feat: remove cohort parameter

Author: glichtner

apps/rest_api/app/routers/recommendation.py

@@ -50,7 +50,6 @@ async def recommendation_criteria(
         data.append(
             {
                 "description": c.description(),
-                "cohort_category": c.category,
             }
         )
 

execution_engine/converter/action/abstract.py

@@ -3,7 +3,6 @@
 
 from fhir.resources.timing import Timing as FHIRTiming
 
-from execution_engine.constants import CohortCategory
 from execution_engine.converter.criterion import CriterionConverter, parse_code
 from execution_engine.converter.goal.abstract import Goal
 from execution_engine.fhir.recommendation import RecommendationPlan
@@ -158,9 +157,7 @@ def to_positive_criterion(self) -> Criterion | LogicalCriterionCombination:
             criteria = [goal.to_criterion() for goal in self.goals]
             if action is not None:
                 criteria.append(action)
-            return LogicalCriterionCombination.And(
-                *criteria, category=CohortCategory.INTERVENTION
-            )
+            return LogicalCriterionCombination.And(*criteria)
         else:
             return action  # type: ignore
 

execution_engine/converter/action/assessment.py

@@ -1,6 +1,5 @@
 from typing import Self, Type
 
-from execution_engine.constants import CohortCategory
 from execution_engine.converter.action.abstract import AbstractAction
 from execution_engine.converter.criterion import parse_code
 from execution_engine.fhir.recommendation import RecommendationPlan
@@ -79,7 +78,6 @@ def _to_criterion(self) -> Criterion | LogicalCriterionCombination | None:
                 )
 
         criterion = cls(
-            category=CohortCategory.INTERVENTION,
             concept=self._code,
             timing=self._timing,
         )

execution_engine/converter/action/body_positioning.py

@@ -1,6 +1,5 @@
 from typing import Self
 
-from execution_engine.constants import CohortCategory
 from execution_engine.converter.action.abstract import AbstractAction
 from execution_engine.converter.criterion import parse_code
 from execution_engine.fhir.recommendation import RecommendationPlan
@@ -53,7 +52,6 @@ def _to_criterion(self) -> Criterion | LogicalCriterionCombination | None:
         """Converts this characteristic to a Criterion."""
 
         return ProcedureOccurrence(
-            category=CohortCategory.INTERVENTION,
             concept=self._code,
             timing=self._timing,
         )

execution_engine/converter/action/drug_administration.py

@@ -6,7 +6,7 @@
 from fhir.resources.dosage import Dosage as FHIRDosage
 
 from execution_engine.clients import omopdb
-from execution_engine.constants import EXT_DOSAGE_CONDITION, CohortCategory
+from execution_engine.constants import EXT_DOSAGE_CONDITION
 from execution_engine.converter.action.abstract import AbstractAction
 from execution_engine.converter.criterion import (
     get_extension_by_url,
@@ -285,15 +285,13 @@ def _to_criterion(self) -> Criterion | LogicalCriterionCombination | None:
         if not self._dosages:
             # no dosages, just return the drug exposure
             return DrugExposure(
-                category=CohortCategory.INTERVENTION,
                 ingredient_concept=self._ingredient_concept,
                 dose=None,
                 route=None,
             )
 
         for dosage in self._dosages:
             drug_action = DrugExposure(
-                category=CohortCategory.INTERVENTION,
                 ingredient_concept=self._ingredient_concept,
                 dose=dosage["dose"],
                 route=dosage.get("route", None),
@@ -316,7 +314,6 @@ def _to_criterion(self) -> Criterion | LogicalCriterionCombination | None:
                     )
 
                 ext_criterion = PointInTimeCriterion(
-                    category=CohortCategory.INTERVENTION,
                     concept=extension["code"],
                     value=extension["value"],
                 )
@@ -326,7 +323,6 @@ def _to_criterion(self) -> Criterion | LogicalCriterionCombination | None:
                 # Thus, the actual drug administration (drug_action, "right") must only be fulfilled if the
                 # condition (ext_criterion, "left") is fulfilled. Thus, we here add this conditional filter.
                 comb = NonCommutativeLogicalCriterionCombination.ConditionalFilter(
-                    category=CohortCategory.INTERVENTION,
                     left=ext_criterion,
                     right=drug_action,
                 )
@@ -338,7 +334,6 @@ def _to_criterion(self) -> Criterion | LogicalCriterionCombination | None:
             result = drug_actions[0]
         else:
             result = LogicalCriterionCombination(
-                category=CohortCategory.INTERVENTION,
                 operator=LogicalCriterionCombination.Operator("OR"),
             )
             result.add_all(drug_actions)

execution_engine/converter/characteristic/codeable_concept.py

@@ -3,7 +3,6 @@
 
 from fhir.resources.evidencevariable import EvidenceVariableCharacteristic
 
-from execution_engine.constants import CohortCategory
 from execution_engine.converter.characteristic.abstract import AbstractCharacteristic
 from execution_engine.fhir.util import get_coding
 from execution_engine.omop.concepts import Concept
@@ -82,7 +81,6 @@ def from_fhir(
     def to_positive_criterion(self) -> Criterion:
         """Converts this characteristic to a Criterion."""
         return self._criterion_class(
-            category=CohortCategory.POPULATION,
             concept=self.value,
             value=None,
             static=self._concept_value_static,

execution_engine/converter/characteristic/value.py

@@ -3,7 +3,6 @@
 
 from fhir.resources.evidencevariable import EvidenceVariableCharacteristic
 
-from execution_engine.constants import CohortCategory
 from execution_engine.converter.characteristic.abstract import AbstractCharacteristic
 from execution_engine.converter.criterion import parse_code, parse_value
 from execution_engine.omop.criterion.concept import ConceptCriterion
@@ -36,7 +35,6 @@ def from_fhir(
     def to_positive_criterion(self) -> ConceptCriterion:
         """Converts this characteristic to a Criterion."""
         return self._criterion_class(
-            category=CohortCategory.POPULATION,
             concept=self.type,
             value=self.value,
             static=self._concept_value_static,

execution_engine/converter/criterion.py

@@ -154,9 +154,7 @@ def to_criterion(self) -> Criterion | LogicalCriterionCombination:
         """
         positive_criterion = self.to_positive_criterion()
         if self._exclude:
-            return LogicalCriterionCombination.Not(
-                positive_criterion, positive_criterion.category
-            )
+            return LogicalCriterionCombination.Not(positive_criterion)
         else:
             return positive_criterion
 

execution_engine/converter/goal/assessment_scale.py

@@ -1,6 +1,6 @@
 from fhir.resources.plandefinition import PlanDefinitionGoal
 
-from execution_engine.constants import SCT_ASSESSMENT_SCALE, CohortCategory
+from execution_engine.constants import SCT_ASSESSMENT_SCALE
 from execution_engine.converter.criterion import parse_code_value
 from execution_engine.converter.goal.abstract import Goal
 from execution_engine.omop.concepts import Concept
@@ -52,7 +52,6 @@ def to_positive_criterion(self) -> Criterion:
         Converts the goal to a criterion.
         """
         return Measurement(
-            category=CohortCategory.INTERVENTION,
             concept=self._code,
             value=self._value,
         )

execution_engine/converter/goal/laboratory_value.py

@@ -1,6 +1,6 @@
 from fhir.resources.plandefinition import PlanDefinitionGoal
 
-from execution_engine.constants import SCT_LAB_FINDINGS_SURVEILLANCE, CohortCategory
+from execution_engine.constants import SCT_LAB_FINDINGS_SURVEILLANCE
 from execution_engine.converter.criterion import parse_code_value
 from execution_engine.converter.goal.abstract import Goal
 from execution_engine.omop.concepts import Concept
@@ -51,7 +51,6 @@ def to_positive_criterion(self) -> Criterion:
         Converts the goal to a criterion.
         """
         return Measurement(
-            category=CohortCategory.INTERVENTION,
             concept=self._code,
             value=self._value,
         )