,3 +117,8 @@
     )
 
     e.execute(cdd, start_datetime=start_datetime, end_datetime=end_datetime)
+
+end_time = time.time()
+runtime_seconds = end_time - start_time
+
+logging.info(f"Total runtime: {runtime_seconds:.2f} seconds")