feat: implement relativeTime extension

Author: glichtner

converter/parser/util.py renamed to execution_engine/converter/parser/util.py

@@ -3,6 +3,7 @@
 
 from execution_engine.omop.criterion.abstract import Criterion
 from execution_engine.omop.criterion.procedure_occurrence import ProcedureOccurrence
+from execution_engine.omop.vocabulary import OMOP_SURGICAL_PROCEDURE
 from execution_engine.util import logic
 from execution_engine.util.temporal_logic_util import Presence
 
@@ -20,8 +21,6 @@ def _wrap_criteria_with_factory(
     :raises ValueError: If an unexpected element type is encountered.
     """
 
-    from digipod.concepts import OMOP_SURGICAL_PROCEDURE
-
     new_expr: logic.Expr
 
     if isinstance(expr, Criterion):
@@ -31,8 +30,16 @@ def _wrap_criteria_with_factory(
         # Create a new combination of the same type with the same operator
         args = []
 
+        interval_criterion = (
+            expr.interval_criterion if hasattr(expr, "interval_criterion") else None
+        )
+
         # Loop through all elements
         for element in expr.args:
+
+            if element == interval_criterion:
+                # interval_criterion must not be wrapped!
+                args.append(element)
             if isinstance(element, logic.Expr):
                 # Recursively wrap nested combinations
                 args.append(_wrap_criteria_with_factory(element, factory))

execution_engine/omop/cohort/graph_builder.py

@@ -37,7 +37,16 @@ def filter_symbols(cls, node: logic.Expr, filter_: logic.Expr) -> logic.Expr:
         if isinstance(node, logic.Symbol):
             return logic.LeftDependentToggle(left=filter_, right=node)
         elif isinstance(node, logic.Expr):
-            converted_args = [cls.filter_symbols(a, filter_) for a in node.args]
+            if hasattr(node, "interval_criterion") and node.interval_criterion:
+                # we must not wrap the interval_criterion
+                interval_criterion = node.interval_criterion
+                converted_args = [
+                    cls.filter_symbols(a, filter_)
+                    for a in node.args
+                    if not a == interval_criterion
+                ] + [interval_criterion]
+            else:
+                converted_args = [cls.filter_symbols(a, filter_) for a in node.args]
 
             if any(a is not b for a, b in zip(node.args, converted_args)):
                 node.update_args(*converted_args)
@@ -64,6 +73,9 @@ def filter_intervention_criteria_by_population(cls, expr: logic.Expr) -> logic.E
         def traverse(
             expr: logic.Expr,
         ) -> None:
+            if expr is None:
+                pass
+
             if isinstance(expr, PopulationInterventionPairExpr):
                 p, i = expr.left, expr.right
 

execution_engine/omop/vocabulary.py

@@ -7,6 +7,7 @@
 OMOP_INTENSIVE_CARE = 32037
 OMOP_INPATIENT_VISIT = 9201
 OMOP_OUTPATIENT_VISIT = 9202
+OMOP_SURGICAL_PROCEDURE = 4301351  # OMOP surgical procedure
 
 
 class VocabularyNotFoundError(Exception):

execution_engine/util/logic.py

@@ -622,6 +622,12 @@ def dict(self, include_id: bool = False) -> dict:
         data = super().dict(include_id=include_id)
 
         if self.interval_criterion:
+
+            if len(self.args) <= 1:
+                raise ValueError(
+                    "More than one argument required if interval_criterion is set"
+                )
+
             args, pop = self.args[:-1], self.args[-1]
 
             if pop != self.interval_criterion:

tests/execution_engine/omop/criterion/combination/test_temporal_combination.py

@@ -13,6 +13,7 @@
 from execution_engine.omop.criterion.noop import NoopCriterion
 from execution_engine.omop.criterion.procedure_occurrence import ProcedureOccurrence
 from execution_engine.omop.db.omop import tables
+from execution_engine.omop.vocabulary import OMOP_SURGICAL_PROCEDURE
 from execution_engine.task.process import get_processing_module
 from execution_engine.util import logic, temporal_logic_util
 from execution_engine.util.enum import TimeIntervalType
@@ -43,8 +44,6 @@
 
 process = get_processing_module()
 
-OMOP_SURGICAL_PROCEDURE = 4301351  # OMOP surgical procedure
-
 
 def intervals_to_df(result, by=None):
     df = intervals_to_df_orig(result, by, process.normalize_interval)