chore(deps): bump the dependencies group across 1 directory with 9 updates

execution_engine/converter/converter.py

@@ -4,7 +4,7 @@
 from fhir.resources.codeableconcept import CodeableConcept
 from fhir.resources.element import Element
 from fhir.resources.extension import Extension
-from fhir.resources.fhirtypes import Boolean
+from fhir.resources.fhirtypes import BooleanType
 from fhir.resources.quantity import Quantity
 from fhir.resources.range import Range
 
@@ -21,7 +21,7 @@
 @staticmethod
 def select_value(
     root: Element, value_prefix: str
-) -> CodeableConcept | Quantity | Range | Boolean:
+) -> CodeableConcept | Quantity | Range | BooleanType:
     """
     Selects the value of a characteristic by datatype.
     """

execution_engine/fhir/client.py

@@ -1,7 +1,7 @@
 import logging
 
 import requests
-from fhir.resources import FHIRAbstractModel, construct_fhir_element
+from fhir.resources import FHIRAbstractModel, get_fhir_model_class
 
 
 class FHIRClient:
@@ -15,7 +15,7 @@ def __init__(self, base_url: str):
         self.base_url = base_url
 
     def fetch_resource(
-        self, element_type: str, canonical_url: str, version: str
+        self, resource_type: str, canonical_url: str, version: str
     ) -> FHIRAbstractModel:
         """
         Get a resource from the FHIR server by its canonical URL.
@@ -24,7 +24,7 @@ def fetch_resource(
 
         try:
             r = requests.get(
-                f"{self.base_url}/{element_type}?url={canonical_url}&version={version}",
+                f"{self.base_url}/{resource_type}?url={canonical_url}&version={version}",
                 timeout=10,
             )
         except ConnectionRefusedError:
@@ -34,4 +34,7 @@ def fetch_resource(
         assert (
             r.status_code == 200
         ), f"Could not get resource: HTTP status code {r.status_code}"
-        return construct_fhir_element(element_type, r.json())
+
+        resource = get_fhir_model_class(resource_type)
+
+        return resource.model_validate(r.json())

execution_engine/omop/db/celida/views.py

@@ -14,84 +14,6 @@
 from execution_engine.util.interval import IntervalType
 
 
-def view_interval_coverage_slow() -> Select:
-    """
-    Return Select statement for view to calculate the full day coverage of recommendation results.
-    """
-
-    one_day = func.cast(concat(1, "day"), INTERVAL)
-    rri = ResultInterval.__table__.alias("rri")
-
-    date_series = select(
-        ExecutionRun.run_id,
-        func.generate_series(
-            func.date_trunc("day", ExecutionRun.observation_start_datetime),
-            func.date_trunc("day", ExecutionRun.observation_end_datetime),
-            one_day,
-        )
-        .cast(Date)
-        .label("day"),
-        ExecutionRun.observation_start_datetime,
-        ExecutionRun.observation_end_datetime,
-    ).cte("date_series")
-
-    interval_coverage = (
-        select(
-            date_series.c.run_id,
-            rri.c.person_id,
-            rri.c.cohort_category,
-            rri.c.pi_pair_id,
-            rri.c.criterion_id,
-            date_series.c.day,
-            func.sum(
-                func.least(
-                    date_series.c.day + one_day,
-                    rri.c.interval_end,
-                    date_series.c.observation_end_datetime,
-                )
-                - func.greatest(
-                    date_series.c.day,
-                    rri.c.interval_start,
-                    date_series.c.observation_start_datetime,
-                )
-            ).label("covered_time"),
-            func.bool_or(rri.c.interval_type == IntervalType.POSITIVE).label(
-                "has_positive"
-            ),
-            func.bool_or(rri.c.interval_type == IntervalType.NO_DATA).label(
-                "has_no_data"
-            ),
-            func.bool_or(rri.c.interval_type == IntervalType.NEGATIVE).label(
-                "has_negative"
-            ),
-        )
-        .select_from(date_series)
-        .outerjoin(rri, (date_series.c.run_id == rri.c.run_id))
-        .filter(
-            rri.c.interval_start < date_series.c.day + one_day,
-            rri.c.interval_end > date_series.c.day,
-        )
-        .group_by(
-            date_series.c.run_id,
-            date_series.c.day,
-            rri.c.person_id,
-            rri.c.cohort_category,
-            rri.c.pi_pair_id,
-            rri.c.criterion_id,
-        )
-    )
-
-    return interval_coverage
-
-
-interval_coverage_slow = view(
-    "interval_coverage_slow",
-    Base.metadata,
-    view_interval_coverage_slow(),
-    schema=SCHEMA_NAME,
-)
-
-
 def view_interval_coverage() -> Select:
     """
     Return Select statement for view to calculate the full day coverage of recommendation results.

execution_engine/omop/db/view.py

@@ -62,11 +62,6 @@ def view(
     :param schema: The schema name.
     :return: The table object.
     """
-    t = table(name, schema=schema)
-
-    t._columns._populate_separate_keys(
-        col._make_proxy(t) for col in selectable.selected_columns
-    )
 
     def view_exists(
         ddl: DDLElement, target: MetaData, connection: Connection, **kw: Any
@@ -85,6 +80,16 @@ def view_doesnt_exist(
         """
         return not view_exists(ddl, target, connection, **kw)
 
+    t = table(
+        name,
+        *(
+            sa.Column(c.name, c.type, primary_key=c.primary_key)
+            for c in selectable.selected_columns
+        ),
+        schema=schema
+    )
+    t.primary_key.update(c for c in t.c if c.primary_key)
+
     sa.event.listen(
         metadata,
         "after_create",
@@ -95,4 +100,5 @@ def view_doesnt_exist(
         "before_drop",
         DropView(name, schema).execute_if(callable_=view_exists),
     )
+
     return t

requirements-dev.txt

@@ -1,5 +1,5 @@
 pytest==8.3.4
-pytest-postgresql==6.1.1
+pytest-postgresql==7.0.0
 tqdm==4.67.1
 pytest-cov==6.0.0
 pytest-env==1.1.5

requirements.txt

@@ -1,19 +1,19 @@
 requests==2.32.3
 python-dotenv==1.0.1
 pyyaml==6.0.2
-fhir.resources==7.1.0
+fhir.resources==8.0.0
 sympy==1.13.3
 pandas==2.2.3
-psycopg[binary]==3.2.4
-sqlalchemy==2.0.37
-pydantic==2.10.5
-pydantic-settings==2.7.1
+psycopg[binary]==3.2.5
+sqlalchemy==2.0.38
+pydantic==2.10.6
+pydantic-settings==2.8.0
 uvicorn[standard]==0.34.0
-fastapi==0.115.6
+fastapi==0.115.8
 pendulum==3.0.0
 networkx==3.4.2
-numpy==2.2.2
-pytz==2024.2
-cython==3.0.11
+numpy==2.2.3
+pytz==2025.1
+cython==3.0.12
 setuptools==75.8.0
 sortedcontainers==2.4.0

tests/execution_engine/fhir/test_recommendation.py

@@ -1,7 +1,7 @@
 from unittest.mock import patch
 
 import pytest
-from fhir.resources import construct_fhir_element
+from fhir.resources import get_fhir_model_class
 
 from execution_engine.constants import CS_PLAN_DEFINITION_TYPE
 from execution_engine.fhir.client import FHIRClient
@@ -20,8 +20,8 @@ def mock_load(self, test_class):
 
     @pytest.fixture
     def mock_fetch_resource_unknown(self):
-        plan_definition = construct_fhir_element(
-            "PlanDefinition",
+
+        plan_definition = get_fhir_model_class("PlanDefinition").model_validate(
             {
                 "status": "draft",
                 "action": [],
@@ -39,8 +39,7 @@ def mock_fetch_resource_unknown(self):
 
     @pytest.fixture
     def mock_fetch_resource_no_partOf(self):
-        plan_definition = construct_fhir_element(
-            "PlanDefinition",
+        plan_definition = get_fhir_model_class("PlanDefinition").model_validate(
             {
                 "status": "draft",
                 "action": [],
@@ -62,8 +61,8 @@ def test_class(self):
 
     @pytest.fixture
     def mock_fetch_recommendation(self, test_class):
-        plan_definition = construct_fhir_element(
-            "PlanDefinition", {"status": "draft", "action": []}
+        plan_definition = get_fhir_model_class("PlanDefinition").model_validate(
+            {"status": "draft", "action": []}
         )
         with patch.object(
             test_class, "fetch_recommendation", return_value=plan_definition
@@ -159,8 +158,8 @@ def test_class(self):
 
     @pytest.fixture
     def mock_fetch_recommendation_plan(self):
-        plan_definition = construct_fhir_element(
-            "PlanDefinition", {"status": "draft", "action": []}
+        plan_definition = get_fhir_model_class("PlanDefinition").model_validate(
+            {"status": "draft", "action": []}
         )
         with patch.object(
             RecommendationPlan,
@@ -171,8 +170,7 @@ def mock_fetch_recommendation_plan(self):
 
     @pytest.fixture
     def mock_fetch_resource_goals(self):
-        plan_definition = construct_fhir_element(
-            "PlanDefinition",
+        plan_definition = get_fhir_model_class("PlanDefinition").model_validate(
             {
                 "status": "draft",
                 "action": [],

tests/recommendation/test_recommendation_base.py

@@ -953,7 +953,10 @@ def get_query(t, category):
                     t.c.cohort_category,
                     t.c.valid_date,
                 )
-                .outerjoin(PopulationInterventionPair)
+                .outerjoin(
+                    PopulationInterventionPair,
+                    PopulationInterventionPair.pi_pair_id == t.c.pi_pair_id,
+                )
                 .where(t.c.criterion_id.is_(None))
                 .where(t.c.cohort_category.in_(category))
             )