chore: remove deprecated function calls

Author: glichtner

execution_engine/execution_engine.py

@@ -277,7 +277,7 @@ def register_recommendation(self, recommendation: cohort.Recommendation) -> None
             ).encode()
 
             rec_json: bytes = recommendation.json()
-            logging.info(f"Storing recommendation {recommendation}")
+            logging.info(f"Storing recommendation {recommendation.description}")
             update_query = (
                 update(recommendation_table)
                 .where(recommendation_table.recommendation_id == recommendation.id)

execution_engine/task/process/rectangle.py

@@ -158,7 +158,7 @@ def forward_fill_intervals(intervals: list[Interval]) -> list[Interval]:
     The last interval for each person is not extended (but may be merged with the previous intervals, if they
     are of the same type).
 
-    :param data: The intervals per person.
+    :param intervals: The intervals per person.
     :return: A DataFrame with the forward filled intervals.
     """
     all_intervals = sorted(
@@ -234,7 +234,7 @@ def complement_intervals(
     The complement of an interval is the interval that is not covered by the original interval.
     The complement of an interval is always of the same type as the original interval.
 
-    :param data: The intervals per person.
+    :param intervals: The intervals per person.
     :param type_: The type of the complement intervals.
     :return: A DataFrame with the complement intervals.
     """

sample.env

@@ -26,7 +26,6 @@ CELIDA_EE_OMOP__DATA_SCHEMA=cds_cdm
 
 ## Execution Engine Result Schema
 CELIDA_EE_OMOP__RESULT_SCHEMA=celida
-CELIDA_EE_OMOP__RESULT_SCHEMA=celida
 
 # Execution Engine Configuration
 ## Timezone used for date/time calculations

tests/execution_engine/converter/test_converter.py

@@ -25,31 +25,31 @@
 
 class TestSelectValue:
     def test_select_value_codeable_concept(self):
-        cc = CodeableConcept.construct()
-        elem = Extension.construct(valueCodeableConcept=cc)
+        cc = CodeableConcept.model_construct()
+        elem = Extension.model_construct(valueCodeableConcept=cc)
         value = select_value(elem, "value")
         assert value == cc
 
     def test_select_value_quantity(self):
-        q = Quantity.construct()
-        elem = Extension.construct(valueQuantity=q)
+        q = Quantity.model_construct()
+        elem = Extension.model_construct(valueQuantity=q)
         value = select_value(elem, "value")
         assert value == q
 
     def test_select_value_range(self):
-        r = Range.construct()
-        elem = Extension.construct(valueRange=r)
+        r = Range.model_construct()
+        elem = Extension.model_construct(valueRange=r)
         value = select_value(elem, "value")
         assert value == r
 
     def test_select_value_boolean(self):
         b = True
-        elem = Extension.construct(valueBoolean=b)
+        elem = Extension.model_construct(valueBoolean=b)
         value = select_value(elem, "value")
         assert value == b
 
     def test_select_value_not_found(self):
-        elem = Extension.construct()
+        elem = Extension.model_construct()
         with pytest.raises(ValueError):
             select_value(elem, "value")
 
@@ -62,25 +62,25 @@ def test_parse_code(self, monkeypatch):
             mock_get_standard_concept,
         )
 
-        coding = Coding.construct(system="http://example.com", code="123")
-        codeable_concept = CodeableConcept.construct(coding=[coding])
+        coding = Coding.model_construct(system="http://example.com", code="123")
+        codeable_concept = CodeableConcept.model_construct(coding=[coding])
         parse_code(codeable_concept)
 
         mock_get_standard_concept.assert_called_once_with("http://example.com", "123")
 
 
 class TestCodeDisplay:
     def test_code_display_with_display(self):
-        coding = Coding.construct(
+        coding = Coding.model_construct(
             system="http://example.com", code="123", display="Example display"
         )
-        codeable_concept = CodeableConcept.construct(coding=[coding])
+        codeable_concept = CodeableConcept.model_construct(coding=[coding])
         display = code_display(codeable_concept)
         assert display == "Example display"
 
     def test_code_display_without_display(self):
-        coding = Coding.construct(system="http://example.com", code="123")
-        codeable_concept = CodeableConcept.construct(coding=[coding])
+        coding = Coding.model_construct(system="http://example.com", code="123")
+        codeable_concept = CodeableConcept.model_construct(coding=[coding])
         display = code_display(codeable_concept)
         assert display == "123"
 
@@ -94,9 +94,9 @@ def test_parse_value_codeable_concept(self, monkeypatch, test_concept):
             mock_get_standard_concept,
         )
 
-        coding = Coding.construct(system="http://example.com", code="123")
-        codeable_concept = CodeableConcept.construct(coding=[coding])
-        elem = Extension.construct(valueCodeableConcept=codeable_concept)
+        coding = Coding.model_construct(system="http://example.com", code="123")
+        codeable_concept = CodeableConcept.model_construct(coding=[coding])
+        elem = Extension.model_construct(valueCodeableConcept=codeable_concept)
 
         value = parse_value(elem, "value")
 
@@ -113,8 +113,8 @@ def test_parse_value_quantity(self, monkeypatch, unit_concept):
             mock_get_standard_unit_concept,
         )
 
-        quantity = Quantity.construct(value=42, code="kg")
-        elem = Extension.construct(valueQuantity=quantity)
+        quantity = Quantity.model_construct(value=42, code="kg")
+        elem = Extension.model_construct(valueQuantity=quantity)
 
         value = parse_value(elem, "value")
 
@@ -130,10 +130,10 @@ def test_parse_value_range(self, monkeypatch, unit_concept):
             mock_get_standard_unit_concept,
         )
 
-        low = Quantity.construct(value=10, code="kg")
-        high = Quantity.construct(value=20, code="kg")
-        range_obj = Range.construct(low=low, high=high)
-        elem = Extension.construct(valueRange=range_obj)
+        low = Quantity.model_construct(value=10, code="kg")
+        high = Quantity.model_construct(value=20, code="kg")
+        range_obj = Range.model_construct(low=low, high=high)
+        elem = Extension.model_construct(valueRange=range_obj)
 
         value = parse_value(elem, "value")
 
@@ -170,7 +170,7 @@ def test_criterion_converter_factory_get(self):
         factory = CriterionConverterFactory()
         factory.register(TestCriterionConverter.MockCriterionConverter)
 
-        element = Element.construct(id="valid")
+        element = Element.model_construct(id="valid")
         converter = factory.get(element)
 
         assert isinstance(
@@ -181,7 +181,7 @@ def test_criterion_converter_factory_no_matching_converter(self):
         factory = CriterionConverterFactory()
         factory.register(TestCriterionConverter.MockCriterionConverter)
 
-        element = Element.construct(id="not-valid")
+        element = Element.model_construct(id="not-valid")
 
         with pytest.raises(ValueError, match="Cannot find a converter"):
             factory.get(element)

tests/execution_engine/fhir/test_util.py

@@ -10,9 +10,9 @@
 class TestUtils:
     @pytest.fixture
     def codeable_concept(self):
-        cc = CodeableConcept.construct(
+        cc = CodeableConcept.model_construct(
             coding=[
-                Coding.construct(
+                Coding.model_construct(
                     system="http://example.com/system",
                     code="example_code",
                     display="Example Code",
@@ -34,16 +34,16 @@ def test_get_coding_with_system_uri(self, codeable_concept):
         assert coding.display == "Example Code"
 
     def test_get_coding_fail(self):
-        cc = CodeableConcept.construct()
+        cc = CodeableConcept.model_construct()
         with pytest.raises(ValueError):
             get_coding(cc)
 
     @pytest.fixture
     def element_with_extension(self):
-        ext = Extension.construct(
+        ext = Extension.model_construct(
             url="http://example.com/extension", valueString="test"
         )
-        elem = Element.construct(extension=[ext])
+        elem = Element.model_construct(extension=[ext])
         return elem
 
     def test_get_extension(self, element_with_extension):
@@ -60,6 +60,6 @@ def test_get_extension_not_found(self, element_with_extension):
         assert extension is None
 
     def test_get_extension_no_extensions(self):
-        elem = Element.construct()
+        elem = Element.model_construct()
         extension = get_extension(elem, "http://example.com/extension")
         assert extension is None

tests/execution_engine/task/process/test_rectangle.py

@@ -3024,7 +3024,7 @@ def to_df(data):
                 ],
             )
             df["interval_start"] = pd.to_datetime(df["interval_start"])
-            df["interval_end"] = pd.to_datetime(df["interval_end"])
+            df["interval_end"] = pd.to_datetime(df["interval_end"], utc=True)
 
             return df