Merge pull request #214 from CODEX-CELIDA/chore/update-deps

Chore/update deps

apps/viz-backend/README.md

@@ -0,0 +1,7 @@
+# Visualization Backend
+
+Run:
+```
+cd app
+uvicorn main:app --reload --port 8081
+```

execution_engine/omop/criterion/abstract.py

@@ -370,7 +370,7 @@ def _filter_base_persons(
     def process_data(
         self,
         data: PersonIntervals,
-        base_data: PersonIntervals,
+        base_data: PersonIntervals | None,
         observation_window: TimeRange,
     ) -> PersonIntervals:
         """
@@ -382,6 +382,7 @@ def process_data(
         :param data: The result of the SQL query.
         :param base_data: The result from the base criterion or None if this is the base criterion. This is used to
             add intervals for all patients that are not in the result of the SQL query.
+            May be None if this is the base criterion.
         :param observation_window: The observation window.
         :return: A processed DataFrame.
         """

execution_engine/omop/criterion/point_in_time.py

@@ -86,7 +86,7 @@ def _create_query(self) -> Select:
     def process_data(
         self,
         data: PersonIntervals,
-        base_data: PersonIntervals,
+        base_data: PersonIntervals | None,
         observation_window: TimeRange,
     ) -> PersonIntervals:
         """
@@ -95,7 +95,7 @@ def process_data(
         Forward fill all intervals and in insert NO_DATA intervals for missing time in observation_window.
 
         :param data: The result of the SQL query.
-        :param base_data: The base data.
+        :param base_data: The base data or None if this is the base criterion.
         :param observation_window: The observation window.
         :return: A processed DataFrame.
         """

requirements-dev.txt

@@ -1,5 +1,5 @@
 pytest==8.3.2
-pytest-postgresql==6.0.0
+pytest-postgresql==6.1.1
 tqdm==4.66.5
 pytest-cov==5.0.0
 pytest-env==1.1.3

requirements.txt

@@ -4,16 +4,16 @@ pyyaml==6.0.2
 fhir.resources==7.1.0
 sympy==1.13.2
 pandas==2.2.2
-psycopg[binary]==3.2.1
+psycopg[binary]==3.2.3
 sqlalchemy==2.0.35
-pydantic==2.8.2
+pydantic==2.9.2
 pydantic-settings==2.5.2
-uvicorn[standard]==0.30.1
+uvicorn[standard]==0.31.0
 fastapi==0.112.0
 pendulum==3.0.0
 networkx==3.3
 numpy==2.0.1
-pytz==2024.1
+pytz==2024.2
 cython==3.0.10
 setuptools==72.1.0
 sortedcontainers==2.4.0

scripts/execute.py

@@ -88,7 +88,7 @@
         )
 
 base_url = "https://www.netzwerk-universitaetsmedizin.de/fhir/codex-celida/guideline/"
-recommendation_package_version = "latest"
+recommendation_package_version = "v1.5.2"
 
 urls = [
     "covid19-inpatient-therapy/recommendation/no-therapeutic-anticoagulation",